Starting phenix.real_space_refine on Fri Oct 23 23:05:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/43if_81903/10_2026/43if_81903.cif Found real_map, /net/cci-nas-00/data/ceres_data/43if_81903/10_2026/43if_81903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/43if_81903/10_2026/43if_81903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/43if_81903/10_2026/43if_81903.map" model { file = "/net/cci-nas-00/data/ceres_data/43if_81903/10_2026/43if_81903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/43if_81903/10_2026/43if_81903.cif" } resolution = 2.87 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= 0.013 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 269 5.49 5 S 12 5.16 5 C 6314 2.51 5 N 2131 2.21 5 O 2660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11386 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 769 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 769 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2752 Classifications: {'DNA': 135} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 134} Chain: "J" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2780 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Time building chain proxies: 2.31, per 1000 atoms: 0.20 Number of scatterers: 11386 At special positions: 0 Unit cell: (76.5, 119, 121.55, 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 12 16.00 P 269 15.00 O 2660 8.00 N 2131 7.00 C 6314 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: 0.80 Conformation dependent library (CDL) restraints added in 234.0 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 72.8% alpha, 3.0% beta 133 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.540A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.614A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.530A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 75 removed outlier: 4.284A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.010A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.522A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.551A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 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: 3.536A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.596A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.608A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.566A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.994A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.552A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.746A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.436A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.785A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.809A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.075A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.510A 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 100 through 102 removed outlier: 6.936A 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: 7.083A 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: 7.288A 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 78 391 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.13 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: 2191 1.33 - 1.45: 3892 1.45 - 1.57: 5493 1.57 - 1.69: 537 1.69 - 1.81: 22 Bond restraints: 12135 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DA J 65 " pdb=" C2' DA J 65 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA I -22 " pdb=" C2' DA I -22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 ... (remaining 12130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 16846 1.91 - 3.82: 667 3.82 - 5.73: 27 5.73 - 7.64: 2 7.64 - 9.55: 1 Bond angle restraints: 17543 Sorted by residual: angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" O4' DA I 17 " pdb=" C4' DA I 17 " pdb=" C3' DA I 17 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 17538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 5187 35.06 - 70.13: 1383 70.13 - 105.19: 19 105.19 - 140.25: 3 140.25 - 175.32: 1 Dihedral angle restraints: 6593 sinusoidal: 4449 harmonic: 2144 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 -140.00 35.32 -175.32 1 3.50e+01 8.16e-04 1.56e+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 84.69 135.31 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 94.84 125.16 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 6590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1188 0.033 - 0.066: 528 0.066 - 0.099: 206 0.099 - 0.132: 69 0.132 - 0.165: 6 Chirality restraints: 1997 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-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 -2.57 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 1994 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 68 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" CG ASP H 68 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP H 68 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP H 68 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" CG ASP F 24 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO G 80 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.020 5.00e-02 4.00e+02 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4957 2.98 - 3.46: 10184 3.46 - 3.94: 20928 3.94 - 4.42: 24260 4.42 - 4.90: 