Starting phenix.real_space_refine on Thu Aug 6 05:52:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8b_29845/08_2026/8g8b_29845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8b_29845/08_2026/8g8b_29845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2026/8g8b_29845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2026/8g8b_29845.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2026/8g8b_29845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2026/8g8b_29845.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 336 5.49 5 S 17 5.16 5 C 7819 2.51 5 N 2611 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 14067 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 863 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3419 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "J" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3469 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1080 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Time building chain proxies: 2.69, per 1000 atoms: 0.19 Number of scatterers: 14067 At special positions: 0 Unit cell: (80.5, 119.14, 172.27, 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 17 16.00 P 336 15.00 O 3284 8.00 N 2611 7.00 C 7819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 391.6 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 74.5% alpha, 2.4% beta 161 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.053A 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 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: 3.736A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.233A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.950A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.363A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.552A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 239 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.928A 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: 6.705A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.125A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.758A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.760A 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: 6.981A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 491 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 389 hydrogen bonds 778 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.41 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: 2622 1.33 - 1.45: 4963 1.45 - 1.57: 6717 1.57 - 1.69: 670 1.69 - 1.81: 28 Bond restraints: 15000 Sorted by residual: bond pdb=" C1' DC J -96 " pdb=" N1 DC J -96 " ideal model delta sigma weight residual 1.468 1.552 -0.084 1.40e-02 5.10e+03 3.56e+01 bond pdb=" C1' DC I 83 " pdb=" N1 DC I 83 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.35e+01 bond pdb=" C1' DC I 85 " pdb=" N1 DC I 85 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.30e+01 bond pdb=" C1' DC I 81 " pdb=" N1 DC I 81 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" C1' DT I 79 " pdb=" N1 DT I 79 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.75e+01 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21229 2.36 - 4.72: 440 4.72 - 7.08: 23 7.08 - 9.44: 1 9.44 - 11.79: 1 Bond angle restraints: 21694 Sorted by residual: angle pdb=" N3 DT J 40 " pdb=" C4 DT J 40 " pdb=" O4 DT J 40 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" C3' DG J -71 " pdb=" C2' DG J -71 " pdb=" C1' DG J -71 " ideal model delta sigma weight residual 102.50 97.20 5.30 1.20e+00 6.94e-01 1.95e+01 angle pdb=" N3 DT I 70 " pdb=" C4 DT I 70 " pdb=" O4 DT I 70 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I 39 " pdb=" C4 DT I 39 " pdb=" O4 DT I 39 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I -52 " pdb=" C4 DT I -52 " pdb=" O4 DT I -52 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 21689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6500 35.81 - 71.62: 1745 71.62 - 107.42: 15 107.42 - 143.23: 2 143.23 - 179.04: 1 Dihedral angle restraints: 8263 sinusoidal: 5648 harmonic: 2615 Sorted by residual: dihedral pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.04 -179.04 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 82 " pdb=" C3' DA I 82 " pdb=" O3' DA I 82 " pdb=" P DC I 83 " ideal model delta sinusoidal sigma weight residual 220.00 80.83 139.17 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 8260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1426 0.034 - 0.067: 691 0.067 - 0.101: 257 0.101 - 0.135: 84 0.135 - 0.168: 10 Chirality restraints: 2468 Sorted by residual: chirality pdb=" C1' DC I 83 " pdb=" O4' DC I 83 " pdb=" C2' DC I 83 " pdb=" N1 DC I 83 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" C1' DC I 85 " pdb=" O4' DC I 85 " pdb=" C2' DC I 85 " pdb=" N1 DC I 85 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" C3' DA I 82 " pdb=" C4' DA I 82 " pdb=" O3' DA I 82 " pdb=" C2' DA I 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 2465 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 79 " 0.023 