Starting phenix.real_space_refine on Wed Aug 5 19:46:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j92_36085/08_2026/8j92_36085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j92_36085/08_2026/8j92_36085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2026/8j92_36085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2026/8j92_36085.map" model { file = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2026/8j92_36085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j92_36085/08_2026/8j92_36085.cif" } resolution = 2.9 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= 0.004 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 298 5.49 5 S 14 5.16 5 C 6641 2.51 5 N 2226 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12003 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 665 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 794 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 794 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3037 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3072 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Time building chain proxies: 2.08, per 1000 atoms: 0.17 Number of scatterers: 12003 At special positions: 0 Unit cell: (115.54, 121.9, 117.66, 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 298 15.00 O 2824 8.00 N 2226 7.00 C 6641 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: 0.59 Conformation dependent library (CDL) restraints added in 282.8 milliseconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 73.3% alpha, 2.9% beta 129 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.538A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.808A 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 25 through 31 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 55 through 82 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 107 removed outlier: 3.537A pdb=" N LEU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 128 through 149 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 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 35 through 46 Processing helix chain 'G' and resid 55 through 82 Processing helix chain 'G' and resid 88 through 99 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 removed outlier: 3.815A pdb=" N GLU H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 127 Processing helix chain 'H' and resid 128 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.159A 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 removed outlier: 6.805A pdb=" N THR B 96 " --> pdb=" O THR G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52 removed outlier: 7.004A pdb=" N ARG C 51 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'C' and resid 110 through 111 removed outlier: 7.105A pdb=" N THR C 110 " --> 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: 7.315A 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 51 through 52 removed outlier: 7.182A pdb=" N ARG G 51 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87 412 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 332 hydrogen bonds 664 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2224 1.33 - 1.45: 4271 1.45 - 1.57: 5714 1.57 - 1.69: 592 1.69 - 1.81: 26 Bond restraints: 12827 Sorted by residual: bond pdb=" O3' DA I -68 " pdb=" P DG I -67 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.20e-02 6.94e+03 3.43e+01 bond pdb=" O3' DG I -73 " pdb=" P DC I -72 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.20e-02 6.94e+03 2.56e+01 bond pdb=" C3' DC I 42 " pdb=" C2' DC I 42 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DC J -58 " pdb=" C2' DC J -58 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 ... (remaining 12822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 17271 1.48 - 2.96: 1245 2.96 - 4.44: 64 4.44 - 5.93: 11 5.93 - 7.41: 3 Bond angle restraints: 18594 Sorted by residual: angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" C4' DG I -74 " pdb=" O4' DG I -74 " pdb=" C1' DG I -74 " ideal model delta sigma weight residual 110.10 105.70 4.40 1.00e+00 1.00e+00 1.93e+01 angle pdb=" N3 DT J -67 " pdb=" C4 DT J -67 " pdb=" O4 DT J -67 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 60 " pdb=" C4 DT I 60 " pdb=" O4 DT I 60 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 18589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 5433 33.69 - 67.39: 1475 67.39 - 101.08: 14 101.08 - 134.77: 2 134.77 - 168.46: 3 Dihedral angle restraints: 6927 sinusoidal: 4772 harmonic: 2155 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 51.54 168.46 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J -58 " pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " pdb=" P DT J -57 " ideal model delta sinusoidal sigma weight residual 220.00 83.96 136.04 1 3.50e+01 8.16e-04 1.35e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 84.70 135.30 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 6924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1202 0.034 - 0.068: 601 0.068 - 0.101: 240 0.101 - 0.135: 73 0.135 - 0.169: 5 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CB ILE H 79 " pdb=" CA ILE H 79 " pdb=" CG1 ILE H 79 " pdb=" CG2 ILE H 79 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" C3' DC I 4 " pdb=" C4' DC I 4 " pdb=" O3' DC I 4 " pdb=" C2' DC I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 2118 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -73 " 0.048 2.00e-02 2.50e+03 2.59e-02 2.02e+01 pdb=" N9 DG I -73 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG I -73 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG I -73 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -73 " -0.031 2.00e-02 2.50e+03 pdb=" C6 DG I -73 " -0.030 2.00e-02 2.50e+03 pdb=" O6 DG I -73 " 0.056 2.00e-02 2.50e+03 pdb=" N1 DG I -73 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I -73 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -73 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG I -73 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -73 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -69 " -0.025 2.00e-02 2.50e+03 1.57e-02 7.39e+00 pdb=" N9 DG I -69 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -69 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DG I -69 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -69 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DG I -69 " -0.027 2.00e-02 2.50e+03 pdb=" O6 DG I -69 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG I -69 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DG I -69 " -0.008 2.00e-02 2.50e+03 pdb=" N2 DG I -69 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -69 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I -69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -70 " -0.014 2.00e-02 2.50e+03 1.35e-02 4.59e+00 pdb=" N1 DT I -70 " 0.034 2.00e-02 2.50e+03 pdb=" C2 DT I -70 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DT I -70 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT I -70 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I -70 " -0.013 2.00e-02 2.50e+03 pdb=" O4 DT I -70 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT I -70 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT I -70 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT I -70 " -0.009 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2219 2.79 - 3.32: 10426 3.32 - 3.84: 23617 3.84 - 4.37: 27847 4.37 - 4.90: 39494 Nonbonded interactions: 103603 Sorted by model distance: nonbonded pdb=" OG SER G 27 " pdb=" O LEU G 32 " model vdw 2.259 3.040 nonbonded pdb=" OG SER C 27 " pdb=" O LEU C 32 " model vdw 2.272 3.040 nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.276 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.278 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.306 3.120 ... (remaining 103598 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:5.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.070 12827 Z= 0.546 Angle : 0.752 7.407 18594 Z= 0.656 Chirality : 0.046 0.169 2121 Planarity : 0.004 0.044 1312 Dihedral : 28.059 168.462 5537 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 2.70 (0.30), residues: 733 helix: 2.45 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.24 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 49 TYR 0.011 0.002 TYR H 65 PHE 0.011 0.001 PHE D 90 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.55 (12827) covalent geometry : angle 0.75151 / 0.66 (18594) hydrogen bonds : bond 0.07540 / 5.03 ( 744) hydrogen bonds : angle 3.41646 / 2.49 ( 1888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.232 Fit side-chains REVERT: A 50 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 84 MET cc_start: 0.7771 (mmm) cc_final: 0.7462 (tpp) REVERT: C 81 ASP cc_start: 0.7890 (m-30) cc_final: 0.7683 (m-30) REVERT: D 72 GLN cc_start: 0.7555 (tt0) cc_final: 0.7204 (tt0) REVERT: G 84 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8359 (mmmm) REVERT: G 104 LYS cc_start: 0.7996 (tttt) cc_final: 0.7735 (mtpt) REVERT: H 147 THR cc_start: 0.7267 (m) cc_final: 0.7029 (p) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.6847 time to fit residues: 125.9687 Evaluate side-chains 101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 ASN D 109 ASN D 120 GLN E 108 ASN F 25 ASN G 33 GLN H 72 GLN H 109 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.177518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127117 restraints weight = 13285.588| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.98 r_work: 0.3207 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12827 Z= 0.143 Angle : 0.626 10.012 18594 Z= 0.369 Chirality : 0.045 0.268 2121 Planarity : 0.004 0.039 1312 Dihedral : 31.421 171.269 4065 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.70 % Allowed : 12.38 % Favored : 83.92 % 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: 733 helix: 2.62 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.21 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 83 TYR 0.010 0.001 TYR C 66 PHE 0.008 0.001 PHE D 90 