32904 Nonbonded interactions: 93233 Sorted by model distance: nonbonded pdb=" O THR A 80 " pdb=" OD1 ASP A 81 " model vdw 2.497 3.040 nonbonded pdb=" O THR E 80 " pdb=" OD1 ASP E 81 " model vdw 2.517 3.040 nonbonded pdb=" O ASP D 51 " pdb=" OD1 ASP D 51 " model vdw 2.525 3.040 nonbonded pdb=" O5' DG I -71 " pdb=" O4' DG I -71 " model vdw 2.537 2.432 nonbonded pdb=" O5' DG I -70 " pdb=" O4' DG I -70 " model vdw 2.556 2.432 ... (remaining 93228 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' } ncs_group { reference = chain 'B' 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: 3.160 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.100 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 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 0.033 12135 Z= 0.524 Angle : 0.738 9.553 17543 Z= 0.646 Chirality : 0.044 0.165 1997 Planarity : 0.004 0.036 1286 Dihedral : 28.411 175.315 5213 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.49 % Allowed : 28.43 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.32), residues: 726 helix: 2.42 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.35 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 45 TYR 0.015 0.001 TYR B 88 PHE 0.009 0.001 PHE F 61 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.52 (12135) covalent geometry : angle 0.73827 / 0.65 (17543) hydrogen bonds : bond 0.11052 / 7.19 ( 734) hydrogen bonds : angle 3.42402 / 2.57 ( 1853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.317 Fit side-chains REVERT: C 15 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7244 (pptt) REVERT: E 73 GLU cc_start: 0.8758 (tt0) cc_final: 0.8549 (tt0) REVERT: G 64 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: G 95 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8755 (tttt) REVERT: H 33 ARG cc_start: 0.6446 (mtt180) cc_final: 0.6012 (mmt180) REVERT: H 82 HIS cc_start: 0.8672 (t-90) cc_final: 0.8117 (m170) outliers start: 3 outliers final: 1 residues processed: 109 average time/residue: 0.8243 time to fit residues: 94.4649 Evaluate side-chains 111 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.098123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061435 restraints weight = 23489.633| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.68 r_work: 0.2792 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12135 Z= 0.168 Angle : 0.618 8.561 17543 Z= 0.364 Chirality : 0.045 0.272 1997 Planarity : 0.004 0.040 1286 Dihedral : 30.667 172.625 3769 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.61 % Allowed : 25.65 % Favored : 71.73 % 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: 2.42 (0.32), residues: 726 helix: 2.57 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.29 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.012 0.001 TYR B 88 PHE 0.008 0.001 PHE F 61 HIS 0.001 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (12135) covalent geometry : angle 0.61784 / 0.36 (17543) hydrogen bonds : bond 0.05774 / 3.81 ( 734) hydrogen bonds : angle 2.84765 / 2.12 ( 1853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.269 Fit side-chains REVERT: A 97 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: C 15 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7325 (pttt) REVERT: D 82 HIS cc_start: 0.8623 (t-90) cc_final: 0.8205 (m170) REVERT: D 113 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: E 73 GLU cc_start: 0.8666 (tt0) cc_final: 0.8429 (tt0) REVERT: G 64 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: G 92 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: G 95 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8848 (tttt) REVERT: H 33 ARG cc_start: 0.6468 (mtt180) cc_final: 0.6140 (mmt180) REVERT: H 68 ASP cc_start: 0.9028 (t0) cc_final: 0.8822 (t0) REVERT: H 82 HIS cc_start: 0.8569 (t-90) cc_final: 0.8095 (m170) outliers start: 16 outliers final: 6 residues processed: 122 average time/residue: 0.8204 time to fit residues: 105.4822 Evaluate side-chains 122 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [78, 88, 67, 82, 14, 76, 53, 57, 45, 38, 73] chunk 78 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061942 restraints weight = 23749.037| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.75 r_work: 0.2803 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12135 Z= 0.153 Angle : 0.590 7.989 17543 Z= 0.350 Chirality : 0.043 0.262 1997 Planarity : 0.004 0.039 1286 Dihedral : 30.698 173.067 3766 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.96 % Allowed : 25.65 % Favored : 72.39 % 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: 2.60 (0.32), residues: 726 helix: 2.71 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.27 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.009 0.001 TYR D 40 PHE 0.008 0.001 PHE F 61 HIS 0.001 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12135) covalent geometry : angle 0.59012 / 0.35 (17543) hydrogen bonds : bond 0.05299 / 3.49 ( 734) hydrogen bonds : angle 2.70570 / 2.01 ( 1853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.222 Fit side-chains REVERT: A 97 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: C 15 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7323 (pttt) REVERT: C 27 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8227 (t) REVERT: D 71 