Starting phenix.real_space_refine on Fri Jul 3 11:08:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8b_29845/07_2026/8g8b_29845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8b_29845/07_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_29845/07_2026/8g8b_29845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8b_29845/07_2026/8g8b_29845.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8b_29845/07_2026/8g8b_29845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8b_29845/07_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-dev-6108/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: 2.74, 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: 0.91 Conformation dependent library (CDL) restraints added in 333.5 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: 1.84 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: 2.80 Time building geometry restraints manager: 1.18 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: 21233 2.36 - 4.72: 436 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- 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= 0.547 Angle : 0.768 11.794 21694 Z= 0.665 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 0.76804 / 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 : 0.357 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: 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: 0.7841 (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: 0.8343 (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: 0.9047 (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: 0.8956 (m110) REVERT: E 65 LEU cc_start: 0.9858 (mt) cc_final: 0.9618 (mt) REVERT: E 94 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8919 (tp30) REVERT: E 109 LEU cc_start: 0.9672 (mt) cc_final: 0.9301 (mt) REVERT: F 26 ILE cc_start: 0.9212 (tp) cc_final: 0.8951 (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: 0.9654 (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: 0.9070 (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: 0.9493 (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: 0.8337 (mt) REVERT: H 109 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9445 (p) outliers start: 15 outliers final: 2 residues processed: 323 average time/residue: 0.1385 time to fit residues: 60.5833 Evaluate side-chains 187 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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: 6.9990 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: 2.8586 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.065714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051608 restraints weight = 152359.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.051944 restraints weight = 98549.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052406 restraints weight = 67477.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052821 restraints weight = 52308.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.053121 restraints weight = 43785.791| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15000 Z= 0.194 Angle : 0.753 9.366 21694 Z= 0.427 Chirality : 0.047 0.275 2468 Planarity : 0.008 0.179 1582 Dihedral : 31.337 178.878 4762 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: 1.43 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.52 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 96 TYR 0.036 0.003 TYR H 80 PHE 0.022 0.003 PHE A 67 TRP 0.005 0.001 TRP X 277 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (15000) covalent geometry : angle 0.75325 / 0.43 (21694) hydrogen bonds : bond 0.06227 / 4.35 ( 880) hydrogen bonds : angle 3.68019 / 2.64 ( 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 249 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.235 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: A 81 ASP cc_start: 0.9391 (m-30) cc_final: 0.9181 (m-30) REVERT: A 89 VAL cc_start: 0.9505 (t) cc_final: 0.9253 (p) REVERT: A 126 LEU cc_start: 0.9458 (mm) cc_final: 0.8917 (tp) REVERT: B 53 GLU cc_start: 0.9219 (tp30) cc_final: 0.8923 (tt0) REVERT: C 25 PHE cc_start: 0.8623 (m-10) cc_final: 0.8145 (m-10) REVERT: C 94 ASN cc_start: 0.9239 (t0) cc_final: 0.8893 (m-40) REVERT: C 101 THR cc_start: 0.8758 (m) cc_final: 0.8482 (t) REVERT: D 34 TYR cc_start: 0.9166 (m-80) cc_final: 0.8657 (m-80) REVERT: D 59 MET cc_start: 0.9753 (mmm) cc_final: 0.9125 (mmm) REVERT: D 73 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8891 (mm-30) REVERT: D 80 TYR cc_start: 0.9099 (m-10) cc_final: 0.8801 (m-80) REVERT: D 89 ARG cc_start: 0.9552 (ttt90) cc_final: 0.9335 (ttt90) REVERT: E 94 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9104 (tp30) REVERT: E 130 ILE cc_start: 0.9490 (mt) cc_final: 0.9267 (tt) REVERT: F 49 LEU cc_start: 0.9618 (mm) cc_final: 0.9356 (mm) REVERT: F 53 GLU cc_start: 0.8925 (tp30) cc_final: 0.8672 (tt0) REVERT: F 64 ASN cc_start: 0.9564 (m-40) cc_final: 0.9342 (m-40) REVERT: F 72 TYR cc_start: 0.8699 (m-80) cc_final: 0.8270 (m-80) REVERT: F 100 PHE cc_start: 0.5688 (m-80) cc_final: 0.5321 (m-80) REVERT: G 25 PHE cc_start: 0.9438 (m-80) cc_final: 0.8878 (m-10) REVERT: G 73 ASN cc_start: 0.8857 (m110) cc_final: 0.8569 (m-40) REVERT: G 94 ASN cc_start: 0.9488 (t0) cc_final: 0.9154 (m-40) REVERT: G 95 LYS cc_start: 0.9517 (mtmm) cc_final: 0.9258 (ptpt) REVERT: G 101 THR cc_start: 0.8763 (m) cc_final: 0.8316 (p) REVERT: H 34 TYR cc_start: 0.9274 (m-80) cc_final: 0.8784 (m-80) REVERT: H 91 ILE cc_start: 0.9755 (mm) cc_final: 0.9513 (mm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1273 time to fit residues: 43.4689 Evaluate side-chains 180 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 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: 2.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 93 GLN ** 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 = 0.3502 r_free = 0.3502 target = 0.062907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048849 restraints weight = 157940.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049652 restraints weight = 96105.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050129 restraints weight = 66536.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050484 restraints weight = 51095.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050638 restraints weight = 41881.758| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15000 Z= 0.205 Angle : 0.716 10.340 21694 Z= 0.410 Chirality : 0.044 0.236 2468 Planarity : 0.007 0.157 1582 Dihedral : 31.634 179.793 4762 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.27), residues: 882 helix: 1.35 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG H 96 TYR 0.034 0.003 TYR B 51 PHE 0.023 0.002 PHE E 67 TRP 0.007 0.002 TRP X 207 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.20 (15000) covalent geometry : angle 0.71619 / 0.41 (21694) hydrogen bonds : bond 0.07448 / 5.17 ( 880) hydrogen bonds : angle 3.71562 / 2.66 ( 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 222 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.363 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: 0.9272 (tp) cc_final: 0.8349 (tt) REVERT: A 70 LEU cc_start: 0.9778 (mt) cc_final: 0.9550 (mt) REVERT: A 81 ASP cc_start: 0.9422 (m-30) cc_final: 0.9218 (m-30) REVERT: A 97 GLU cc_start: 0.9444 (pp20) cc_final: 0.8946 (pt0) REVERT: A 126 LEU cc_start: 0.9361 (mm) cc_final: 0.9103 (tp) REVERT: B 53 GLU cc_start: 0.9471 (tp30) cc_final: 0.9075 (tt0) REVERT: B 88 TYR cc_start: 0.9593 (m-80) cc_final: 0.9366 (m-80) REVERT: B 100 PHE cc_start: 0.6950 (m-80) cc_final: 0.5992 (m-10) REVERT: C 25 PHE cc_start: 0.8522 (m-10) cc_final: 0.8056 (m-10) REVERT: C 94 ASN cc_start: 0.9237 (t0) cc_final: 0.8834 (m-40) REVERT: C 101 THR cc_start: 0.8710 (m) cc_final: 0.8465 (p) REVERT: C 102 ILE cc_start: 0.7557 (tt) cc_final: 0.7242 (tt) REVERT: D 34 TYR cc_start: 0.9323 (m-80) cc_final: 0.8551 (m-80) REVERT: D 59 MET cc_start: 0.9745 (mmm) cc_final: 0.9186 (mmm) REVERT: D 63 VAL cc_start: 0.9719 (t) cc_final: 0.9477 (t) REVERT: D 64 ASN cc_start: 0.9476 (m-40) cc_final: 0.9046 (m110) REVERT: D 65 ASP cc_start: 0.9694 (t0) cc_final: 0.9333 (t0) REVERT: E 84 PHE cc_start: 0.9451 (m-80) cc_final: 0.9157 (m-80) REVERT: E 94 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9249 (mm-30) REVERT: E 99 TYR cc_start: 0.9701 (t80) cc_final: 0.9492 (t80) REVERT: F 26 ILE cc_start: 0.8666 (tp) cc_final: 0.8457 (tp) REVERT: F 53 GLU cc_start: 0.8942 (tp30) cc_final: 0.8701 (tt0) REVERT: F 100 PHE cc_start: 0.6234 (m-80) cc_final: 0.5503 (m-80) REVERT: G 25 PHE cc_start: 0.9537 (m-80) cc_final: 0.8890 (m-10) REVERT: G 56 GLU cc_start: 0.8551 (tt0) cc_final: 0.7922 (tt0) REVERT: G 73 ASN cc_start: 0.8643 (m110) cc_final: 0.8341 (m110) REVERT: G 91 GLU cc_start: 0.9813 (pm20) cc_final: 0.9609 (pm20) REVERT: G 94 ASN cc_start: 0.9442 (t0) cc_final: 0.9109 (m-40) REVERT: G 95 LYS cc_start: 0.9664 (mtmm) cc_final: 0.9371 (mttt) REVERT: G 101 THR cc_start: 0.8574 (m) cc_final: 0.8335 (p) REVERT: H 34 TYR cc_start: 0.9199 (m-80) cc_final: 0.8454 (m-80) REVERT: H 64 ASN cc_start: 0.9598 (m-40) cc_final: 0.9333 (m110) REVERT: H 91 ILE cc_start: 0.9655 (mm) cc_final: 0.9407 (mm) REVERT: H 98 LEU cc_start: 0.7890 (mt) cc_final: 0.6861 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1176 time to fit residues: 36.3917 Evaluate side-chains 177 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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: 20.0000 chunk 87 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN F 64 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.060474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047102 restraints weight = 160971.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.047396 restraints weight = 100438.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047687 restraints weight = 69297.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.048170 restraints weight = 55566.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048396 restraints weight = 44983.426| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15000 Z= 0.233 Angle : 0.727 12.201 21694 Z= 0.417 Chirality : 0.044 0.243 2468 Planarity : 0.007 0.124 1582 Dihedral : 31.908 179.889 4762 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.13 % Allowed : 2.51 % Favored : 97.36 % 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: 1.15 (0.27), residues: 882 helix: 1.11 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.08 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 69 TYR 0.037 0.003 TYR F 51 PHE 0.019 0.002 PHE A 67 TRP 0.010 0.001 TRP X 207 HIS 0.022 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.23 (15000) covalent geometry : angle 0.72724 / 0.42 (21694) hydrogen bonds : bond 0.08567 / 5.91 ( 880) hydrogen bonds : angle 3.79662 / 2.73 ( 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 213 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.265 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: A 60 LEU cc_start: 0.9112 (tp) cc_final: 0.8141 (tt) REVERT: A 81 ASP cc_start: 0.9466 (m-30) cc_final: 0.9256 (m-30) REVERT: A 97 GLU cc_start: 0.9391 (pp20) cc_final: 0.8935 (pt0) REVERT: A 126 LEU cc_start: 0.9511 (mm) cc_final: 0.9132 (tp) REVERT: B 53 GLU cc_start: 0.9662 (tp30) cc_final: 0.9234 (tt0) REVERT: B 97 LEU cc_start: 0.9568 (tp) cc_final: 0.9351 (tp) REVERT: B 98 TYR cc_start: 0.8096 (m-10) cc_final: 0.7892 (m-80) REVERT: C 25 PHE cc_start: 0.8520 (m-10) cc_final: 0.7987 (m-10) REVERT: C 94 ASN cc_start: 0.9247 (t0) cc_final: 0.8900 (t0) REVERT: C 101 THR cc_start: 0.8728 (m) cc_final: 0.8406 (p) REVERT: D 34 TYR cc_start: 0.9386 (m-80) cc_final: 0.8699 (m-80) REVERT: D 59 MET cc_start: 0.9723 (mmm) cc_final: 0.9186 (mmm) REVERT: D 63 VAL cc_start: 0.9721 (t) cc_final: 0.9482 (t) REVERT: D 98 LEU cc_start: 0.8271 (mm) cc_final: 0.7928 (mm) REVERT: E 94 GLU cc_start: 0.9598 (mm-30) cc_final: 0.9321 (mm-30) REVERT: F 53 GLU cc_start: 0.9049 (tp30) cc_final: 0.8806 (tt0) REVERT: F 72 TYR cc_start: 0.8557 (m-80) cc_final: 0.8312 (m-80) REVERT: G 25 PHE cc_start: 0.9344 (m-10) cc_final: 0.8710 (m-10) REVERT: G 73 ASN cc_start: 0.8779 (m110) cc_final: 0.8527 (m110) REVERT: G 94 ASN cc_start: 0.9369 (t0) cc_final: 0.8996 (m-40) REVERT: G 101 THR