HIS 0.006 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12827) covalent geometry : angle 0.62622 / 0.37 (18594) hydrogen bonds : bond 0.04962 / 3.45 ( 744) hydrogen bonds : angle 2.84854 / 2.04 ( 1888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.329 Fit side-chains REVERT: A 53 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8161 (ttmm) REVERT: A 120 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8120 (mtt) REVERT: C 70 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: C 81 ASP cc_start: 0.8093 (m-30) cc_final: 0.7891 (m-30) REVERT: D 72 GLN cc_start: 0.7961 (tt0) cc_final: 0.7666 (tt0) REVERT: D 118 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: G 82 ASN cc_start: 0.7937 (t0) cc_final: 0.7579 (t0) REVERT: G 84 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8391 (mmtp) REVERT: G 104 LYS cc_start: 0.8234 (tttt) cc_final: 0.7987 (mtpt) REVERT: H 72 GLN cc_start: 0.8391 (mt0) cc_final: 0.8158 (mt0) REVERT: H 96 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: H 133 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7155 (mptt) REVERT: H 147 THR cc_start: 0.7270 (m) cc_final: 0.7015 (p) outliers start: 23 outliers final: 7 residues processed: 121 average time/residue: 0.9268 time to fit residues: 118.3611 Evaluate side-chains 117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 133 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN F 25 ASN H 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.170638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120395 restraints weight = 13314.305| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 0.85 r_work: 0.3114 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12827 Z= 0.190 Angle : 0.671 10.387 18594 Z= 0.384 Chirality : 0.047 0.273 2121 Planarity : 0.005 0.041 1312 Dihedral : 31.627 170.793 4065 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.34 % Allowed : 13.50 % Favored : 82.15 % 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: 2.40 (0.30), residues: 733 helix: 2.22 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.33 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 45 TYR 0.025 0.003 TYR F 88 PHE 0.015 0.002 PHE H 146 HIS 0.004 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (12827) covalent geometry : angle 0.67137 / 0.38 (18594) hydrogen bonds : bond 0.05620 / 3.88 ( 744) hydrogen bonds : angle 2.98235 / 2.16 ( 1888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.320 Fit side-chains REVERT: A 53 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8265 (ttmm) REVERT: A 59 GLU cc_start: 0.7763 (pp20) cc_final: 0.7245 (pt0) REVERT: A 120 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8200 (mtt) REVERT: D 72 GLN cc_start: 0.7806 (tt0) cc_final: 0.7506 (tt0) REVERT: D 96 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7581 (tp30) REVERT: D 118 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: E 49 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7913 (mtm110) REVERT: G 82 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7512 (t0) REVERT: G 84 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8413 (mmmm) REVERT: H 96 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: H 111 LYS cc_start: 0.7630 (tttp) cc_final: 0.7125 (mmtm) REVERT: H 118 GLU cc_start: 0.8151 (mp0) cc_final: 0.7949 (mp0) REVERT: H 133 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7133 (mptt) REVERT: H 147 THR cc_start: 0.7288 (m) cc_final: 0.7035 (p) outliers start: 27 outliers final: 10 residues processed: 129 average time/residue: 0.8913 time to fit residues: 121.5737 Evaluate side-chains 126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 133 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN H 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.172130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121279 restraints weight = 13258.583| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.03 r_work: 0.3106 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12827 Z= 0.139 Angle : 0.626 9.893 18594 Z= 0.363 Chirality : 0.045 0.260 2121 Planarity : 0.004 0.040 1312 Dihedral : 31.578 171.825 4065 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.34 % Allowed : 15.76 % Favored : 79.90 % 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: 2.68 (0.31), residues: 733 helix: 2.44 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.25 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.013 0.002 TYR F 51 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (12827) covalent geometry : angle 0.62579 / 0.36 (18594) hydrogen bonds : bond 0.04764 / 3.31 ( 744) hydrogen bonds : angle 2.90443 / 2.09 ( 1888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.271 Fit side-chains REVERT: A 53 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8214 (ttmm) REVERT: A 59 GLU cc_start: 0.7872 (pp20) cc_final: 0.7323 (pt0) REVERT: A 120 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8174 (mtt) REVERT: A 129 ARG cc_start: 0.7912 (tpt90) cc_final: 0.7610 (tpt-90) REVERT: D 72 