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: D 82 HIS cc_start: 0.8574 (t-90) cc_final: 0.8118 (m170) REVERT: D 113 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: E 73 GLU cc_start: 0.8649 (tt0) cc_final: 0.8383 (tt0) REVERT: G 95 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8825 (tttt) REVERT: H 33 ARG cc_start: 0.6468 (mtt180) cc_final: 0.6133 (mmt180) REVERT: H 68 ASP cc_start: 0.9067 (t0) cc_final: 0.8782 (t0) REVERT: H 82 HIS cc_start: 0.8585 (t-90) cc_final: 0.8066 (m170) outliers start: 12 outliers final: 6 residues processed: 121 average time/residue: 0.7786 time to fit residues: 99.3363 Evaluate side-chains 120 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [8, 36, 77, 74, 13, 95, 78, 42, 86, 87, 0] chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 95 GLN E 113 HIS G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059284 restraints weight = 23489.287| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.72 r_work: 0.2738 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12135 Z= 0.244 Angle : 0.667 8.513 17543 Z= 0.378 Chirality : 0.048 0.270 1997 Planarity : 0.005 0.042 1286 Dihedral : 30.980 172.891 3766 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.74 % Allowed : 23.20 % Favored : 72.06 % 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: 2.33 (0.32), residues: 726 helix: 2.51 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.33 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 86 TYR 0.017 0.002 TYR H 42 PHE 0.012 0.002 PHE D 65 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (12135) covalent geometry : angle 0.66720 / 0.38 (17543) hydrogen bonds : bond 0.06800 / 4.48 ( 734) hydrogen bonds : angle 2.88065 / 2.15 ( 1853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.269 Fit side-chains REVERT: A 64 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (mtmm) REVERT: A 97 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: C 15 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7266 (pptt) REVERT: C 104 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8571 (mm-40) REVERT: D 71 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: D 82 HIS cc_start: 0.8738 (t-90) cc_final: 0.8333 (m170) REVERT: D 113 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: D 120 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8636 (tptp) REVERT: E 73 GLU cc_start: 0.8733 (tt0) cc_final: 0.8497 (tt0) REVERT: G 92 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: G 95 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8816 (tttt) REVERT: H 33 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6193 (mmt180) REVERT: H 68 ASP cc_start: 0.9098 (t0) cc_final: 0.8791 (t0) REVERT: H 82 HIS cc_start: 0.8606 (t-90) cc_final: 0.8151 (m170) outliers start: 29 outliers final: 11 residues processed: 127 average time/residue: 0.7907 time to fit residues: 105.8973 Evaluate side-chains 128 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [86, 58, 25, 51, 13, 32, 64, 36, 23, 48, 43] chunk 86 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 0.0170 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062143 restraints weight = 23497.092| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.69 r_work: 0.2808 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12135 Z= 0.143 Angle : 0.597 7.906 17543 Z= 0.350 Chirality : 0.044 0.279 1997 Planarity : 0.004 0.039 1286 Dihedral : 30.880 173.455 3766 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.12 % Allowed : 25.82 % Favored : 72.06 % 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 (0.32), residues: 726 helix: 2.76 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.34 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.011 0.001 TYR D 40 PHE 0.007 0.001 PHE F 61 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12135) covalent geometry : angle 0.59672 / 0.35 (17543) hydrogen bonds : bond 0.05132 / 3.38 ( 734) hydrogen bonds : angle 2.63970 / 1.96 ( 1853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.291 Fit side-chains REVERT: A 97 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: C 15 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7235 (pptt) REVERT: D 71 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: D 82 HIS cc_start: 0.8591 (t70) cc_final: 0.8097 (m170) REVERT: E 73 GLU cc_start: 0.8580 (tt0) cc_final: 0.8286 (tt0) REVERT: G 92 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: G 95 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8796 (tttt) REVERT: H 33 ARG cc_start: 0.6519 (mtt180) cc_final: 0.6123 (mmt180) REVERT: H 68 ASP cc_start: 0.9059 (t0) cc_final: 0.8726 (t0) REVERT: H 82 HIS cc_start: 0.8576 (t-90) cc_final: 0.8047 (m170) outliers start: 13 outliers final: 7 residues processed: 119 average time/residue: 0.8119 time to fit residues: 101.9130 Evaluate side-chains 122 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [9, 84, 68, 34, 8, 82, 11, 57, 4, 94, 19] chunk 9 optimal weight: 0.1980 chunk 84 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063360 restraints weight = 23688.153| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.70 r_work: 0.2839 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12135 Z= 0.136 Angle : 0.570 8.127 17543 Z= 0.337 Chirality : 0.042 0.261 1997 Planarity : 0.004 