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 79 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT I 79 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 79 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DT I 79 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 79 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 79 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DT I 79 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT I 79 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 79 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 56 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C GLY F 56 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY F 56 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL F 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO G 80 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.025 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 146 2.63 - 3.20: 11304 3.20 - 3.76: 26958 3.76 - 4.33: 36243 4.33 - 4.90: 50059 Nonbonded interactions: 124710 Sorted by model distance: nonbonded pdb=" O2 DC I 85 " pdb=" N2 DG J -85 " model vdw 2.061 3.120 nonbonded pdb=" N6 DA I 72 " pdb=" N3 DT J -72 " model vdw 2.065 2.560 nonbonded pdb=" CD PRO E 30 " pdb=" OE1 GLU X 209 " model vdw 2.132 3.440 nonbonded pdb=" N1 DA I 72 " pdb=" O2 DT J -72 " model vdw 2.152 2.496 nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.276 3.040 ... (remaining 124705 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 38 through 133) selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } 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=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.040 Set scattering table: 0.040 Process input model: 12.770 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 0.084 15000 Z= 0.548 Angle : 0.776 11.794 21694 Z= 0.672 Chirality : 0.046 0.168 2468 Planarity : 0.004 0.044 1582 Dihedral : 28.756 179.040 6571 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.07 % Rotamer: Outliers : 1.98 % Allowed : 17.15 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.27), residues: 882 helix: 1.93 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.013 0.002 TYR H 80 PHE 0.012 0.002 PHE E 67 TRP 0.022 0.003 TRP X 277 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.55 (15000) covalent geometry : angle 0.77571 / 0.67 (21694) hydrogen bonds : bond 0.12470 / 8.50 ( 880) hydrogen bonds : angle 5.37206 / 3.90 ( 2227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 312 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9228 (mt) cc_final: 0.8846 (tp) REVERT: A 89 VAL cc_start: 0.9748 (t) cc_final: 0.9395 (m) REVERT: A 90 MET cc_start: 0.9569 (mmp) cc_final: 0.9326 (mmm) REVERT: A 99 TYR cc_start: 0.8162 (t80) cc_final: 0.7840 (t80) REVERT: A 106 ASP cc_start: 0.9386 (m-30) cc_final: 0.8954 (t0) REVERT: A 110 CYS cc_start: 0.9720 (m) cc_final: 0.9434 (m) REVERT: B 53 GLU cc_start: 0.9278 (tp30) cc_final: 0.8811 (tt0) REVERT: B 59 LYS cc_start: 0.9633 (tppp) cc_final: 0.9388 (tppp) REVERT: B 61 PHE cc_start: 0.9349 (t80) cc_final: 0.8959 (t80) REVERT: B 66 ILE cc_start: 0.9625 (mt) cc_final: 0.9422 (tt) REVERT: C 51 LEU cc_start: 0.9717 (tp) cc_final: 0.9504 (tp) REVERT: C 75 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8430 (mmmt) REVERT: C 94 ASN cc_start: 0.9568 (t0) cc_final: 0.9178 (m-40) REVERT: C 101 THR cc_start: 0.9445 (m) cc_final: 0.9049 (t) REVERT: D 34 TYR cc_start: 0.9188 (m-80) cc_final: 0.8727 (m-80) REVERT: D 64 ASN cc_start: 0.9598 (m-40) cc_final: 0.8957 (m110) REVERT: E 65 LEU cc_start: 0.9858 (mt) cc_final: 0.9598 (mt) REVERT: E 94 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8917 (tp30) REVERT: E 109 LEU cc_start: 0.9672 (mt) cc_final: 0.9302 (mt) REVERT: F 26 ILE cc_start: 0.9212 (tp) cc_final: 0.8952 (tp) REVERT: F 46 ILE cc_start: 0.9314 (mt) cc_final: 0.8878 (tp) REVERT: F 51 TYR cc_start: 0.8810 (m-80) cc_final: 0.8470 (m-80) REVERT: F 53 GLU cc_start: 0.9195 (tp30) cc_final: 0.8912 (tt0) REVERT: F 64 ASN cc_start: 0.9661 (m-40) cc_final: 0.9248 (m-40) REVERT: F 74 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9102 (mt-10) REVERT: G 25 PHE cc_start: 0.8966 (m-80) cc_final: 0.8594 (m-10) REVERT: G 51 LEU cc_start: 0.9900 (tp) cc_final: 0.9655 (tp) REVERT: G 56 GLU cc_start: 0.8697 (tt0) cc_final: 0.7532 (tt0) REVERT: G 73 ASN cc_start: 0.9480 (m110) cc_final: 0.9069 (m110) REVERT: G 93 LEU cc_start: 0.9811 (mt) cc_final: 0.9580 (tp) REVERT: G 94 ASN cc_start: 0.9749 (t0) cc_final: 0.9359 (m-40) REVERT: G 101 THR cc_start: 0.9441 (m) cc_final: 0.9144 (p) REVERT: H 34 TYR cc_start: 0.9144 (m-80) cc_final: 0.8306 (m-10) REVERT: H 41 VAL cc_start: 0.9742 (t) cc_final: 0.9492 (p) REVERT: H 58 ILE cc_start: 0.9776 (mt) cc_final: 0.9432 (mt) REVERT: H 59 MET cc_start: 0.9744 (mmm) cc_final: 0.9533 (mmm) REVERT: H 64 ASN cc_start: 0.9453 (m-40) cc_final: 0.9223 (m110) REVERT: H 76 ARG cc_start: 0.9617 (mtm-85) cc_final: 0.9298 (ptp-110) REVERT: H 90 GLU cc_start: 0.9535 (mp0) cc_final: 0.9034 (mp0) REVERT: H 98 LEU cc_start: 0.8787 (mt) cc_final: 0.8338 (mt) REVERT: H 109 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9445 (p) outliers start: 15 outliers final: 1 residues processed: 323 average time/residue: 0.1355 time to fit residues: 59.4687 Evaluate side-chains 184 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN D 81 ASN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.066000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.051878 restraints weight = 152533.