GLN cc_start: 0.7834 (tt0) cc_final: 0.7550 (tt0) REVERT: D 96 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: D 111 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8441 (mmtp) REVERT: D 118 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: E 49 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7982 (mtm110) REVERT: G 84 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8445 (mmmm) REVERT: H 96 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: H 111 LYS cc_start: 0.7640 (tttp) cc_final: 0.7125 (mmtm) REVERT: H 133 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7187 (mptt) REVERT: H 147 THR cc_start: 0.7266 (m) cc_final: 0.6992 (p) outliers start: 27 outliers final: 8 residues processed: 122 average time/residue: 0.8435 time to fit residues: 108.7424 Evaluate side-chains 123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 133 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120587 restraints weight = 13349.838| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.10 r_work: 0.3089 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12827 Z= 0.144 Angle : 0.603 9.712 18594 Z= 0.354 Chirality : 0.044 0.266 2121 Planarity : 0.004 0.042 1312 Dihedral : 31.530 171.823 4065 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.18 % Allowed : 16.72 % Favored : 79.10 % 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: 2.78 (0.30), residues: 733 helix: 2.51 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.22 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.017 0.002 TYR F 88 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (12827) covalent geometry : angle 0.60316 / 0.35 (18594) hydrogen bonds : bond 0.04653 / 3.22 ( 744) hydrogen bonds : angle 2.83845 / 2.04 ( 1888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.314 Fit side-chains REVERT: A 53 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8297 (ttmm) REVERT: A 59 GLU cc_start: 0.8025 (pp20) cc_final: 0.7489 (pt0) REVERT: A 129 ARG cc_start: 0.7929 (tpt90) cc_final: 0.7686 (tpt-90) REVERT: D 72 GLN cc_start: 0.7886 (tt0) cc_final: 0.7603 (tt0) REVERT: D 96 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7745 (tp30) REVERT: D 111 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8497 (mmtp) REVERT: E 49 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7993 (mtm110) REVERT: G 84 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8445 (mmmm) REVERT: G 104 LYS cc_start: 0.8441 (tttt) cc_final: 0.8191 (mtpt) REVERT: H 96 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: H 109 ASN cc_start: 0.8377 (m-40) cc_final: 0.8154 (m110) REVERT: H 111 LYS cc_start: 0.7660 (tttp) cc_final: 0.7194 (mmtm) REVERT: H 147 THR cc_start: 0.7259 (m) cc_final: 0.6994 (p) outliers start: 26 outliers final: 10 residues processed: 129 average time/residue: 0.8250 time to fit residues: 112.5485 Evaluate side-chains 124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121435 restraints weight = 13360.519| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.84 r_work: 0.3142 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12827 Z= 0.139 Angle : 0.591 9.447 18594 Z= 0.346 Chirality : 0.043 0.259 2121 Planarity : 0.004 0.042 1312 Dihedral : 31.427 174.026 4065 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.89 % Allowed : 18.65 % Favored : 78.46 % 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: 2.93 (0.30), residues: 733 helix: 2.62 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 42 TYR 0.011 0.002 TYR F 51 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (12827) covalent geometry : angle 0.59123 / 0.35 (18594) hydrogen bonds : bond 0.04355 / 3.02 ( 744) hydrogen bonds : angle 2.80094 / 2.00 ( 1888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.393 Fit side-chains REVERT: A 53 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8210 (ttmm) REVERT: A 59 GLU cc_start: 0.7908 (pp20) cc_final: 0.7252 (pt0) REVERT: B 68 ASP cc_start: 0.8802 (m-30) cc_final: 0.8447 (m-30) REVERT: D 72 GLN cc_start: 0.7776 (tt0) cc_final: 0.7472 (tt0) REVERT: D 111 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8370 (mmtp) REVERT: D 118 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: E 56 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8100 (ttmt) REVERT: E 120 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7774 (mtm) REVERT: F 84 MET cc_start: 0.8801 (tpp) cc_final: 0.8596 (mmm) REVERT: F 92 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7934 (mtp-110) REVERT: G 84 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8514 (mmtp) REVERT: H 96 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: H 100 SER cc_start: 0.9156 (p) cc_final: 0.8758 (m) REVERT: H 104 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7232 (mmtp) REVERT: H 111 LYS cc_start: 0.7476 (tttp) cc_final: 0.6981 (mmtm) REVERT: H 147 THR cc_start: 0.7183 (m) cc_final: 0.6871 (p) outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 0.7872 time to fit residues: 105.6861 Evaluate side-chains 