Starting phenix.real_space_refine on Fri Jul 3 02:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybj_39119/07_2026/8ybj_39119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybj_39119/07_2026/8ybj_39119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2026/8ybj_39119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2026/8ybj_39119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2026/8ybj_39119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2026/8ybj_39119.map" } resolution = 2.38 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= 0.003 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 289 5.49 5 S 14 5.16 5 C 6606 2.51 5 N 2246 2.21 5 O 2798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11953 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} 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: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.37, per 1000 atoms: 0.20 Number of scatterers: 11953 At special positions: 0 Unit cell: (75.26, 120.84, 116.6, 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 289 15.00 O 2798 8.00 N 2246 7.00 C 6606 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: 0.89 Conformation dependent library (CDL) restraints added in 215.9 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.4% alpha, 2.9% beta 144 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.709A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.772A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.653A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.752A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.558A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.501A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.575A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.897A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.945A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.551A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.907A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.095A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.24 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: 1548 1.32 - 1.44: 4687 1.44 - 1.57: 5915 1.57 - 1.69: 579 1.69 - 1.81: 24 Bond restraints: 12753 Sorted by residual: bond pdb=" C5' DT I 55 " pdb=" C4' DT I 55 " ideal model delta sigma weight residual 1.512 1.552 -0.040 7.00e-03 2.04e+04 3.31e+01 bond pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 1.512 1.550 -0.038 7.00e-03 2.04e+04 2.89e+01 bond pdb=" N3 DC I 7 " pdb=" C4 DC I 7 " ideal model delta sigma weight residual 1.335 1.300 0.035 7.00e-03 2.04e+04 2.47e+01 bond pdb=" C5 DT J -57 " pdb=" C6 DT J -57 " ideal model delta sigma weight residual 1.339 1.372 -0.033 7.00e-03 2.04e+04 2.20e+01 bond pdb=" N3 DC J 3 " pdb=" C4 DC J 3 " ideal model delta sigma weight residual 1.335 1.302 0.033 7.00e-03 2.04e+04 2.19e+01 ... (remaining 12748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 16494 1.64 - 3.29: 1686 3.29 - 4.93: 248 4.93 - 6.58: 31 6.58 - 8.22: 5 Bond angle restraints: 18464 Sorted by residual: angle pdb=" O5' DA I 50 " pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 109.40 115.83 -6.43 8.00e-01 1.56e+00 6.46e+01 angle pdb=" O5' DT J -16 " pdb=" C5' DT J -16 " pdb=" C4' DT J -16 " ideal model delta sigma weight residual 109.40 115.29 -5.89 8.00e-01 1.56e+00 5.42e+01 angle pdb=" O5' DT I 55 " pdb=" C5' DT I 55 " pdb=" C4' DT I 55 " ideal model delta sigma weight residual 109.40 114.36 -4.96 8.00e-01 1.56e+00 3.85e+01 angle pdb=" O5' DC I 7 " pdb=" C5' DC I 7 " pdb=" C4' DC I 7 " ideal model delta sigma weight residual 109.40 114.07 -4.67 8.00e-01 1.56e+00 3.41e+01 angle pdb=" O5' DC I 35 " pdb=" C5' DC I 35 " pdb=" C4' DC I 35 " ideal model delta sigma weight residual 109.40 113.89 -4.49 8.00e-01 1.56e+00 3.15e+01 ... (remaining 18459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4408 17.67 - 35.33: 1035 35.33 - 53.00: 1144 53.00 - 70.67: 319 70.67 - 88.33: 24 Dihedral angle restraints: 6930 sinusoidal: 4738 harmonic: 2192 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1662 0.070 - 0.139: 384 0.139 - 0.209: 38 0.209 - 0.279: 12 0.279 - 0.348: 4 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C4' DC I -70 " pdb=" C5' DC I -70 " pdb=" O4' DC I -70 " pdb=" C3' DC I -70 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA LYS G 74 " pdb=" N LYS G 74 " pdb=" C LYS G 74 " pdb=" CB LYS G 74 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ASN G 73 " pdb=" N ASN G 73 " pdb=" C ASN G 73 " pdb=" CB ASN G 73 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2097 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J -24 " 0.050 2.00e-02 2.50e+03 6.62e-02 1.10e+02 pdb=" N1 DT J -24 " 0.046 2.00e-02 2.50e+03 pdb=" C2 DT J -24 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DT J -24 " -0.117 2.00e-02 2.50e+03 pdb=" N3 DT J -24 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DT J -24 " 0.027 2.00e-02 2.50e+03 pdb=" O4 DT J -24 " 0.080 2.00e-02 2.50e+03 pdb=" C5 DT J -24 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT J -24 " -0.125 2.00e-02 2.50e+03 pdb=" C6 DT J -24 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 55 " 0.095 2.00e-02 2.50e+03 6.04e-02 9.12e+01 pdb=" N1 DT I 55 " 0.038 2.00e-02 2.50e+03 pdb=" C2 DT I 55 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT I 55 " -0.093 2.00e-02 2.50e+03 pdb=" N3 DT I 55 " -0.015 2.00e-02 2.50e+03 pdb=" C4 DT I 55 " 0.021 2.00e-02 2.50e+03 pdb=" O4 DT I 55 " 0.100 2.00e-02 2.50e+03 pdb=" C5 DT I 55 " -0.033 