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052279 restraints weight = 96693.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.052661 restraints weight = 67227.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.053112 restraints weight = 53443.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.053279 restraints weight = 43733.565| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15000 Z= 0.192 Angle : 0.755 10.685 21694 Z= 0.426 Chirality : 0.046 0.272 2468 Planarity : 0.008 0.178 1582 Dihedral : 31.226 179.275 4762 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.27), residues: 882 helix: 1.53 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 131 TYR 0.035 0.002 TYR H 80 PHE 0.022 0.003 PHE A 67 TRP 0.004 0.001 TRP X 277 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (15000) covalent geometry : angle 0.75547 / 0.43 (21694) hydrogen bonds : bond 0.06088 / 4.27 ( 880) hydrogen bonds : angle 3.66548 / 2.62 ( 2227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9492 (mp) cc_final: 0.9243 (mt) REVERT: A 60 LEU cc_start: 0.9181 (mt) cc_final: 0.8521 (tp) REVERT: A 81 ASP cc_start: 0.9382 (m-30) cc_final: 0.9175 (m-30) REVERT: A 89 VAL cc_start: 0.9500 (t) cc_final: 0.9084 (p) REVERT: A 90 MET cc_start: 0.9666 (mmp) cc_final: 0.9439 (mmm) REVERT: A 97 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 126 LEU cc_start: 0.9433 (mm) cc_final: 0.8895 (tp) REVERT: B 53 GLU cc_start: 0.9198 (tp30) cc_final: 0.8893 (tt0) REVERT: C 25 PHE cc_start: 0.8458 (m-10) cc_final: 0.7929 (m-10) REVERT: C 94 ASN cc_start: 0.9229 (t0) cc_final: 0.8885 (m-40) REVERT: C 101 THR cc_start: 0.8664 (m) cc_final: 0.8388 (t) REVERT: C 102 ILE cc_start: 0.7892 (tt) cc_final: 0.7667 (tt) REVERT: D 34 TYR cc_start: 0.9315 (m-80) cc_final: 0.9063 (m-80) REVERT: D 59 MET cc_start: 0.9769 (mmm) cc_final: 0.9166 (mmm) REVERT: D 68 GLU cc_start: 0.9560 (mt-10) cc_final: 0.9047 (pt0) REVERT: D 73 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8825 (mm-30) REVERT: D 80 TYR cc_start: 0.9065 (m-10) cc_final: 0.8788 (m-80) REVERT: E 94 GLU cc_start: 0.9616 (mm-30) cc_final: 0.9187 (mm-30) REVERT: E 130 ILE cc_start: 0.9437 (mt) cc_final: 0.9215 (tt) REVERT: F 26 ILE cc_start: 0.8614 (tp) cc_final: 0.8374 (tp) REVERT: F 49 LEU cc_start: 0.9597 (mm) cc_final: 0.9332 (mm) REVERT: F 53 GLU cc_start: 0.8880 (tp30) cc_final: 0.8659 (tt0) REVERT: F 72 TYR cc_start: 0.8687 (m-80) cc_final: 0.8299 (m-80) REVERT: F 100 PHE cc_start: 0.5111 (m-80) cc_final: 0.4450 (m-80) REVERT: G 25 PHE cc_start: 0.9426 (m-80) cc_final: 0.8859 (m-10) REVERT: G 73 ASN cc_start: 0.8855 (m110) cc_final: 0.8566 (m-40) REVERT: G 94 ASN cc_start: 0.9470 (t0) cc_final: 0.9140 (m-40) REVERT: G 95 LYS cc_start: 0.9493 (mtmm) cc_final: 0.9246 (ptpt) REVERT: G 101 THR cc_start: 0.8741 (m) cc_final: 0.8415 (p) REVERT: H 34 TYR cc_start: 0.9253 (m-80) cc_final: 0.8682 (m-80) REVERT: H 41 VAL cc_start: 0.9706 (t) cc_final: 0.9501 (t) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1336 time to fit residues: 45.0949 Evaluate side-chains 176 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.064297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050308 restraints weight = 157181.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.050742 restraints weight = 97339.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051101 restraints weight = 66516.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.051498 restraints weight = 52965.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.051737 restraints weight = 44200.536| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15000 Z= 0.183 Angle : 0.706 9.187 21694 Z= 0.403 Chirality : 0.044 0.250 2468 Planarity : 0.007 0.168 1582 Dihedral : 31.397 179.413 4762 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.27), residues: 882 helix: 1.39 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.36 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 35 TYR 0.017 0.003 TYR C 39 PHE 0.017 0.002 PHE A 67 TRP 0.023 0.004 TRP X 277 HIS 0.012 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (15000) covalent geometry : angle 0.70612 / 0.40 (21694) hydrogen bonds : bond 0.06088 / 4.25 ( 880) hydrogen bonds : angle 3.63449 / 2.59 ( 2227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9018 (tppt) cc_final: 0.8511 (tttm) REVERT: A 81 ASP cc_start: 0.9454 (m-30) cc_final: 0.9201 (m-30) REVERT: A 89 VAL cc_start: 0.9469 (t) cc_final: 0.9127 (p) REVERT: A 90 MET cc_start: 0.9674 (mmp) cc_final: 0.9456 (mmm) REVERT: A 126 LEU cc_start: 0.9451 (mm) cc_final: 0.9168 (tp) REVERT: B 53 GLU cc_start: 0.9544 (tp30) cc_final: 0.8946 (tt0) REVERT: B 98 TYR cc_start: 0.7854 (m-10) cc_final: 0.7528 (m-10) REVERT: C 25 PHE cc_start: 0.8809 (m-10) cc_final: 0.8476 (m-10) REVERT: C 94 ASN cc_start: 0.9232 (t0) cc_final: 0.8840 (m-40) REVERT: C 101 THR cc_start: 0.8737 (m) cc_final: 0.8482 (p) REVERT: C 102 ILE cc_start: 0.7386 (tt) cc_final: 0.7023 (tt) REVERT: D 34 TYR cc_start: 0.9243 (m-80) cc_final: 0.9030 (m-80) REVERT: D 59 MET cc_start: 0.9766 (mmm) cc_final: 0.9237 (mmm) REVERT: D 68 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8904 (pt0) REVERT: D 80 TYR cc_start: 0.9082 (m-10) cc_final: 0.8876 (m-10) REVERT: E 67 PHE cc_start: 0.9678 (t80) cc_final: 0.9449 (t80) REVERT: E 84 PHE cc_start: 0.9464 (m-80) cc_final: 0.9176 (m-80) REVERT: E 94 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9206 (mm-30) REVERT: E 99 TYR cc_start: 0.9648 (t80) cc_final: 0.9443 (t80) REVERT: F 53 GLU cc_start: 0.8945 (tp30) cc_final: 0.8683 (tt0) REVERT: F 72 TYR cc_start: 0.8825 (m-80) cc_final: 0.8475 (m-80) REVERT: F 100 PHE cc_start: 0.5721 (m-80) cc_final: 0.4991 (m-80) REVERT: G 25 PHE cc_start: 0.9553 (m-80) cc_final: 0.8792 (m-10) REVERT: G 56 GLU cc_start: 0.8532 (tt0) cc_final: 0.7773 (tt0) REVERT: G 73 ASN cc_start: 0.8673 (m110) cc_final: 0.8336 (m110) REVERT: G 91 GLU cc_start: 0.9819 (pm20) cc_final: 0.9592 (pm20) REVERT: G 94 ASN cc_start: 0.9449 (t0) cc_final: 0.9102 (m-40) REVERT: G 95 LYS cc_start: 0.9671 (mtmm) cc_final: 0.9359 (mttt) REVERT: G 101 THR cc_start: 0.8680 (m) cc_final: 0.8379 (p) REVERT: H 34 TYR cc_start: 0.9166 (m-80) cc_final: 0.8377 (m-80) REVERT: H 64 ASN cc_start: 0.9605 (m-40) cc_final: 0.9316 (m110) REVERT: H 76 ARG cc_start: 0.9836 (mpt-90) cc_final: 0.9455 (ptp-110) outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.1240 time to fit residues: 39.0912 Evaluate side-chains 168 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 40.0000 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 HIS E 108 ASN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.062887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.048989 restraints weight = 157125.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049340 restraints weight = 101676.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.049866 restraints weight = 69218.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050223 restraints weight = 52352.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.050393 restraints weight = 42886.942| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15000 Z= 0.176 Angle : 0.688 10.120 21694 Z= 0.395 Chirality : 0.043 0.247 2468 Planarity : 0.006 0.134 1582 Dihedral : 31.495 179.224 4762 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.40 % Allowed : 1.72 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.27), residues: 882 helix: 1.28 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 96 TYR 0.035 0.002 TYR F 51 PHE 0.014 0.002 PHE A 67 TRP 0.016 0.003 TRP X 277 HIS 0.018 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.18 (15000) covalent geometry : angle 0.68822 / 0.39 (21694) hydrogen bonds : bond 0.06082 / 4.21 ( 880) hydrogen bonds : angle 3.59217 / 2.60 ( 2227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9083 (mt) cc_final: 0.8396 (tp) REVERT: A 96 SER cc_start: 0.9120 (p) cc_final: 0.8791 (p) REVERT: A 97 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8149 (mt-10) REVERT: A 126 LEU cc_start: 0.9506 (mm) cc_final: 0.9112 (tp) REVERT: B 53 GLU cc_start: 0.9566 (tp30) cc_final: 0.9068 (tt0) REVERT: B 71 THR cc_start: 0.9697 (OUTLIER) cc_final: 0.9243 (t) REVERT: C 25 PHE cc_start: 0.8844 (m-10) cc_final: 0.8492 (m-10) REVERT: C 94 ASN cc_start: 0.9267 (t0) cc_final: 0.8866 (m-40) REVERT: C 101 THR cc_start: 0.8777 (m) cc_final: 0.8514 (p) REVERT: D 34 TYR cc_start: 0.9335 (m-80) cc_final: 0.8835 (m-80) REVERT: D 59 MET cc_start: 0.9794 (mmm) cc_final: 0.9245 (mmm) REVERT: D 98 LEU cc_start: 0.8592 (mm) cc_final: 0.8157 (mt) REVERT: E 94 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9211 (mm-30) REVERT: F 53 GLU cc_start: 0.9026 (tp30) cc_final: 0.8763 (tt0) REVERT: F 84 MET cc_start: 0.9801 (mmp) cc_final: 0.9410 (tmm) REVERT: F 100 PHE cc_start: 0.6384 (m-80) cc_final: 0.5238 (m-10) REVERT: G 25 PHE cc_start: 0.9465 (m-80) cc_final: 0.8977 (m-10) REVERT: G 73 ASN cc_start: 0.8536 (m110) cc_final: 0.8206 (m110) REVERT: G 91 GLU cc_start: 0.9818 (pm20) cc_final: 0.9604 (pm20) REVERT: G 94 ASN cc_start: 0.9454 (t0) cc_final: 0.9097 (m-40) REVERT: G 95 LYS cc_start: 0.9673 (mtmm) cc_final: 0.9378 (mttt) REVERT: G 101 THR cc_start: 0.8770 (m) cc_final: 0.8472 (p) REVERT: H 34 TYR cc_start: 0.9346 (m-80) cc_final: 0.8646 (m-80) outliers start: 3 outliers final: 1 residues processed: 216 average time/residue: 0.1168 time to fit residues: 35.9378 Evaluate side-chains 164 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 0.0980 chunk 26 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 92 optimal weight: 40.0000 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 chunk 45 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.062791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048724 restraints weight = 156186.