cc_start: 0.8602 (m) cc_final: 0.8343 (p) REVERT: H 34 TYR cc_start: 0.9369 (m-80) cc_final: 0.8746 (m-80) REVERT: H 64 ASN cc_start: 0.9515 (m-40) cc_final: 0.9210 (m110) REVERT: H 90 GLU cc_start: 0.9673 (mp0) cc_final: 0.9452 (mp0) REVERT: H 110 GLU cc_start: 0.9670 (mm-30) cc_final: 0.9337 (mm-30) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.1227 time to fit residues: 36.6750 Evaluate side-chains 159 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 10.0000 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 64 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** 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 = 0.3458 r_free = 0.3458 target = 0.060759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047407 restraints weight = 160660.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047759 restraints weight = 99090.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048238 restraints weight = 67858.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.048584 restraints weight = 51544.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.048696 restraints weight = 42497.714| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15000 Z= 0.177 Angle : 0.688 11.591 21694 Z= 0.395 Chirality : 0.044 0.252 2468 Planarity : 0.005 0.095 1582 Dihedral : 31.941 179.597 4762 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 1.17 (0.27), residues: 882 helix: 1.11 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.00 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 96 TYR 0.031 0.002 TYR H 80 PHE 0.011 0.002 PHE B 100 TRP 0.010 0.001 TRP X 207 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (15000) covalent geometry : angle 0.68796 / 0.39 (21694) hydrogen bonds : bond 0.06265 / 4.34 ( 880) hydrogen bonds : angle 3.75562 / 2.73 ( 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 205 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.330 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 60 LEU cc_start: 0.9050 (tp) cc_final: 0.8118 (tt) REVERT: A 81 ASP cc_start: 0.9477 (m-30) cc_final: 0.9275 (m-30) REVERT: A 96 SER cc_start: 0.9215 (p) cc_final: 0.8991 (p) REVERT: A 97 GLU cc_start: 0.9367 (pp20) cc_final: 0.8925 (pt0) REVERT: A 126 LEU cc_start: 0.9420 (mm) cc_final: 0.9047 (tp) REVERT: B 53 GLU cc_start: 0.9620 (tp30) cc_final: 0.9205 (tt0) REVERT: B 97 LEU cc_start: 0.9572 (tp) cc_final: 0.9364 (tp) REVERT: C 25 PHE cc_start: 0.8875 (m-10) cc_final: 0.8628 (m-10) REVERT: C 94 ASN cc_start: 0.9238 (t0) cc_final: 0.8883 (t0) REVERT: C 101 THR cc_start: 0.8826 (m) cc_final: 0.8512 (p) REVERT: D 34 TYR cc_start: 0.9399 (m-80) cc_final: 0.9122 (m-80) REVERT: D 59 MET cc_start: 0.9744 (mmm) cc_final: 0.9310 (mmm) REVERT: D 98 LEU cc_start: 0.8286 (mm) cc_final: 0.7453 (mm) REVERT: E 94 GLU cc_start: 0.9625 (mm-30) cc_final: 0.9272 (mm-30) REVERT: E 99 TYR cc_start: 0.9452 (t80) cc_final: 0.9231 (t80) REVERT: E 119 ILE cc_start: 0.8856 (pt) cc_final: 0.8632 (pt) REVERT: F 53 GLU cc_start: 0.9027 (tp30) cc_final: 0.8728 (tt0) REVERT: F 72 TYR cc_start: 0.8564 (m-80) cc_final: 0.8282 (m-80) REVERT: G 25 PHE cc_start: 0.9334 (m-10) cc_final: 0.8546 (m-10) REVERT: G 73 ASN cc_start: 0.8650 (m110) cc_final: 0.8332 (m110) REVERT: G 91 GLU cc_start: 0.9869 (pm20) cc_final: 0.9637 (pm20) REVERT: G 94 ASN cc_start: 0.9347 (t0) cc_final: 0.9000 (m-40) REVERT: G 101 THR cc_start: 0.8579 (m) cc_final: 0.8309 (p) REVERT: H 34 TYR cc_start: 0.9415 (m-80) cc_final: 0.8792 (m-80) REVERT: H 64 ASN cc_start: 0.9594 (m-40) cc_final: 0.9377 (m110) REVERT: H 76 ARG cc_start: 0.9578 (ptp-110) cc_final: 0.9345 (mtm-85) REVERT: H 110 GLU cc_start: 0.9670 (mm-30) cc_final: 0.9419 (mm-30) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1117 time to fit residues: 32.3311 Evaluate side-chains 163 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 6.9990 chunk 78 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 98 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS B 27 GLN ** D 106 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.059242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.046150 restraints weight = 164088.