127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 104 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 85 optimal weight: 50.0000 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121546 restraints weight = 13317.570| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.85 r_work: 0.3138 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12827 Z= 0.138 Angle : 0.582 9.547 18594 Z= 0.342 Chirality : 0.043 0.250 2121 Planarity : 0.004 0.042 1312 Dihedral : 31.371 174.607 4065 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.05 % Allowed : 18.81 % Favored : 78.14 % 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: 2.93 (0.30), residues: 733 helix: 2.59 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.09 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 41 TYR 0.011 0.002 TYR F 51 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12827) covalent geometry : angle 0.58207 / 0.34 (18594) hydrogen bonds : bond 0.04358 / 3.00 ( 744) hydrogen bonds : angle 2.78912 / 2.00 ( 1888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.333 Fit side-chains REVERT: A 53 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8231 (ttmm) REVERT: B 68 ASP cc_start: 0.8760 (m-30) cc_final: 0.8522 (m-30) REVERT: D 72 GLN cc_start: 0.7784 (tt0) cc_final: 0.7482 (tt0) REVERT: D 111 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8341 (mmtp) REVERT: D 118 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: E 56 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8120 (ttmt) REVERT: F 92 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7918 (mtp-110) REVERT: G 84 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8532 (mmtp) REVERT: H 96 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: H 100 SER cc_start: 0.9141 (p) cc_final: 0.8794 (m) REVERT: H 107 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7457 (ttm110) REVERT: H 111 LYS cc_start: 0.7405 (tttp) cc_final: 0.6953 (mmtm) REVERT: H 147 THR cc_start: 0.7174 (m) cc_final: 0.6870 (p) outliers start: 19 outliers final: 10 residues processed: 124 average time/residue: 0.7607 time to fit residues: 99.6787 Evaluate side-chains 128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 118 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 40.0000 chunk 84 optimal weight: 40.0000 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.169064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118523 restraints weight = 13231.011| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.91 r_work: 0.3067 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12827 Z= 0.196 Angle : 0.668 10.350 18594 Z= 0.376 Chirality : 0.047 0.273 2121 Planarity : 0.005 0.042 1312 Dihedral : 31.557 173.082 4065 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.70 % Allowed : 18.17 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.30), residues: 733 helix: 2.23 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.29 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 42 TYR 0.019 0.003 TYR F 88 PHE 0.014 0.002 PHE A 67 HIS 0.004 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (12827) covalent geometry : angle 0.66756 / 0.38 (18594) hydrogen bonds : bond 0.05417 / 3.73 ( 744) hydrogen bonds : angle 2.97889 / 2.15 ( 1888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.337 Fit side-chains REVERT: A 53 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8364 (ttmm) REVERT: B 68 ASP cc_start: 0.8888 (m-30) cc_final: 0.8508 (m-30) REVERT: D 72 GLN cc_start: 0.7813 (tt0) cc_final: 0.7503 (tt0) REVERT: D 111 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8505 (mmtp) REVERT: D 118 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: E 56 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8117 (ttmt) REVERT: F 92 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7969 (mtp-110) REVERT: G 82 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7682 (t0) REVERT: G 84 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8538 (mmtp) REVERT: H 96 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: H 110 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8265 (mtpp) REVERT: H 111 LYS cc_start: 0.7686 (tttp) cc_final: 0.7180 (mmtm) REVERT: H 147 THR cc_start: 0.7214 (m) cc_final: 0.6927 (p) outliers start: 23 outliers final: 8 residues processed: 132 average time/residue: 0.7824 time to fit residues: 108.9871 Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 110 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.170192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118936 restraints weight = 13211.187| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.85 r_work: 0.3093 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12827 Z= 0.148 Angle : 0.627 9.863 18594 Z= 0.359 Chirality : 0.045 0.247 2121 Planarity : 0.005 0.043 1312 Dihedral : 31.513 173.211 4065 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.57 % Allowed : 20.26 % Favored : 77.17 % 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: 2.47 (0.30), residues: 733 helix: 2.27 