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.049562 restraints weight = 94507.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.050059 restraints weight = 65252.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050338 restraints weight = 49957.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.050434 restraints weight = 41436.006| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15000 Z= 0.164 Angle : 0.689 11.155 21694 Z= 0.391 Chirality : 0.043 0.242 2468 Planarity : 0.006 0.106 1582 Dihedral : 31.478 178.577 4762 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 882 helix: 1.35 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.04 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 96 TYR 0.019 0.002 TYR A 99 PHE 0.015 0.002 PHE F 61 TRP 0.011 0.002 TRP X 277 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (15000) covalent geometry : angle 0.68878 / 0.39 (21694) hydrogen bonds : bond 0.05104 / 3.54 ( 880) hydrogen bonds : angle 3.55939 / 2.58 ( 2227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8727 (mt) cc_final: 0.8183 (tp) REVERT: A 81 ASP cc_start: 0.9455 (m-30) cc_final: 0.9242 (m-30) REVERT: A 96 SER cc_start: 0.8937 (p) cc_final: 0.8728 (p) REVERT: A 97 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8293 (mt-10) REVERT: A 126 LEU cc_start: 0.9464 (mm) cc_final: 0.9078 (tp) REVERT: B 53 GLU cc_start: 0.9506 (tp30) cc_final: 0.8964 (tt0) REVERT: B 96 THR cc_start: 0.8223 (m) cc_final: 0.7931 (m) REVERT: C 25 PHE cc_start: 0.8796 (m-10) cc_final: 0.8277 (m-10) REVERT: C 94 ASN cc_start: 0.9194 (t0) cc_final: 0.8809 (m-40) REVERT: C 101 THR cc_start: 0.8653 (m) cc_final: 0.8389 (p) REVERT: D 34 TYR cc_start: 0.9379 (m-80) cc_final: 0.9179 (m-80) REVERT: D 59 MET cc_start: 0.9772 (mmm) cc_final: 0.9263 (mmm) REVERT: D 65 ASP cc_start: 0.9701 (t0) cc_final: 0.9333 (t0) REVERT: D 97 LEU cc_start: 0.9115 (tt) cc_final: 0.8901 (tt) REVERT: D 98 LEU cc_start: 0.8612 (mm) cc_final: 0.8204 (mt) REVERT: E 94 GLU cc_start: 0.9619 (mm-30) cc_final: 0.9234 (mm-30) REVERT: E 99 TYR cc_start: 0.9680 (t80) cc_final: 0.9273 (t80) REVERT: E 119 ILE cc_start: 0.8758 (pt) cc_final: 0.8501 (pt) REVERT: F 53 GLU cc_start: 0.8945 (tp30) cc_final: 0.8657 (tt0) REVERT: F 72 TYR cc_start: 0.8599 (m-80) cc_final: 0.8220 (m-80) REVERT: F 100 PHE cc_start: 0.6161 (m-80) cc_final: 0.5468 (m-80) REVERT: G 25 PHE cc_start: 0.9485 (m-80) cc_final: 0.8908 (m-10) REVERT: G 73 ASN cc_start: 0.8573 (m110) cc_final: 0.8265 (m110) REVERT: G 94 ASN cc_start: 0.9396 (t0) cc_final: 0.9059 (m-40) REVERT: G 101 THR cc_start: 0.8672 (m) cc_final: 0.8377 (p) REVERT: H 34 TYR cc_start: 0.9254 (m-80) cc_final: 0.8637 (m-80) REVERT: H 110 GLU cc_start: 0.9582 (mm-30) cc_final: 0.9145 (mm-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1279 time to fit residues: 38.5900 Evaluate side-chains 166 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 117 optimal weight: 40.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 106 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.060115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046760 restraints weight = 161735.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.047117 restraints weight = 100515.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047574 restraints weight = 68436.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047923 restraints weight = 52836.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.048055 restraints weight = 43357.461| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15000 Z= 0.211 Angle : 0.727 13.154 21694 Z= 0.414 Chirality : 0.043 0.239 2468 Planarity : 0.006 0.068 1582 Dihedral : 31.701 178.783 4762 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 1.85 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.27), residues: 882 helix: 1.11 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.04 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 96 TYR 0.037 0.003 TYR H 80 PHE 0.016 0.002 PHE D 67 TRP 0.011 0.002 TRP X 277 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.21 (15000) covalent geometry : angle 0.72741 / 0.41 (21694) hydrogen bonds : bond 0.08393 / 5.79 ( 880) hydrogen bonds : angle 3.80143 / 2.73 ( 2227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8784 (mt) cc_final: 0.8246 (tp) REVERT: A 81 ASP cc_start: 0.9468 (m-30) cc_final: 0.9261 (m-30) REVERT: A 97 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 99 TYR cc_start: 0.9218 (t80) cc_final: 0.8969 (t80) REVERT: A 126 LEU cc_start: 0.9517 (mm) cc_final: 0.9147 (tp) REVERT: B 53 GLU cc_start: 0.9528 (tp30) cc_final: 0.9068 (tt0) REVERT: C 25 PHE cc_start: 0.8834 (m-10) cc_final: 0.8559 (m-10) REVERT: C 94 ASN cc_start: 0.9254 (t0) cc_final: 0.8911 (t0) REVERT: C 101 THR cc_start: 0.8755 (m) cc_final: 0.8394 (p) REVERT: D 59 MET cc_start: 0.9761 (mmm) cc_final: 