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046488 restraints weight = 101732.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046773 restraints weight = 69213.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047065 restraints weight = 55942.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047409 restraints weight = 46471.393| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15000 Z= 0.207 Angle : 0.718 15.821 21694 Z= 0.409 Chirality : 0.044 0.241 2468 Planarity : 0.006 0.131 1582 Dihedral : 32.047 179.327 4762 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.40 % Allowed : 1.45 % 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: 0.98 (0.27), residues: 882 helix: 0.94 (0.19), residues: 665 sheet: None (None), residues: 0 loop : 0.04 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 186 TYR 0.026 0.003 TYR B 98 PHE 0.017 0.002 PHE B 61 TRP 0.011 0.001 TRP X 207 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.21 (15000) covalent geometry : angle 0.71826 / 0.41 (21694) hydrogen bonds : bond 0.07850 / 5.42 ( 880) hydrogen bonds : angle 3.86246 / 2.81 ( 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 207 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.350 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 90 MET cc_start: 0.9634 (mmp) cc_final: 0.9427 (mmp) REVERT: A 103 LEU cc_start: 0.9546 (tt) cc_final: 0.9277 (tt) REVERT: A 126 LEU cc_start: 0.9522 (mm) cc_final: 0.9180 (tp) REVERT: B 59 LYS cc_start: 0.9451 (tptp) cc_final: 0.9069 (tppt) REVERT: B 97 LEU cc_start: 0.9403 (tp) cc_final: 0.9153 (tp) REVERT: C 94 ASN cc_start: 0.9720 (t0) cc_final: 0.9303 (t0) REVERT: C 101 THR cc_start: 0.9502 (m) cc_final: 0.9296 (p) REVERT: D 34 TYR cc_start: 0.9238 (m-80) cc_final: 0.9020 (m-80) REVERT: D 59 MET cc_start: 0.9587 (mmm) cc_final: 0.9270 (mmm) REVERT: D 65 ASP cc_start: 0.9571 (t70) cc_final: 0.9361 (t0) REVERT: D 79 HIS cc_start: 0.9632 (t-90) cc_final: 0.9376 (t-90) REVERT: D 98 LEU cc_start: 0.9221 (mm) cc_final: 0.9020 (mt) REVERT: E 90 MET cc_start: 0.9335 (ttp) cc_final: 0.9120 (ttp) REVERT: E 94 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8898 (mm-30) REVERT: F 53 GLU cc_start: 0.9556 (tp30) cc_final: 0.9307 (tt0) REVERT: F 59 LYS cc_start: 0.9581 (ptpp) cc_final: 0.9335 (pttm) REVERT: G 25 PHE cc_start: 0.8894 (m-10) cc_final: 0.8638 (m-10) REVERT: G 73 ASN cc_start: 0.9172 (m110) cc_final: 0.8800 (m110) REVERT: G 91 GLU cc_start: 0.9674 (pm20) cc_final: 0.9278 (pm20) REVERT: G 94 ASN cc_start: 0.9703 (t0) cc_final: 0.9323 (t0) REVERT: G 101 THR cc_start: 0.9383 (m) cc_final: 0.9025 (p) REVERT: H 34 TYR cc_start: 0.9102 (m-80) cc_final: 0.8306 (m-80) REVERT: H 59 MET cc_start: 0.9727 (mmp) cc_final: 0.9464 (mmm) REVERT: H 64 ASN cc_start: 0.9496 (m-40) cc_final: 0.9123 (m110) REVERT: H 65 ASP cc_start: 0.9628 (t70) cc_final: 0.9316 (t0) REVERT: H 69 ARG cc_start: 0.9620 (mmm-85) cc_final: 0.9156 (ttm110) REVERT: H 73 GLU cc_start: 0.8810 (mp0) cc_final: 0.8411 (mp0) REVERT: H 76 ARG cc_start: 0.9627 (ptp-110) cc_final: 0.9219 (mtm110) outliers start: 3 outliers final: 0 residues processed: 206 average time/residue: 0.1198 time to fit residues: 35.0875 Evaluate side-chains 145 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 81 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 85 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** 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 = 0.3450 r_free = 0.3450 target = 0.060118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046894 restraints weight = 160417.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.047227 restraints weight = 98637.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.047524 restraints weight = 66962.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047966 restraints weight = 53518.