0.042 1286 Dihedral : 30.783 172.933 3766 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.29 % Allowed : 26.47 % Favored : 71.24 % 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: 2.83 (0.32), residues: 726 helix: 2.90 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.011 0.001 TYR D 40 PHE 0.006 0.001 PHE F 61 HIS 0.001 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (12135) covalent geometry : angle 0.57031 / 0.34 (17543) hydrogen bonds : bond 0.04602 / 3.02 ( 734) hydrogen bonds : angle 2.54815 / 1.90 ( 1853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.285 Fit side-chains REVERT: A 94 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: A 97 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: C 15 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7277 (pptt) REVERT: C 27 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8257 (t) REVERT: D 71 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: D 82 HIS cc_start: 0.8475 (t70) cc_final: 0.8023 (m170) REVERT: E 73 GLU cc_start: 0.8594 (tt0) cc_final: 0.8312 (tt0) REVERT: G 95 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8910 (tttt) REVERT: H 33 ARG cc_start: 0.6530 (mtt180) cc_final: 0.6155 (mmt180) REVERT: H 68 ASP cc_start: 0.9044 (t0) cc_final: 0.8757 (t0) REVERT: H 82 HIS cc_start: 0.8514 (t-90) cc_final: 0.8042 (m170) outliers start: 14 outliers final: 5 residues processed: 120 average time/residue: 0.7696 time to fit residues: 97.4148 Evaluate side-chains 120 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [54, 59, 65, 90, 15, 22, 42, 91, 13, 49, 39] chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.099794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063434 restraints weight = 23732.884| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.70 r_work: 0.2840 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12135 Z= 0.137 Angle : 0.578 9.015 17543 Z= 0.339 Chirality : 0.042 0.266 1997 Planarity : 0.004 0.044 1286 Dihedral : 30.808 173.419 3766 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.29 % Allowed : 26.96 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.32), residues: 726 helix: 2.93 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.014 0.001 TYR D 83 PHE 0.007 0.001 PHE B 61 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (12135) covalent geometry : angle 0.57845 / 0.34 (17543) hydrogen bonds : bond 0.04538 / 2.98 ( 734) hydrogen bonds : angle 2.53009 / 1.88 ( 1853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.176 Fit side-chains REVERT: A 94 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: A 97 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: C 15 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7274 (pptt) REVERT: D 71 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: D 82 HIS cc_start: 0.8474 (t70) cc_final: 0.8031 (m170) REVERT: E 73 GLU cc_start: 0.8608 (tt0) cc_final: 0.8314 (tt0) REVERT: G 95 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8807 (tttt) REVERT: H 33 ARG cc_start: 0.6520 (mtt180) cc_final: 0.6163 (mmt180) REVERT: H 68 ASP cc_start: 0.9052 (t0) cc_final: 0.8758 (t0) REVERT: H 82 HIS cc_start: 0.8511 (t-90) cc_final: 0.8048 (m170) outliers start: 14 outliers final: 7 residues processed: 120 average time/residue: 0.7493 time to fit residues: 94.9752 Evaluate side-chains 119 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [70, 64, 52, 12, 16, 46, 43, 37, 3, 94, 82] chunk 70 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.0050 chunk 46 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.099844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063408 restraints weight = 23593.022| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.70 r_work: 0.2840 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12135 Z= 0.139 Angle : 0.578 9.747 17543 Z= 0.338 Chirality : 0.042 0.265 1997 Planarity : 0.004 0.037 1286 Dihedral : 30.811 173.111 3766 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.45 % Allowed : 27.12 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.32), residues: 726 helix: 2.95 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 86 TYR 0.015 0.001 TYR D 83 PHE 0.007 0.001 PHE B 61 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12135) covalent geometry : angle 0.57814 / 0.34 (17543) hydrogen bonds : bond 0.04564 / 2.99 ( 734) hydrogen bonds : angle 2.51117 / 1.87 ( 1853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.295 Fit side-chains REVERT: A 64 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8522 (mtmm) REVERT: A 94 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: A 97 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: C 15 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7270 (pptt) REVERT: C 27 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8254 (t) REVERT: D 71 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: D 82 HIS cc_start: 0.8473 (t70) cc_final: 0.8027 (m170) REVERT: E 73 GLU cc_start: 0.8613 (tt0) cc_final: 0.8316 (tt0) REVERT: G 92 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: G 95 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8918 (tttt) REVERT: H 33 ARG cc_start: 0.6492 (mtt180) cc_final: 0.6128 (mmt180) REVERT: H 68 ASP cc_start: 0.9049 (t0) cc_final: 0.8752 (t0) REVERT: H 82 HIS