0.9461 (tpp) REVERT: D 64 ASN cc_start: 0.9357 (m110) cc_final: 0.9145 (m110) REVERT: D 98 LEU cc_start: 0.8747 (mm) cc_final: 0.8410 (mm) REVERT: E 94 GLU cc_start: 0.9626 (mm-30) cc_final: 0.9282 (mm-30) REVERT: F 53 GLU cc_start: 0.9180 (tp30) cc_final: 0.8961 (tt0) REVERT: F 97 LEU cc_start: 0.9353 (tt) cc_final: 0.9032 (tp) REVERT: F 100 PHE cc_start: 0.6816 (m-80) cc_final: 0.6263 (m-80) REVERT: G 25 PHE cc_start: 0.9299 (m-10) cc_final: 0.8703 (m-10) REVERT: G 73 ASN cc_start: 0.8620 (m110) cc_final: 0.8311 (m110) REVERT: G 91 GLU cc_start: 0.9852 (pm20) cc_final: 0.9565 (pm20) REVERT: G 94 ASN cc_start: 0.9353 (t0) cc_final: 0.9068 (m-40) REVERT: G 101 THR cc_start: 0.8710 (m) cc_final: 0.8375 (p) REVERT: H 34 TYR cc_start: 0.9392 (m-80) cc_final: 0.8797 (m-80) REVERT: H 98 LEU cc_start: 0.8525 (tp) cc_final: 0.8248 (tp) REVERT: H 110 GLU cc_start: 0.9602 (mm-30) cc_final: 0.9089 (mm-30) REVERT: H 117 LYS cc_start: 0.9688 (ptpp) cc_final: 0.9362 (ptmm) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1263 time to fit residues: 35.0559 Evaluate side-chains 153 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 109 optimal weight: 30.0000 chunk 81 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.058388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.044980 restraints weight = 164198.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045688 restraints weight = 98528.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.046110 restraints weight = 67699.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.046290 restraints weight = 52665.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.046438 restraints weight = 44790.491| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15000 Z= 0.214 Angle : 0.731 13.287 21694 Z= 0.418 Chirality : 0.044 0.233 2468 Planarity : 0.005 0.057 1582 Dihedral : 32.043 178.868 4762 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.13 % Allowed : 1.45 % Favored : 98.42 % 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: 1.03 (0.27), residues: 882 helix: 1.04 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 35 TYR 0.027 0.003 TYR B 72 PHE 0.016 0.002 PHE A 104 TRP 0.012 0.002 TRP X 207 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.21 (15000) covalent geometry : angle 0.73078 / 0.42 (21694) hydrogen bonds : bond 0.07735 / 5.37 ( 880) hydrogen bonds : angle 3.90596 / 2.85 ( 2227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9497 (m-30) cc_final: 0.9290 (m-30) REVERT: A 99 TYR cc_start: 0.9347 (t80) cc_final: 0.9133 (t80) REVERT: A 126 LEU cc_start: 0.9516 (mm) cc_final: 0.9200 (tp) REVERT: B 53 GLU cc_start: 0.9568 (tp30) cc_final: 0.9111 (tt0) REVERT: C 25 PHE cc_start: 0.8362 (m-10) cc_final: 0.8076 (m-10) REVERT: C 94 ASN cc_start: 0.9263 (t0) cc_final: 0.8961 (t0) REVERT: C 101 THR cc_start: 0.8714 (m) cc_final: 0.8326 (p) REVERT: D 34 TYR cc_start: 0.9463 (m-80) cc_final: 0.9215 (m-80) REVERT: D 59 MET cc_start: 0.9773 (mmm) cc_final: 0.9236 (mmm) REVERT: D 64 ASN cc_start: 0.9361 (m-40) cc_final: 0.9143 (m110) REVERT: D 98 LEU cc_start: 0.8665 (mm) cc_final: 0.8302 (mm) REVERT: E 94 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9204 (tp30) REVERT: F 26 ILE cc_start: 0.9207 (tp) cc_final: 0.9003 (tp) REVERT: F 53 GLU cc_start: 0.9222 (tp30) cc_final: 0.8940 (tt0) REVERT: F 68 ASP cc_start: 0.9291 (m-30) cc_final: 0.8122 (m-30) REVERT: F 72 TYR cc_start: 0.9409 (m-80) cc_final: 0.9019 (m-80) REVERT: F 92 ARG cc_start: 0.8910 (tmm160) cc_final: 0.8607 (tmm-80) REVERT: F 97 LEU cc_start: 0.9350 (tt) cc_final: 0.9020 (tp) REVERT: F 100 PHE cc_start: 0.7377 (m-80) cc_final: 0.7079 (m-10) REVERT: G 25 PHE cc_start: 0.9249 (m-10) cc_final: 0.8402 (m-10) REVERT: G 73 ASN cc_start: 0.8555 (m110) cc_final: 0.8298 (m110) REVERT: G 94 ASN cc_start: 0.9337 (t0) cc_final: 0.9011 (m-40) REVERT: G 101 THR cc_start: 0.8889 (m) cc_final: 0.8600 (p) REVERT: H 34 TYR cc_start: 0.9488 (m-80) cc_final: 0.8881 (m-80) REVERT: H 73 GLU cc_start: 0.9260 (mp0) cc_final: 0.8978 (mp0) REVERT: H 97 LEU cc_start: 0.9207 (tp) cc_final: 0.8780 (tp) REVERT: H 98 LEU cc_start: 0.8489 (tp) cc_final: 0.8266 (tp) REVERT: H 110 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9323 (mm-30) REVERT: H 117 LYS cc_start: 0.9694 (ptpp) cc_final: 0.9441 (ptmm) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.1325 time to fit residues: 35.9683 Evaluate side-chains 149 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 104 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 40.0000 chunk 92 optimal weight: 40.0000 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.058512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045104 restraints weight = 163960.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045842 restraints weight = 97656.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.046279 restraints weight = 67481.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046518 restraints weight = 52016.