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.048057 restraints weight = 44696.064| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15000 Z= 0.164 Angle : 0.698 13.137 21694 Z= 0.400 Chirality : 0.044 0.226 2468 Planarity : 0.005 0.069 1582 Dihedral : 31.995 178.852 4762 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 882 helix: 0.95 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.01 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 186 TYR 0.020 0.002 TYR C 57 PHE 0.041 0.002 PHE C 25 TRP 0.010 0.001 TRP X 207 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (15000) covalent geometry : angle 0.69799 / 0.40 (21694) hydrogen bonds : bond 0.05346 / 3.72 ( 880) hydrogen bonds : angle 3.82456 / 2.80 ( 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 200 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.390 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: A 90 MET cc_start: 0.9619 (mmp) cc_final: 0.9406 (mmp) REVERT: A 126 LEU cc_start: 0.9494 (mm) cc_final: 0.9149 (tp) REVERT: B 59 LYS cc_start: 0.9430 (tptp) cc_final: 0.9047 (tppt) REVERT: B 97 LEU cc_start: 0.9337 (tp) cc_final: 0.9104 (tp) REVERT: C 94 ASN cc_start: 0.9698 (t0) cc_final: 0.9267 (t0) REVERT: D 59 MET cc_start: 0.9555 (mmm) cc_final: 0.9326 (mmm) REVERT: D 79 HIS cc_start: 0.9619 (t-90) cc_final: 0.9368 (t-90) REVERT: D 98 LEU cc_start: 0.9385 (mm) cc_final: 0.8891 (mt) REVERT: E 94 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8740 (tp30) REVERT: E 120 MET cc_start: 0.8619 (tpt) cc_final: 0.8410 (tpt) REVERT: F 53 GLU cc_start: 0.9517 (tp30) cc_final: 0.9293 (tt0) REVERT: F 59 LYS cc_start: 0.9569 (ptpp) cc_final: 0.9342 (pttm) REVERT: G 25 PHE cc_start: 0.8792 (m-10) cc_final: 0.8556 (m-10) REVERT: G 73 ASN cc_start: 0.9201 (m110) cc_final: 0.8838 (m110) REVERT: G 91 GLU cc_start: 0.9649 (pm20) cc_final: 0.9268 (pm20) REVERT: G 94 ASN cc_start: 0.9680 (t0) cc_final: 0.9236 (m-40) REVERT: G 101 THR cc_start: 0.9361 (m) cc_final: 0.9003 (p) REVERT: H 34 TYR cc_start: 0.9059 (m-80) cc_final: 0.8240 (m-80) REVERT: H 59 MET cc_start: 0.9728 (mmp) cc_final: 0.9446 (mmm) REVERT: H 65 ASP cc_start: 0.9597 (t70) cc_final: 0.9235 (t0) REVERT: H 69 ARG cc_start: 0.9613 (mmm-85) cc_final: 0.9158 (ttm110) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1220 time to fit residues: 34.6315 Evaluate side-chains 152 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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: 3.9990 chunk 54 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 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 = 0.3408 r_free = 0.3408 target = 0.057862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044505 restraints weight = 166150.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045137 restraints weight = 99936.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045704 restraints weight = 70104.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.045862 restraints weight = 53292.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.046043 restraints weight = 46226.609| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15000 Z= 0.218 Angle : 0.731 15.951 21694 Z= 0.418 Chirality : 0.043 0.216 2468 Planarity : 0.006 0.105 1582 Dihedral : 32.152 179.149 4762 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.73 (0.27), residues: 882 helix: 0.77 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.08 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 131 TYR 0.037 0.003 TYR H 80 PHE 0.024 0.002 PHE F 100 TRP 0.012 0.001 TRP X 207 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.22 (15000) covalent geometry : angle 0.73084 / 0.42 (21694) hydrogen bonds : bond 0.08758 / 6.07 ( 880) hydrogen bonds : angle 4.07970 / 2.97 ( 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 184 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.278 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: A 81 ASP cc_start: 0.9557 (m-30) cc_final: 0.9334 (m-30) REVERT: A 126 LEU cc_start: 0.9511 (mm) cc_final: 0.9209 (tp) REVERT: B 59 LYS cc_start: 0.9342 (tptp) cc_final: 0.9136 (tppt) REVERT: B 97 LEU cc_start: 0.9568 (tp) cc_final: 0.9360 (tp) REVERT: C 25 PHE cc_start: 0.7966 (m-10) cc_final: 0.7691 (m-80) REVERT: C 94 ASN cc_start: 0.9256 (t0) cc_final: 0.8973 (t0) REVERT: D 59 MET cc_start: 0.9773 (mmm) cc_final: 0.9424 (mmm) REVERT: D 98 LEU cc_start: 0.8438 (mm) cc_final: 0.8130 (mt) REVERT: E 94 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9238 (mm-30) REVERT: E 124 ILE cc_start: 0.9628 (mt) cc_final: 0.9323 (mt) REVERT: F 26 ILE cc_start: 0.9162 (tp) cc_final: 0.8955 (tp) REVERT: F 72 TYR cc_start: 0.8659 (m-80) cc_final: 0.8407 (m-80) REVERT: G 25 PHE cc_start: 0.9091 (m-10) cc_final: 0.8465 (m-10) REVERT: G 73 ASN cc_start: 0.8558 (m110) cc_final: 0.8266 (m110) REVERT: G 94 ASN cc_start: 0.9357 (t0) cc_final: 0.9006 (m-40) REVERT: G 101 THR cc_start: 0.8696 (m) cc_final: 0.8326 (p) REVERT: H 34 TYR cc_start: 0.9459 (m-80) cc_final: 0.8890 (m-80) REVERT: H 64 ASN cc_start: 0.9475 (m-40) cc_final: 0.9202 (m110) REVERT: H 76 ARG cc_start: 0.9658 (ptp-110) cc_final: 0.9400 (mtm110) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1166 time to fit residues: 30.7681 Evaluate side-chains 137 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 20.0000 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.059667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.046441 restraints weight = 161795.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046782 restraints weight = 100386.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047123 restraints weight = 68282.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.047546 restraints weight = 54345.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047651 restraints weight = 44015.495| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15000 Z= 0.155 Angle : 0.696 12.911 21694 Z= 0.400 Chirality : 0.043 0.229 2468 Planarity : 0.005 0.072 1582 Dihedral : 32.025 178.704 4762 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 0.78 (0.27), residues: 882 helix: 0.82 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.11 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 131 TYR 0.022 0.002 TYR H 80 PHE 0.021 0.002 PHE F 61 TRP 0.010 0.001 TRP X 207 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (15000) covalent geometry : angle 0.69595 / 0.40 (21694) hydrogen bonds : bond 0.04662 / 3.23 ( 880) hydrogen bonds : angle 3.96125 / 2.89 ( 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 190 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.259 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 81 ASP cc_start: 0.9559 (m-30) cc_final: 0.9316 (m-30) REVERT: A 115 LYS cc_start: 0.9482 (mppt) cc_final: 0.9219 (mmtm) REVERT: A 126 LEU cc_start: 0.9481 (mm) cc_final: 0.9204 (tp) REVERT: B 97 LEU cc_start: 0.9566 (tp) cc_final: 0.9336 (tp) REVERT: C 25 PHE cc_start: 0.8035 (m-10) cc_final: 0.7812 (m-80) REVERT: C 94 ASN cc_start: 0.9251 (t0) cc_final: 0.8922 (t0) REVERT: C 112 GLN cc_start: 0.9491 (tp40) cc_final: 0.9229 (tp-100) REVERT: D 59 MET cc_start: 0.9759 (mmm) cc_final: 0.9413 (mmm) REVERT: D 98 LEU cc_start: 0.8622 (mm) cc_final: 0.7666 (mm) REVERT: E 94 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9235 (mm-30) REVERT: F 100 PHE cc_start: 0.7532 (m-80) cc_final: 0.7201 (m-80) REVERT: G 25 PHE cc_start: 0.9107 (m-10) cc_final: 0.8463 (m-10) REVERT: G 73 ASN cc_start: 0.8484 (m110) cc_final: 0.8241 (m110) REVERT: G 91 GLU cc_start: 0.9823 (pm20) cc_final: 0.9614 (pm20) REVERT: G 94 ASN cc_start: 0.9310 (t0) cc_final: 0.8997 (m-40) REVERT: G 101 THR cc_start: 0.8702 (m) cc_final: 0.8371 (p) REVERT: H 34 TYR cc_start: 0.9433 (m-80) cc_final: 0.8825 (m-80) REVERT: H 59 MET cc_start: 0.9807 (mmp) cc_final: 0.9592 (mmm) REVERT: H 76 ARG cc_start: 0.9716 (ptp-110) cc_final: 0.9308 (ptt-90) REVERT: H 110 GLU cc_start: 0.9738 (mm-30) cc_final: 0.9427 (mm-30) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1214 time to fit residues: 32.1648 Evaluate side-chains 148 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 0.9980 chunk 88 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.059129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045930 restraints weight = 163394.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.046414 restraints weight = 98100.