cc_start: 0.8523 (t-90) cc_final: 0.8054 (m170) outliers start: 15 outliers final: 8 residues processed: 119 average time/residue: 0.7754 time to fit residues: 97.4422 Evaluate side-chains 125 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [84, 53, 36, 28, 76, 69, 5, 27, 13, 85, 90] chunk 84 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.099400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062901 restraints weight = 23372.452| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.69 r_work: 0.2828 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12135 Z= 0.157 Angle : 0.597 10.839 17543 Z= 0.345 Chirality : 0.042 0.267 1997 Planarity : 0.004 0.038 1286 Dihedral : 30.841 173.112 3766 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.96 % Allowed : 27.78 % Favored : 70.26 % 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: 2.84 (0.32), residues: 726 helix: 2.92 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.29 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.012 0.001 TYR B 88 PHE 0.008 0.001 PHE F 61 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (12135) covalent geometry : angle 0.59719 / 0.35 (17543) hydrogen bonds : bond 0.04843 / 3.18 ( 734) hydrogen bonds : angle 2.54265 / 1.90 ( 1853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.306 Fit side-chains REVERT: A 64 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8523 (mtmm) REVERT: A 97 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: C 15 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7252 (pptt) REVERT: C 27 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8250 (t) REVERT: D 71 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: D 82 HIS cc_start: 0.8520 (t70) cc_final: 0.8070 (m170) REVERT: E 73 GLU cc_start: 0.8624 (tt0) cc_final: 0.8323 (tt0) REVERT: G 95 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8884 (tttt) REVERT: H 33 ARG cc_start: 0.6515 (mtt180) cc_final: 0.6125 (mmt180) REVERT: H 68 ASP cc_start: 0.9061 (t0) cc_final: 0.8732 (t0) REVERT: H 82 HIS cc_start: 0.8540 (t-90) cc_final: 0.8045 (m170) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 0.7968 time to fit residues: 97.6276 Evaluate side-chains 120 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [53, 22, 25, 52, 49, 68, 37, 10, 66, 36, 80] chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.061096 restraints weight = 24438.088| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.90 r_work: 0.2778 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12135 Z= 0.139 Angle : 0.592 10.907 17543 Z= 0.342 Chirality : 0.042 0.263 1997 Planarity : 0.004 0.036 1286 Dihedral : 30.840 173.202 3766 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.12 % Allowed : 27.61 % Favored : 70.26 % 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: 2.87 (0.32), residues: 726 helix: 2.95 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.29 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.014 0.001 TYR D 83 PHE 0.007 0.001 PHE F 61 HIS 0.001 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (12135) covalent geometry : angle 0.59173 / 0.34 (17543) hydrogen bonds : bond 0.04728 / 3.11 ( 734) hydrogen bonds : angle 2.54010 / 1.89 ( 1853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.197 Fit side-chains REVERT: A 64 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8243 (mtmm) REVERT: A 97 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: C 15 LYS cc_start: 0.7933 (mmmt) cc_final: 0.6911 (pptt) REVERT: D 71 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: D 82 HIS cc_start: 0.8468 (t70) cc_final: 0.7728 (m170) REVERT: E 73 GLU cc_start: 0.8397 (tt0) cc_final: 0.8086 (tt0) REVERT: G 95 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8548 (tttt) REVERT: H 33 ARG cc_start: 0.6539 (mtt180) cc_final: 0.6050 (mmt180) REVERT: H 68 ASP cc_start: 0.8869 (t0) cc_final: 0.8475 (t0) REVERT: H 82 HIS cc_start: 0.8506 (t-90) cc_final: 0.7735 (m170) outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 0.7796 time to fit residues: 95.3879 Evaluate side-chains 120 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [84, 27, 26, 17, 61, 51, 94, 67, 29, 73, 38] chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 10.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.097967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061258 restraints weight = 24385.378| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.89 r_work: 0.2780 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12135 Z= 0.144 Angle : 0.592 11.221 17543 Z= 0.342 Chirality : 0.042 0.267 1997 Planarity : 0.004 0.037 1286 Dihedral : 30.838 173.185 3766 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.63 % Allowed : 27.78 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.32), residues: 726 helix: 2.96 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.31 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.015 0.001 TYR D 83 PHE 0.008 0.001 PHE F 61 HIS 0.001 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (12135) covalent geometry : angle 0.59156 / 0.34 (17543) hydrogen bonds : bond 0.04717 / 3.10 ( 734) hydrogen bonds : angle 2.52563 / 1.88 ( 1853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3173.96 seconds wall clock time: 54 minutes 56.47 seconds (3296.47 seconds total)