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046656 restraints weight = 43213.235| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15000 Z= 0.176 Angle : 0.709 11.941 21694 Z= 0.406 Chirality : 0.043 0.237 2468 Planarity : 0.005 0.068 1582 Dihedral : 32.032 178.394 4762 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 0.88 (0.27), residues: 882 helix: 0.94 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 131 TYR 0.022 0.002 TYR C 57 PHE 0.036 0.002 PHE E 67 TRP 0.012 0.002 TRP X 207 HIS 0.008 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.18 (15000) covalent geometry : angle 0.70866 / 0.41 (21694) hydrogen bonds : bond 0.06386 / 4.43 ( 880) hydrogen bonds : angle 3.91592 / 2.85 ( 2227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9520 (m-30) cc_final: 0.9314 (m-30) REVERT: A 99 TYR cc_start: 0.9318 (t80) cc_final: 0.9117 (t80) REVERT: A 126 LEU cc_start: 0.9508 (mm) cc_final: 0.9179 (tp) REVERT: B 53 GLU cc_start: 0.9565 (tp30) cc_final: 0.9093 (tt0) REVERT: C 25 PHE cc_start: 0.8289 (m-10) cc_final: 0.7920 (m-10) REVERT: C 39 TYR cc_start: 0.9004 (m-10) cc_final: 0.8791 (m-80) REVERT: C 94 ASN cc_start: 0.9222 (t0) cc_final: 0.8873 (t0) REVERT: C 101 THR cc_start: 0.8652 (m) cc_final: 0.8241 (p) REVERT: D 34 TYR cc_start: 0.9448 (m-80) cc_final: 0.9192 (m-80) REVERT: D 59 MET cc_start: 0.9750 (mmm) cc_final: 0.9417 (tpp) REVERT: D 98 LEU cc_start: 0.8915 (mm) cc_final: 0.8544 (mm) REVERT: E 94 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9052 (tp30) REVERT: E 124 ILE cc_start: 0.9537 (mt) cc_final: 0.9291 (mt) REVERT: F 53 GLU cc_start: 0.9198 (tp30) cc_final: 0.8993 (tt0) REVERT: F 68 ASP cc_start: 0.9237 (m-30) cc_final: 0.8790 (m-30) REVERT: F 72 TYR cc_start: 0.9344 (m-80) cc_final: 0.8968 (m-80) REVERT: F 96 THR cc_start: 0.9280 (p) cc_final: 0.9056 (t) REVERT: G 25 PHE cc_start: 0.9063 (m-10) cc_final: 0.8406 (m-10) REVERT: G 73 ASN cc_start: 0.8513 (m110) cc_final: 0.8236 (m110) REVERT: G 94 ASN cc_start: 0.9346 (t0) cc_final: 0.8971 (m-40) REVERT: G 101 THR cc_start: 0.8877 (m) cc_final: 0.8581 (p) REVERT: H 34 TYR cc_start: 0.9449 (m-80) cc_final: 0.8884 (m-80) REVERT: H 64 ASN cc_start: 0.9524 (m-40) cc_final: 0.9260 (m110) REVERT: H 76 ARG cc_start: 0.9617 (ptp-110) cc_final: 0.9373 (mtm110) REVERT: H 97 LEU cc_start: 0.8996 (tp) cc_final: 0.8738 (tp) REVERT: H 110 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9325 (mm-30) REVERT: H 117 LYS cc_start: 0.9735 (ptpp) cc_final: 0.9475 (ptmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1302 time to fit residues: 35.0336 Evaluate side-chains 139 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 8.9990 chunk 34 optimal weight: 0.0670 chunk 87 optimal weight: 40.0000 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.057794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044383 restraints weight = 166377.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.045157 restraints weight = 98729.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045613 restraints weight = 68443.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045856 restraints weight = 51509.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.046042 restraints weight = 42912.007| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15000 Z= 0.185 Angle : 0.712 11.728 21694 Z= 0.407 Chirality : 0.043 0.232 2468 Planarity : 0.005 0.055 1582 Dihedral : 32.044 178.622 4762 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 882 helix: 0.93 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 186 TYR 0.022 0.002 TYR F 88 PHE 0.044 0.003 PHE F 61 TRP 0.013 0.002 TRP X 207 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 (15000) covalent geometry : angle 0.71167 / 0.41 (21694) hydrogen bonds : bond 0.06832 / 4.76 ( 880) hydrogen bonds : angle 3.97285 / 2.91 ( 2227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9628 (mmp) cc_final: 0.9403 (mmp) REVERT: A 124 ILE cc_start: 0.9737 (tp) cc_final: 0.9429 (tp) REVERT: A 126 LEU cc_start: 0.9539 (mm) cc_final: 0.9289 (tp) REVERT: B 63 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9036 (mt-10) REVERT: B 97 LEU cc_start: 0.9336 (tp) cc_final: 0.9122 (tp) REVERT: C 94 ASN cc_start: 0.9697 (t0) cc_final: 0.9348 (t0) REVERT: C 112 GLN cc_start: 0.9546 (tp40) cc_final: 0.9059 (tp-100) REVERT: D 59 MET cc_start: 0.9633 (mmm) cc_final: 0.9410 (tpp) REVERT: D 64 ASN cc_start: 0.9318 (m110) cc_final: 0.9075 (m110) REVERT: D 67 PHE cc_start: 0.9512 (t80) cc_final: 0.9206 (t80) REVERT: D 70 ILE cc_start: 0.9431 (tp) cc_final: 0.9212 (tp) REVERT: D 79 HIS cc_start: 0.9651 (t-90) cc_final: 0.9381 (t-90) REVERT: D 98 LEU cc_start: 0.9422 (mm) cc_final: 0.9041 (mm) REVERT: E 94 GLU cc_start: 0.9440 (mm-30) cc_final: 0.8889 (mm-30) REVERT: E 124 ILE cc_start: 0.9899 (mt) cc_final: 0.9598 (mt) REVERT: F 26 ILE cc_start: 0.9492 (tp) cc_final: 0.9290 (tp) REVERT: F 53 GLU cc_start: 0.9579 (tp30) cc_final: 0.9341 (tt0) REVERT: F 68 ASP cc_start: 0.9346 (m-30) cc_final: 0.9112 (m-30) REVERT: F 72 TYR cc_start: 0.8833 (m-80) cc_final: 0.8471 (m-80) REVERT: G 25 PHE cc_start: 0.8807 (m-10) cc_final: 