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.046949 restraints weight = 66898.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.047182 restraints weight = 51502.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047300 restraints weight = 43267.070| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15000 Z= 0.161 Angle : 0.704 12.436 21694 Z= 0.407 Chirality : 0.043 0.221 2468 Planarity : 0.005 0.068 1582 Dihedral : 31.904 178.557 4762 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.70 (0.27), residues: 882 helix: 0.75 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -0.13 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 69 TYR 0.029 0.002 TYR H 80 PHE 0.026 0.002 PHE B 61 TRP 0.011 0.001 TRP X 207 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (15000) covalent geometry : angle 0.70438 / 0.41 (21694) hydrogen bonds : bond 0.05309 / 3.68 ( 880) hydrogen bonds : angle 3.97041 / 2.88 ( 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 185 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.385 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: A 90 MET cc_start: 0.9646 (mmp) cc_final: 0.9436 (mmp) REVERT: A 126 LEU cc_start: 0.9506 (mm) cc_final: 0.9265 (tp) REVERT: B 63 GLU cc_start: 0.9523 (mt-10) cc_final: 0.9044 (mt-10) REVERT: B 97 LEU cc_start: 0.9350 (tp) cc_final: 0.9075 (tp) REVERT: C 94 ASN cc_start: 0.9678 (t0) cc_final: 0.9287 (t0) REVERT: C 112 GLN cc_start: 0.9514 (tp40) cc_final: 0.9145 (tp-100) REVERT: D 34 TYR cc_start: 0.9161 (m-80) cc_final: 0.8794 (m-80) REVERT: D 64 ASN cc_start: 0.9410 (m110) cc_final: 0.8919 (m110) REVERT: D 67 PHE cc_start: 0.9465 (t80) cc_final: 0.9219 (t80) REVERT: D 79 HIS cc_start: 0.9626 (t-90) cc_final: 0.9388 (t-90) REVERT: D 98 LEU cc_start: 0.9445 (mm) cc_final: 0.9060 (mm) REVERT: E 94 GLU cc_start: 0.9423 (mm-30) cc_final: 0.8824 (mm-30) REVERT: F 26 ILE cc_start: 0.9414 (tp) cc_final: 0.9199 (tp) REVERT: F 72 TYR cc_start: 0.8837 (m-80) cc_final: 0.8427 (m-80) REVERT: G 25 PHE cc_start: 0.8815 (m-10) cc_final: 0.8565 (m-10) REVERT: G 73 ASN cc_start: 0.9069 (m110) cc_final: 0.8717 (m110) REVERT: G 91 GLU cc_start: 0.9656 (pm20) cc_final: 0.9437 (pm20) REVERT: G 94 ASN cc_start: 0.9717 (t0) cc_final: 0.9300 (m-40) REVERT: G 101 THR cc_start: 0.9348 (m) cc_final: 0.8952 (p) REVERT: H 34 TYR cc_start: 0.9091 (m-80) cc_final: 0.8295 (m-80) REVERT: H 59 MET cc_start: 0.9754 (mmp) cc_final: 0.9409 (mmm) REVERT: H 97 LEU cc_start: 0.9289 (tp) cc_final: 0.8998 (tp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1125 time to fit residues: 29.8976 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 : 0.242 ------------------------------------------------------------------------------- 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: 4.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.058379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045002 restraints weight = 164758.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045737 restraints weight = 98641.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.046223 restraints weight = 68273.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.046478 restraints weight = 52294.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046649 restraints weight = 43843.465| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15000 Z= 0.169 Angle : 0.690 13.267 21694 Z= 0.401 Chirality : 0.042 0.217 2468 Planarity : 0.005 0.052 1582 Dihedral : 31.929 178.716 4762 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.67 (0.27), residues: 882 helix: 0.73 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -0.14 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 186 TYR 0.051 0.003 TYR H 80 PHE 0.023 0.002 PHE F 61 TRP 0.012 0.001 TRP X 207 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (15000) covalent geometry : angle 0.69031 / 0.40 (21694) hydrogen bonds : bond 0.05802 / 4.05 ( 880) hydrogen bonds : angle 3.98206 / 2.89 ( 2227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.89 seconds wall clock time: 34 minutes 36.74 seconds (2076.74 seconds total)