2.00e-02 2.50e+03 pdb=" C7 DT I 55 " -0.063 2.00e-02 2.50e+03 pdb=" C6 DT I 55 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 5 " -0.101 2.00e-02 2.50e+03 6.31e-02 8.96e+01 pdb=" N1 DC I 5 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DC I 5 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC I 5 " 0.067 2.00e-02 2.50e+03 pdb=" N3 DC I 5 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 5 " 0.023 2.00e-02 2.50e+03 pdb=" N4 DC I 5 " -0.107 2.00e-02 2.50e+03 pdb=" C5 DC I 5 " 0.078 2.00e-02 2.50e+03 pdb=" C6 DC I 5 " 0.051 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 4264 2.93 - 3.43: 10430 3.43 - 3.92: 24382 3.92 - 4.41: 27712 4.41 - 4.90: 36602 Nonbonded interactions: 103390 Sorted by model distance: nonbonded pdb=" N ASP D 51 " pdb=" OD1 ASP D 51 " model vdw 2.443 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.467 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.486 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.504 3.040 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.521 3.120 ... (remaining 103385 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 40 through 135) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = chain 'D' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.640 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.009 0.058 12753 Z= 0.791 Angle : 1.022 8.220 18464 Z= 0.915 Chirality : 0.060 0.348 2100 Planarity : 0.012 0.112 1335 Dihedral : 28.235 88.333 5518 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % 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: 2.32 (0.29), residues: 742 helix: 2.20 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 35 TYR 0.036 0.003 TYR G 39 PHE 0.008 0.002 PHE E 67 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.79 (12753) covalent geometry : angle 1.02156 / 0.91 (18464) hydrogen bonds : bond 0.12210 / 7.98 ( 782) hydrogen bonds : angle 3.69658 / 2.69 ( 1951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8312 (tpt90) REVERT: C 15 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7683 (mtmt) REVERT: C 95 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8498 (tttp) REVERT: E 97 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8852 (mt-10) REVERT: G 95 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7913 (tttt) REVERT: H 93 GLU cc_start: 0.8887 (mp0) cc_final: 0.8483 (mp0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.9378 time to fit residues: 147.3516 Evaluate side-chains 137 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 38 ASN D 84 ASN E 68 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.165943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117782 restraints weight = 10867.376| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.13 r_work: 0.3103 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12753 Z= 0.147 Angle : 0.656 7.373 18464 Z= 0.385 Chirality : 0.048 0.216 2100 Planarity : 0.004 0.034 1335 Dihedral : 30.958 100.774 4021 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.28 % Allowed : 13.08 % Favored : 85.65 % 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: 2.89 (0.30), residues: 742 helix: 2.68 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.26 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.012 0.001 TYR F 51 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.15 (12753) covalent geometry : angle 0.65589 / 0.38 (18464) hydrogen bonds : bond 0.05351 / 3.56 ( 782) hydrogen bonds : angle 2.97968 / 2.17 ( 1951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7229 (mtt180) REVERT: C 15 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7457 (mtmt) REVERT: C 36 LYS cc_start: 0.8749 (mppt) cc_final: 0.8304 (mmtp) REVERT: E 97 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8672 (mt-10) REVERT: G 95 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7757 (tttt) REVERT: H 93 GLU cc_start: 0.8744 (mp0) cc_final: 0.8347 (mp0) REVERT: H 112 SER cc_start: 0.8755 (m) cc_final: 0.8532 (t) outliers start: 8 outliers final: 2 residues processed: 148 average time/residue: 0.9047 time to fit residues: 140.6414 Evaluate side-chains 145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118793 restraints weight = 11192.419| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.15 r_work: 0.3118 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12753 Z= 0.136 Angle : 0.588 6.713 18464 Z= 0.355 Chirality : 0.044 0.217 2100 Planarity : 0.004 0.039 1335 Dihedral : 30.972 107.085 4021 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.44 % Allowed : 12.76 % Favored : 85.81 % 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: 3.15 (0.30), residues: 742 helix: 2.87 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 92 TYR 0.009 0.001 TYR B 51 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.14 (12753) covalent geometry : angle 0.58849 / 0.36 (18464) hydrogen bonds : bond 0.04894 / 3.27 ( 782) hydrogen bonds : angle 2.80710 / 2.04 ( 1951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7364 (ttt90) cc_final: 0.7113 (mtt180) REVERT: B 93 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: C 15 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7474 (mtmt) REVERT: G 95 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7766 (tttt) outliers start: 9 outliers final: 4 residues processed: 146 average time/residue: 0.9447 time to fit residues: 144.5909 Evaluate side-chains 145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 50.0000 