0.8527 (m-10) REVERT: G 73 ASN cc_start: 0.9124 (m110) cc_final: 0.8756 (m110) REVERT: G 91 GLU cc_start: 0.9677 (pm20) cc_final: 0.9338 (pm20) REVERT: G 94 ASN cc_start: 0.9719 (t0) cc_final: 0.9291 (m-40) REVERT: G 101 THR cc_start: 0.9420 (m) cc_final: 0.9117 (p) REVERT: H 34 TYR cc_start: 0.9068 (m-80) cc_final: 0.8430 (m-80) REVERT: H 59 MET cc_start: 0.9731 (mmp) cc_final: 0.9445 (mmm) REVERT: H 64 ASN cc_start: 0.9518 (m-40) cc_final: 0.9134 (m110) REVERT: H 73 GLU cc_start: 0.9109 (mp0) cc_final: 0.8798 (mp0) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1329 time to fit residues: 34.8935 Evaluate side-chains 138 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 0.7980 chunk 88 optimal weight: 50.0000 chunk 6 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044815 restraints weight = 164174.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.045628 restraints weight = 98744.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046071 restraints weight = 68377.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.046308 restraints weight = 52306.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.046521 restraints weight = 43640.168| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15000 Z= 0.162 Angle : 0.715 11.972 21694 Z= 0.406 Chirality : 0.043 0.243 2468 Planarity : 0.005 0.051 1582 Dihedral : 31.972 178.363 4762 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.74 (0.27), residues: 882 helix: 0.82 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 186 TYR 0.035 0.003 TYR F 88 PHE 0.032 0.002 PHE A 104 TRP 0.012 0.002 TRP X 207 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (15000) covalent geometry : angle 0.71525 / 0.41 (21694) hydrogen bonds : bond 0.05295 / 3.70 ( 880) hydrogen bonds : angle 3.92286 / 2.87 ( 2227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8522 (m-30) cc_final: 0.8250 (m-30) REVERT: A 126 LEU cc_start: 0.9543 (mm) cc_final: 0.9272 (tp) REVERT: B 97 LEU cc_start: 0.9356 (tp) cc_final: 0.9148 (tp) REVERT: C 94 ASN cc_start: 0.9689 (t0) cc_final: 0.9291 (t0) REVERT: C 112 GLN cc_start: 0.9543 (tp40) cc_final: 0.9192 (tp-100) REVERT: D 59 MET cc_start: 0.9608 (mmm) cc_final: 0.9348 (tpp) REVERT: D 63 VAL cc_start: 0.9679 (t) cc_final: 0.9474 (m) REVERT: D 64 ASN cc_start: 0.9319 (m110) cc_final: 0.9029 (m-40) REVERT: D 67 PHE cc_start: 0.9477 (t80) cc_final: 0.9197 (t80) REVERT: D 79 HIS cc_start: 0.9662 (t-90) cc_final: 0.9383 (t-90) REVERT: D 98 LEU cc_start: 0.9299 (mm) cc_final: 0.8979 (mm) REVERT: E 94 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8470 (mm-30) REVERT: E 120 MET cc_start: 0.8962 (tpt) cc_final: 0.8757 (tpt) REVERT: E 124 ILE cc_start: 0.9896 (mt) cc_final: 0.9578 (mt) REVERT: F 26 ILE cc_start: 0.9466 (tp) cc_final: 0.9249 (tp) REVERT: F 53 GLU cc_start: 0.9584 (tp30) cc_final: 0.9315 (tt0) REVERT: F 68 ASP cc_start: 0.9327 (m-30) cc_final: 0.9089 (m-30) REVERT: F 72 TYR cc_start: 0.8874 (m-80) cc_final: 0.8525 (m-80) REVERT: G 25 PHE cc_start: 0.8669 (m-10) cc_final: 0.8415 (m-10) REVERT: G 73 ASN cc_start: 0.9099 (m110) cc_final: 0.8738 (m110) REVERT: G 91 GLU cc_start: 0.9691 (pm20) cc_final: 0.9374 (pm20) REVERT: G 94 ASN cc_start: 0.9735 (t0) cc_final: 0.9323 (m-40) REVERT: G 95 LYS cc_start: 0.9687 (ptpp) cc_final: 0.9485 (pttm) REVERT: G 101 THR cc_start: 0.9451 (m) cc_final: 0.9138 (p) REVERT: H 34 TYR cc_start: 0.9053 (m-80) cc_final: 0.8363 (m-80) REVERT: H 59 MET cc_start: 0.9714 (mmp) cc_final: 0.9449 (mmm) REVERT: H 64 ASN cc_start: 0.9533 (m-40) cc_final: 0.9184 (m110) REVERT: H 73 GLU cc_start: 0.8990 (mp0) cc_final: 0.8747 (mp0) REVERT: H 76 ARG cc_start: 0.9594 (ptp-110) cc_final: 0.8963 (mtm110) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1300 time to fit residues: 35.9264 Evaluate side-chains 142 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.058244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044959 restraints weight = 164713.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045606 restraints weight = 98962.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045930 restraints weight = 68958.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046328 restraints weight = 55026.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046492 restraints weight = 44497.408| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15000 Z= 0.159 Angle : 0.701 11.514 21694 Z= 0.400 Chirality : 0.043 0.241 2468 Planarity : 0.005 0.052 1582 Dihedral : 31.850 178.257 4762 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.77 (0.27), residues: 882 helix: 0.84 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 186 TYR 0.032 0.002 TYR F 88 PHE 0.031 0.002 PHE C 25 TRP 0.012 0.002 TRP X 207 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (15000) covalent geometry : angle 0.70077 / 0.40 (21694) hydrogen bonds : bond 0.05249 / 3.67 ( 880) hydrogen bonds : angle 3.88522 / 2.84 ( 2227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.48 seconds wall clock time: 37 minutes 35.50 seconds (2255.50 seconds total)