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.30 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.023 0.002 TYR F 88 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (12827) covalent geometry : angle 0.62670 / 0.36 (18594) hydrogen bonds : bond 0.04798 / 3.31 ( 744) hydrogen bonds : angle 2.93006 / 2.11 ( 1888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.312 Fit side-chains REVERT: A 53 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: B 68 ASP cc_start: 0.8864 (m-30) cc_final: 0.8498 (m-30) REVERT: D 72 GLN cc_start: 0.7770 (tt0) cc_final: 0.7440 (tt0) REVERT: D 111 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8453 (mmtp) REVERT: D 118 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: E 56 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8138 (ttmt) REVERT: F 92 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7896 (mtp-110) REVERT: G 82 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7676 (t0) REVERT: G 84 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8541 (mmtp) REVERT: G 104 LYS cc_start: 0.8406 (tttt) cc_final: 0.8159 (mtpt) REVERT: H 96 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: H 100 SER cc_start: 0.9128 (p) cc_final: 0.8746 (m) REVERT: H 104 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7058 (mmtp) REVERT: H 111 LYS cc_start: 0.7624 (tttp) cc_final: 0.7121 (mmtm) REVERT: H 147 THR cc_start: 0.7260 (m) cc_final: 0.6965 (p) outliers start: 16 outliers final: 6 residues processed: 125 average time/residue: 0.7632 time to fit residues: 100.6664 Evaluate side-chains 125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 50.0000 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.170674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119502 restraints weight = 13324.862| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.87 r_work: 0.3103 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12827 Z= 0.131 Angle : 0.613 9.622 18594 Z= 0.354 Chirality : 0.044 0.253 2121 Planarity : 0.004 0.042 1312 Dihedral : 31.479 173.273 4065 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.57 % Allowed : 20.42 % Favored : 77.01 % 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: 2.63 (0.30), residues: 733 helix: 2.39 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.24 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.024 0.002 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.13 (12827) covalent geometry : angle 0.61338 / 0.35 (18594) hydrogen bonds : bond 0.04533 / 3.13 ( 744) hydrogen bonds : angle 2.91091 / 2.10 ( 1888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.238 Fit side-chains REVERT: A 53 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8207 (ttmm) REVERT: A 59 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: A 115 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7913 (mmtm) REVERT: B 68 ASP cc_start: 0.8865 (m-30) cc_final: 0.8501 (m-30) REVERT: D 72 GLN cc_start: 0.7751 (tt0) cc_final: 0.7421 (tt0) REVERT: D 111 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8355 (mmtp) REVERT: D 118 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: E 56 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8100 (ttmt) REVERT: F 92 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7877 (mtp-110) REVERT: G 82 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7649 (t0) REVERT: G 84 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8520 (mmtp) REVERT: G 104 LYS cc_start: 0.8411 (tttt) cc_final: 0.8200 (mtpt) REVERT: H 96 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: H 100 SER cc_start: 0.9117 (p) cc_final: 0.8738 (m) REVERT: H 104 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7009 (mmtp) REVERT: H 111 LYS cc_start: 0.7597 (tttp) cc_final: 0.7072 (mmtm) REVERT: H 147 THR cc_start: 0.7238 (m) cc_final: 0.6932 (p) outliers start: 16 outliers final: 6 residues processed: 124 average time/residue: 0.7776 time to fit residues: 101.9239 Evaluate side-chains 125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.170032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119079 restraints weight = 13308.070| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 0.88 r_work: 0.3089 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12827 Z= 0.165 Angle : 0.627 10.291 18594 Z= 0.359 Chirality : 0.045 0.262 2121 Planarity : 0.005 0.043 1312 Dihedral : 31.450 172.045 4065 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.57 % Allowed : 20.74 % Favored : 76.69 % 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: 2.52 (0.30), residues: 733 helix: 2.32 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.28 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 42 TYR 0.013 0.002 TYR F 88 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (12827) covalent geometry : angle 0.62675 / 0.36 (18594) hydrogen bonds : bond 0.04818 / 3.32 ( 744) hydrogen bonds : angle 2.91502 / 2.10 ( 1888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4076.08 seconds wall clock time: 69 minutes 49.05 seconds (4189.05 seconds total)