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.162063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113526 restraints weight = 10982.262| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.15 r_work: 0.3032 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12753 Z= 0.227 Angle : 0.718 6.844 18464 Z= 0.404 Chirality : 0.053 0.229 2100 Planarity : 0.006 0.043 1335 Dihedral : 31.324 109.031 4021 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.07 % Allowed : 12.28 % Favored : 85.65 % 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: 2.46 (0.30), residues: 742 helix: 2.41 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.56 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 40 TYR 0.020 0.003 TYR B 88 PHE 0.009 0.002 PHE D 70 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (12753) covalent geometry : angle 0.71814 / 0.40 (18464) hydrogen bonds : bond 0.07088 / 4.78 ( 782) hydrogen bonds : angle 3.04923 / 2.22 ( 1951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.279 Fit side-chains REVERT: B 93 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: C 15 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7518 (mtmt) REVERT: D 82 HIS cc_start: 0.8198 (t-90) cc_final: 0.7794 (m-70) REVERT: E 97 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8795 (mt-10) REVERT: G 95 LYS cc_start: 0.8451 (ttmt) cc_final: 0.7764 (tttt) REVERT: H 93 GLU cc_start: 0.8738 (mp0) cc_final: 0.8383 (mp0) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.9382 time to fit residues: 140.7797 Evaluate side-chains 145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 94 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.163665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115298 restraints weight = 10933.371| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.13 r_work: 0.3070 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12753 Z= 0.146 Angle : 0.668 12.134 18464 Z= 0.378 Chirality : 0.048 0.224 2100 Planarity : 0.005 0.046 1335 Dihedral : 31.306 110.429 4021 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.07 % Allowed : 12.92 % Favored : 85.01 % 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: 2.67 (0.30), residues: 742 helix: 2.57 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.49 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.013 0.002 TYR F 51 PHE 0.009 0.001 PHE E 67 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (12753) covalent geometry : angle 0.66828 / 0.38 (18464) hydrogen bonds : bond 0.05504 / 3.68 ( 782) hydrogen bonds : angle 3.02349 / 2.21 ( 1951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7517 (mtmt) REVERT: E 97 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8724 (mt-10) REVERT: G 95 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7734 (tttt) REVERT: H 93 GLU cc_start: 0.8721 (mp0) cc_final: 0.8350 (mp0) outliers start: 13 outliers final: 5 residues processed: 146 average time/residue: 0.9029 time to fit residues: 138.3888 Evaluate side-chains 146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 87 optimal weight: 40.0000 chunk 97 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.161420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112814 restraints weight = 10911.608| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.15 r_work: 0.3024 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12753 Z= 0.251 Angle : 0.731 7.039 18464 Z= 0.409 Chirality : 0.054 0.221 2100 Planarity : 0.006 0.040 1335 Dihedral : 31.359 117.628 4021 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.23 % Allowed : 12.92 % Favored : 84.85 % 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 (0.29), residues: 742 helix: 2.27 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.67 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 40 TYR 0.025 0.003 TYR B 88 PHE 0.010 0.002 PHE E 67 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 (12753) covalent geometry : angle 0.73085 / 0.41 (18464) hydrogen bonds : bond 0.07280 / 4.90 ( 782) hydrogen bonds : angle 3.08105 / 2.24 ( 1951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7559 (mtmt) REVERT: E 97 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8817 (mt-10) REVERT: G 95 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7759 (tttt) REVERT: H 93 GLU cc_start: 0.8776 (mp0) cc_final: 0.8378 (mp0) outliers start: 14 outliers final: 8 residues processed: 143 average time/residue: 0.9297 time to fit residues: 139.3104 Evaluate side-chains 145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.163002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114535 restraints weight = 10870.324| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.13 r_work: 0.3049 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12753 Z= 0.145 Angle : 0.675 7.881 18464 Z= 0.382 Chirality : 0.048 0.216 2100 Planarity : 0.005 0.061 1335 Dihedral : 31.348 118.168 4021 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.44 % Allowed : 14.19 % Favored : 84.37 % 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: 2.50 (0.30), residues: 742 helix: 2.45 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.017 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12753) covalent geometry : angle 0.67511 / 0.38 (18464) hydrogen bonds : bond 0.05887 / 3.94 ( 782) hydrogen bonds : angle 3.04846 / 2.22 ( 1951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7535 (mtmt) REVERT: D 68 ASP cc_start: 0.9142 (t0) cc_final: 0.8840 (t0) REVERT: E 97 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8776 (mt-10) REVERT: G 95 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7736 (tttt) REVERT: H 93 GLU cc_start: 0.8760 (mp0) cc_final: 0.8403 (mp0) outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.9041 time to fit residues: 133.9047 Evaluate side-chains 144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.163398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115091 restraints weight = 10897.005| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.13 r_work: 0.3059 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12753 Z= 0.155 Angle : 0.656 7.412 18464 Z= 0.375 Chirality : 0.048 0.214 2100 Planarity : 0.005 0.059 1335 Dihedral : 31.280 119.171 4021 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.12 % Allowed : 14.51 % Favored : 84.37 % 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: 2.66 (0.30), residues: 742 helix: 2.55 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.49 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.014 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12753) covalent geometry : angle 0.65634 / 0.37 (18464) hydrogen bonds : bond 0.05635 / 3.76 ( 782) hydrogen bonds : angle 2.96207 / 2.16 ( 1951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7538 (mtmt) REVERT: E 97 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8771 (mt-10) REVERT: G 95 LYS cc_start: 0.8456 (ttmt) cc_final: 0.7761 (tttt) REVERT: H 93 GLU cc_start: 0.8778 (mp0) cc_final: 0.8365 (mp0) outliers start: 7 outliers final: 6 residues processed: 143 average time/residue: 0.9127 time to fit residues: 136.9293 Evaluate side-chains 146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.163636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115367 restraints weight = 10950.642| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.14 r_work: 0.3063 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12753 Z= 0.161 Angle : 0.637 6.194 18464 Z= 0.367 Chirality : 0.047 0.205 2100 Planarity : 0.005 0.077 1335 Dihedral : 31.181 122.506 4021 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.44 % Allowed : 14.35 % Favored : 84.21 % 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: 2.69 (0.30), residues: 742 helix: 2.56 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.019 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (12753) covalent geometry : angle 0.63706 / 0.37 (18464) hydrogen bonds : bond 0.05546 / 3.71 ( 782) hydrogen bonds : angle 2.91674 / 2.13 ( 1951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7534 (mtmt) REVERT: C 91 GLU cc_start: 0.8077 (tt0) cc_final: 0.7786 (pm20) REVERT: D 71 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: E 97 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8777 (mt-10) REVERT: G 95 LYS cc_start: 0.8456 (ttmt) cc_final: 0.7763 (tttt) REVERT: H 93 GLU cc_start: 0.8772 (mp0) cc_final: 0.8330 (mp0) outliers start: 9 outliers final: 7 residues processed: 143 average time/residue: 0.9179 time to fit residues: 137.6147 Evaluate side-chains 146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 91 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.162357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113533 restraints weight = 10964.717| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.13 r_work: 0.3035 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12753 Z= 0.228 Angle : 0.708 7.535 18464 Z= 0.397 Chirality : 0.051 0.215 2100 Planarity : 0.006 0.069 1335 Dihedral : 31.319 127.590 4021 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.44 % Allowed : 14.51 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.29), residues: 742 helix: 2.34 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.64 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 52 TYR 0.041 0.003 TYR B 88 PHE 0.010 0.002 PHE E 67 HIS 0.006 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (12753) covalent geometry : angle 0.70813 / 0.40 (18464) hydrogen bonds : bond 0.06829 / 4.59 ( 782) hydrogen bonds : angle 3.02644 / 2.20 ( 1951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7561 (mtmt) REVERT: D 71 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: E 97 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8797 (mt-10) REVERT: G 95 LYS cc_start: 0.8461 (ttmt) cc_final: 0.7769 (tttt) REVERT: H 93 GLU cc_start: 0.8763 (mp0) cc_final: 0.8350 (mp0) outliers start: 9 outliers final: 7 residues processed: 139 average time/residue: 0.9360 time to fit residues: 136.5122 Evaluate side-chains 144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.164687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116183 restraints weight = 10973.078| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.12 r_work: 0.3075 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 12753 Z= 0.136 Angle : 0.640 9.619 18464 Z= 0.369 Chirality : 0.046 0.211 2100 Planarity : 0.005 0.072 1335 Dihedral : 31.226 128.912 4021 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.28 % Allowed : 14.51 % Favored : 84.21 % 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: 2.72 (0.30), residues: 742 helix: 2.59 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 52 TYR 0.022 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.14 (12753) covalent geometry : angle 0.63992 / 0.37 (18464) hydrogen bonds : bond 0.05219 / 3.48 ( 782) hydrogen bonds : angle 2.92717 / 2.13 ( 1951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5024.58 seconds wall clock time: 85 minutes 58.22 seconds (5158.22 seconds total)