Starting phenix.real_space_refine on Sat Aug 23 18:10:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8b_29845/08_2025/8g8b_29845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8b_29845/08_2025/8g8b_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2025/8g8b_29845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2025/8g8b_29845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2025/8g8b_29845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8b_29845/08_2025/8g8b_29845.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 2.98, per 1000 atoms: 0.21 Number of scatterers: 14067 At special positions: 0 Unit cell: (80.5, 119.14, 172.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 336 15.00 O 3284 8.00 N 2611 7.00 C 7819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 397.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.28 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: 3.24 Time building geometry restraints manager: 1.46 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=" N THR E 32 " pdb=" CA THR E 32 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.60e+00 bond pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.32e-02 5.74e+03 6.27e+00 bond pdb=" N TYR E 41 " pdb=" CA TYR E 41 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.86e+00 bond pdb=" C1' DC J -96 " pdb=" N1 DC J -96 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.20e+00 bond pdb=" C1' DC I 83 " pdb=" N1 DC I 83 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.88e+00 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21469 2.36 - 4.72: 201 4.72 - 7.08: 20 7.08 - 9.44: 3 9.44 - 11.79: 1 Bond angle restraints: 21694 Sorted by residual: angle pdb=" O3' DG J -71 " pdb=" C3' DG J -71 " pdb=" C2' DG J -71 " ideal model delta sigma weight residual 111.50 103.17 8.33 1.50e+00 4.44e-01 3.08e+01 angle pdb=" O3' DG J -73 " pdb=" C3' DG J -73 " pdb=" C2' DG J -73 " ideal model delta sigma weight residual 111.50 104.37 7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" O3' DA I 78 " pdb=" C3' DA I 78 " pdb=" C2' DA I 78 " ideal model delta sigma weight residual 111.50 104.62 6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.49 -11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C4' DC I 75 " pdb=" C3' DC I 75 " pdb=" O3' DC I 75 " ideal model delta sigma weight residual 110.00 104.22 5.78 1.50e+00 4.44e-01 1.48e+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 - 0.041: 1952 0.041 - 0.083: 438 0.083 - 0.124: 63 0.124 - 0.165: 10 0.165 - 0.206: 5 Chirality restraints: 2468 Sorted by residual: chirality pdb=" C3' DC I 75 " pdb=" C4' DC I 75 " pdb=" O3' DC I 75 " pdb=" C2' DC I 75 " both_signs ideal model delta sigma weight residual False -2.66 -2.87 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DT J -76 " pdb=" C4' DT J -76 " pdb=" O3' DT J -76 " pdb=" C2' DT J -76 " both_signs ideal model delta sigma weight residual False -2.66 -2.85 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C3' DG J -71 " pdb=" C4' DG J -71 " pdb=" O3' DG J -71 " pdb=" C2' DG J -71 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.50e-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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.080 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.004 0.062 15000 Z= 0.208 Angle : 0.639 11.794 21694 Z= 0.388 Chirality : 0.036 0.206 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 aren 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 covalent geometry : bond 0.00450 (15000) covalent geometry : angle 0.63909 (21694) hydrogen bonds : bond 0.12470 ( 880) hydrogen bonds : angle 5.37206 ( 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 : 0.473 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: 0.9719 (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: 0.9177 (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: 0.8809 (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: 0.8338 (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: 0.1485 time to fit residues: 64.7500 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 : 0.247 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: B 64 ASN B 75 HIS D 81 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.048949 restraints weight = 154676.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.049820 restraints weight = 92890.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050163 restraints weight = 64300.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.050581 restraints weight = 51431.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.050843 restraints weight = 42283.236| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15000 Z= 0.213 Angle : 0.649 11.594 21694 Z= 0.382 Chirality : 0.036 0.169 2468 Planarity : 0.007 0.163 1582 Dihedral : 31.146 177.646 4762 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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 aren not related in a simple way. whole: 1.90 (0.27), residues: 882 helix: 1.80 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 281 TYR 0.029 0.003 TYR H 80 PHE 0.019 0.002 PHE X 278 TRP 0.008 0.002 TRP X 207 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (15000) covalent geometry : angle 0.64873 (21694) hydrogen bonds : bond 0.05745 ( 880) hydrogen bonds : angle 3.49863 ( 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 243 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.389 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: A 48 LEU cc_start: 0.9656 (mp) cc_final: 0.9421 (mt) REVERT: A 89 VAL cc_start: 0.9428 (t) cc_final: 0.9152 (t) REVERT: A 126 LEU cc_start: 0.9380 (mm) cc_final: 0.9131 (tp) REVERT: B 53 GLU cc_start: 0.9287 (tp30) cc_final: 0.8825 (tt0) REVERT: B 97 LEU cc_start: 0.9597 (tp) cc_final: 0.9397 (tp) REVERT: B 100 PHE cc_start: 0.6488 (m-80) cc_final: 0.5568 (m-10) REVERT: C 25 PHE cc_start: 0.8622 (m-10) cc_final: 0.8237 (m-10) REVERT: C 94 ASN cc_start: 0.9210 (t0) cc_final: 0.8813 (m-40) REVERT: C 101 THR cc_start: 0.8698 (m) cc_final: 0.8370 (p) REVERT: D 59 MET cc_start: 0.9748 (mmm) cc_final: 0.9330 (mmm) REVERT: D 64 ASN cc_start: 0.9503 (m-40) cc_final: 0.9298 (m-40) REVERT: D 70 ILE cc_start: 0.9155 (tp) cc_final: 0.8881 (tp) REVERT: D 73 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8977 (mm-30) REVERT: D 80 TYR cc_start: 0.9095 (m-10) cc_final: 0.8826 (m-10) REVERT: E 94 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9229 (mm-30) REVERT: E 99 TYR cc_start: 0.9601 (t80) cc_final: 0.9137 (t80) REVERT: F 26 ILE cc_start: 0.8739 (tp) cc_final: 0.8206 (tp) REVERT: F 49 LEU cc_start: 0.9582 (mm) cc_final: 0.9322 (mm) REVERT: F 57 VAL cc_start: 0.9542 (t) cc_final: 0.9193 (p) REVERT: F 72 TYR cc_start: 0.8721 (m-80) cc_final: 0.8363 (m-80) REVERT: F 100 PHE cc_start: 0.5735 (m-80) cc_final: 0.5272 (m-80) REVERT: G 25 PHE cc_start: 0.9521 (m-80) cc_final: 0.8881 (m-10) REVERT: G 56 GLU cc_start: 0.8602 (tt0) cc_final: 0.7973 (tt0) REVERT: G 73 ASN cc_start: 0.8574 (m110) cc_final: 0.8268 (m110) REVERT: G 94 ASN cc_start: 0.9386 (t0) cc_final: 0.9036 (m-40) REVERT: G 101 THR cc_start: 0.8693 (m) cc_final: 0.8316 (p) REVERT: H 34 TYR cc_start: 0.9366 (m-80) cc_final: 0.9081 (m-80) REVERT: H 73 GLU cc_start: 0.9525 (tp30) cc_final: 0.8616 (tp30) REVERT: H 86 ILE cc_start: 0.8908 (mm) cc_final: 0.8545 (mm) REVERT: H 90 GLU cc_start: 0.9600 (mp0) cc_final: 0.9048 (mm-30) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1596 time to fit residues: 52.9091 Evaluate side-chains 169 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 0.8980 chunk 27 optimal weight: 9.9990 chunk 111 optimal weight: 40.0000 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 113 HIS D 106 HIS E 108 ASN F 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.059827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.046523 restraints weight = 163157.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046831 restraints weight = 100610.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047371 restraints weight = 69594.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047688 restraints weight = 53140.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047826 restraints weight = 43930.663| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15000 Z= 0.222 Angle : 0.623 11.210 21694 Z= 0.369 Chirality : 0.035 0.140 2468 Planarity : 0.005 0.061 1582 Dihedral : 31.442 177.396 4762 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % 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 aren not related in a simple way. whole: 1.73 (0.27), residues: 882 helix: 1.63 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -0.20 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.013 0.002 TYR F 51 PHE 0.012 0.002 PHE B 61 TRP 0.010 0.001 TRP X 207 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00482 (15000) covalent geometry : angle 0.62339 (21694) hydrogen bonds : bond 0.06197 ( 880) hydrogen bonds : angle 3.49159 ( 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 219 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.222 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: A 48 LEU cc_start: 0.9548 (mp) cc_final: 0.9327 (mt) REVERT: A 79 LYS cc_start: 0.9270 (mmpt) cc_final: 0.9061 (mmtm) REVERT: A 90 MET cc_start: 0.9670 (mmp) cc_final: 0.9426 (mmp) REVERT: A 126 LEU cc_start: 0.9554 (mm) cc_final: 0.9287 (tp) REVERT: B 59 LYS cc_start: 0.9485 (tptp) cc_final: 0.9269 (tppt) REVERT: B 88 TYR cc_start: 0.9296 (m-10) cc_final: 0.9025 (m-10) REVERT: B 97 LEU cc_start: 0.9382 (tp) cc_final: 0.8985 (tp) REVERT: B 98 TYR cc_start: 0.7935 (m-10) cc_final: 0.7617 (m-10) REVERT: C 94 ASN cc_start: 0.9721 (t0) cc_final: 0.9306 (t0) REVERT: C 101 THR cc_start: 0.9439 (m) cc_final: 0.9226 (p) REVERT: C 112 GLN cc_start: 0.9492 (tp40) cc_final: 0.9027 (tp-100) REVERT: D 34 TYR cc_start: 0.9166 (m-80) cc_final: 0.8725 (m-80) REVERT: D 59 MET cc_start: 0.9643 (mmm) cc_final: 0.9193 (mmm) REVERT: D 65 ASP cc_start: 0.9597 (t0) cc_final: 0.9273 (t0) REVERT: D 79 HIS cc_start: 0.9596 (t-90) cc_final: 0.9354 (t-90) REVERT: D 98 LEU cc_start: 0.9248 (mm) cc_final: 0.8761 (mm) REVERT: D 102 GLU cc_start: 0.9468 (tp30) cc_final: 0.9232 (tm-30) REVERT: D 103 LEU cc_start: 0.9735 (mt) cc_final: 0.9287 (mt) REVERT: E 74 ILE cc_start: 0.9659 (mt) cc_final: 0.9242 (mt) REVERT: E 90 MET cc_start: 0.9351 (ttp) cc_final: 0.9127 (ttp) REVERT: E 94 GLU cc_start: 0.9479 (mm-30) cc_final: 0.8993 (mm-30) REVERT: E 105 GLU cc_start: 0.9583 (tp30) cc_final: 0.9352 (tm-30) REVERT: E 106 ASP cc_start: 0.9177 (m-30) cc_final: 0.8890 (m-30) REVERT: E 110 CYS cc_start: 0.9719 (m) cc_final: 0.9004 (t) REVERT: F 26 ILE cc_start: 0.9258 (tp) cc_final: 0.9026 (tp) REVERT: F 74 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8863 (tm-30) REVERT: F 100 PHE cc_start: 0.8279 (m-80) cc_final: 0.8021 (m-80) REVERT: G 73 ASN cc_start: 0.9170 (m110) cc_final: 0.8760 (m110) REVERT: G 94 ASN cc_start: 0.9700 (t0) cc_final: 0.9244 (m-40) REVERT: G 101 THR cc_start: 0.9366 (m) cc_final: 0.8958 (p) REVERT: H 34 TYR cc_start: 0.9200 (m-80) cc_final: 0.8305 (m-80) REVERT: H 59 MET cc_start: 0.9761 (mmp) cc_final: 0.9412 (mmm) REVERT: H 76 ARG cc_start: 0.9594 (ptp-110) cc_final: 0.9270 (ptp-110) REVERT: H 113 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8881 (pttm) outliers start: 1 outliers final: 1 residues processed: 218 average time/residue: 0.1301 time to fit residues: 39.1795 Evaluate side-chains 158 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 10.0000 chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 44 GLN E 108 ASN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.052639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040083 restraints weight = 177456.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.040338 restraints weight = 108243.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040789 restraints weight = 74010.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.041030 restraints weight = 55855.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041167 restraints weight = 46352.508| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 15000 Z= 0.368 Angle : 0.784 16.022 21694 Z= 0.454 Chirality : 0.042 0.170 2468 Planarity : 0.007 0.066 1582 Dihedral : 32.963 177.450 4762 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 882 helix: 0.62 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -0.47 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 131 TYR 0.021 0.003 TYR D 80 PHE 0.030 0.003 PHE F 61 TRP 0.018 0.002 TRP X 207 HIS 0.010 0.003 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00803 (15000) covalent geometry : angle 0.78371 (21694) hydrogen bonds : bond 0.12319 ( 880) hydrogen bonds : angle 4.43124 ( 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 189 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.370 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: A 81 ASP cc_start: 0.9334 (m-30) cc_final: 0.9108 (m-30) REVERT: A 120 MET cc_start: 0.8933 (tpt) cc_final: 0.8450 (tpp) REVERT: A 126 LEU cc_start: 0.9682 (mm) cc_final: 0.9387 (tp) REVERT: C 25 PHE cc_start: 0.8444 (m-10) cc_final: 0.7833 (m-80) REVERT: C 39 TYR cc_start: 0.9213 (m-10) cc_final: 0.8957 (m-80) REVERT: C 90 ASP cc_start: 0.8345 (t0) cc_final: 0.8130 (t70) REVERT: C 94 ASN cc_start: 0.9368 (t0) cc_final: 0.8955 (t0) REVERT: C 101 THR cc_start: 0.9069 (m) cc_final: 0.8728 (t) REVERT: C 112 GLN cc_start: 0.9330 (tp40) cc_final: 0.8879 (tp-100) REVERT: D 59 MET cc_start: 0.9806 (mmm) cc_final: 0.9159 (mmm) REVERT: D 64 ASN cc_start: 0.9455 (m-40) cc_final: 0.9224 (m-40) REVERT: D 79 HIS cc_start: 0.9751 (t-90) cc_final: 0.9488 (t-90) REVERT: D 98 LEU cc_start: 0.8797 (mm) cc_final: 0.8536 (mt) REVERT: D 102 GLU cc_start: 0.9885 (tp30) cc_final: 0.9635 (tm-30) REVERT: D 103 LEU cc_start: 0.9783 (mt) cc_final: 0.9391 (mt) REVERT: E 85 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8907 (tp-100) REVERT: E 94 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9325 (mm-30) REVERT: E 99 TYR cc_start: 0.9526 (t80) cc_final: 0.9210 (t80) REVERT: E 115 LYS cc_start: 0.9215 (mppt) cc_final: 0.8978 (mptt) REVERT: F 29 ILE cc_start: 0.9586 (mp) cc_final: 0.9253 (tp) REVERT: G 25 PHE cc_start: 0.8861 (m-10) cc_final: 0.7289 (m-10) REVERT: G 56 GLU cc_start: 0.8879 (tt0) cc_final: 0.7265 (tt0) REVERT: G 73 ASN cc_start: 0.8774 (m110) cc_final: 0.8527 (m110) REVERT: G 94 ASN cc_start: 0.9438 (t0) cc_final: 0.9131 (t0) REVERT: H 34 TYR cc_start: 0.9699 (m-80) cc_final: 0.9441 (m-80) REVERT: H 59 MET cc_start: 0.9786 (mmp) cc_final: 0.9508 (mmp) REVERT: H 64 ASN cc_start: 0.9580 (m-40) cc_final: 0.9360 (m-40) REVERT: H 73 GLU cc_start: 0.9781 (mm-30) cc_final: 0.9531 (mm-30) REVERT: H 76 ARG cc_start: 0.9656 (ptp-110) cc_final: 0.9347 (ptp-110) REVERT: H 98 LEU cc_start: 0.9232 (tp) cc_final: 0.8999 (tp) REVERT: H 113 LYS cc_start: 0.9466 (ptpp) cc_final: 0.9029 (pttp) REVERT: H 117 LYS cc_start: 0.9676 (ptpp) cc_final: 0.9302 (ptmm) REVERT: H 122 LYS cc_start: 0.9211 (tmmt) cc_final: 0.8956 (tmmt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1284 time to fit residues: 34.2120 Evaluate side-chains 135 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.043204 restraints weight = 171195.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.043557 restraints weight = 102136.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044110 restraints weight = 67453.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044415 restraints weight = 49667.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044635 restraints weight = 40360.376| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15000 Z= 0.188 Angle : 0.638 12.367 21694 Z= 0.372 Chirality : 0.035 0.158 2468 Planarity : 0.004 0.043 1582 Dihedral : 32.210 176.698 4762 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.27), residues: 882 helix: 1.13 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.25 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 53 TYR 0.032 0.002 TYR B 72 PHE 0.015 0.002 PHE G 25 TRP 0.012 0.002 TRP X 207 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00406 (15000) covalent geometry : angle 0.63780 (21694) hydrogen bonds : bond 0.05343 ( 880) hydrogen bonds : angle 3.76952 ( 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 197 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.340 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: 0.9439 (m-30) cc_final: 0.9195 (m-30) REVERT: A 109 LEU cc_start: 0.9407 (mt) cc_final: 0.9194 (mt) REVERT: A 126 LEU cc_start: 0.9616 (mm) cc_final: 0.9332 (tt) REVERT: B 97 LEU cc_start: 0.9504 (tp) cc_final: 0.9289 (tp) REVERT: C 25 PHE cc_start: 0.8170 (m-10) cc_final: 0.7504 (m-80) REVERT: C 83 LEU cc_start: 0.9668 (mp) cc_final: 0.9324 (mp) REVERT: C 94 ASN cc_start: 0.9280 (t0) cc_final: 0.9004 (t0) REVERT: C 101 THR cc_start: 0.8862 (m) cc_final: 0.8516 (t) REVERT: C 112 GLN cc_start: 0.9322 (tp40) cc_final: 0.8957 (tp-100) REVERT: D 34 TYR cc_start: 0.9636 (m-80) cc_final: 0.9203 (m-80) REVERT: D 64 ASN cc_start: 0.9354 (m-40) cc_final: 0.9094 (m110) REVERT: D 73 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8999 (mm-30) REVERT: D 79 HIS cc_start: 0.9748 (t-90) cc_final: 0.9523 (t-90) REVERT: D 98 LEU cc_start: 0.8390 (mm) cc_final: 0.7961 (mm) REVERT: D 102 GLU cc_start: 0.9918 (tp30) cc_final: 0.9706 (tm-30) REVERT: D 103 LEU cc_start: 0.9755 (mt) cc_final: 0.9494 (mt) REVERT: E 85 GLN cc_start: 0.9174 (tp-100) cc_final: 0.8949 (tp-100) REVERT: E 94 GLU cc_start: 0.9659 (mm-30) cc_final: 0.9232 (mm-30) REVERT: E 99 TYR cc_start: 0.9540 (t80) cc_final: 0.9247 (t80) REVERT: F 100 PHE cc_start: 0.7764 (m-80) cc_final: 0.7249 (m-80) REVERT: G 25 PHE cc_start: 0.8691 (m-10) cc_final: 0.7945 (m-10) REVERT: G 73 ASN cc_start: 0.8576 (m110) cc_final: 0.8374 (m110) REVERT: G 94 ASN cc_start: 0.9421 (t0) cc_final: 0.9179 (t0) REVERT: G 101 THR cc_start: 0.8869 (m) cc_final: 0.8554 (p) REVERT: H 34 TYR cc_start: 0.9659 (m-80) cc_final: 0.9313 (m-80) REVERT: H 59 MET cc_start: 0.9778 (mmp) cc_final: 0.9560 (mmm) REVERT: H 73 GLU cc_start: 0.9740 (mm-30) cc_final: 0.9371 (mt-10) REVERT: H 98 LEU cc_start: 0.8924 (tp) cc_final: 0.7848 (tp) REVERT: H 110 GLU cc_start: 0.9643 (mm-30) cc_final: 0.9209 (mm-30) REVERT: H 113 LYS cc_start: 0.9561 (ptpp) cc_final: 0.9286 (pttm) REVERT: H 117 LYS cc_start: 0.9765 (ptpp) cc_final: 0.9468 (ptmm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1356 time to fit residues: 37.2807 Evaluate side-chains 139 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.053264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040731 restraints weight = 176339.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.041471 restraints weight = 102570.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041872 restraints weight = 69061.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.042127 restraints weight = 52265.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042253 restraints weight = 42523.898| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15000 Z= 0.269 Angle : 0.678 14.719 21694 Z= 0.397 Chirality : 0.037 0.158 2468 Planarity : 0.006 0.056 1582 Dihedral : 32.416 176.929 4762 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.27), residues: 882 helix: 0.83 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 131 TYR 0.023 0.002 TYR F 88 PHE 0.015 0.002 PHE B 61 TRP 0.014 0.002 TRP X 207 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00584 (15000) covalent geometry : angle 0.67766 (21694) hydrogen bonds : bond 0.08573 ( 880) hydrogen bonds : angle 4.06483 ( 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 175 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9347 (m-30) cc_final: 0.9122 (m-30) REVERT: A 126 LEU cc_start: 0.9698 (mm) cc_final: 0.9459 (tp) REVERT: B 66 ILE cc_start: 0.9583 (mt) cc_final: 0.9341 (tt) REVERT: B 97 LEU cc_start: 0.9496 (tp) cc_final: 0.9242 (tp) REVERT: B 100 PHE cc_start: 0.7306 (m-10) cc_final: 0.7099 (m-10) REVERT: C 25 PHE cc_start: 0.8474 (m-10) cc_final: 0.7832 (m-10) REVERT: C 90 ASP cc_start: 0.8290 (t0) cc_final: 0.8077 (t70) REVERT: C 94 ASN cc_start: 0.9450 (t0) cc_final: 0.9069 (t0) REVERT: C 101 THR cc_start: 0.9023 (m) cc_final: 0.8733 (p) REVERT: C 102 ILE cc_start: 0.8074 (tt) cc_final: 0.7835 (tt) REVERT: C 112 GLN cc_start: 0.9361 (tp40) cc_final: 0.8926 (tp-100) REVERT: D 34 TYR cc_start: 0.9697 (m-80) cc_final: 0.9487 (m-80) REVERT: D 64 ASN cc_start: 0.9373 (m-40) cc_final: 0.9121 (m-40) REVERT: D 73 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9224 (mm-30) REVERT: D 79 HIS cc_start: 0.9739 (t-90) cc_final: 0.9494 (t-90) REVERT: D 98 LEU cc_start: 0.8814 (mm) cc_final: 0.8360 (mm) REVERT: D 102 GLU cc_start: 0.9917 (tp30) cc_final: 0.9690 (tm-30) REVERT: D 103 LEU cc_start: 0.9796 (mt) cc_final: 0.9402 (mt) REVERT: E 81 ASP cc_start: 0.9593 (m-30) cc_final: 0.9344 (t0) REVERT: E 94 GLU cc_start: 0.9612 (mm-30) cc_final: 0.9210 (mm-30) REVERT: E 115 LYS cc_start: 0.9409 (mppt) cc_final: 0.9196 (mptt) REVERT: F 60 VAL cc_start: 0.9651 (t) cc_final: 0.9394 (t) REVERT: G 25 PHE cc_start: 0.8834 (m-10) cc_final: 0.7917 (m-10) REVERT: G 56 GLU cc_start: 0.8571 (tt0) cc_final: 0.7373 (tt0) REVERT: G 64 GLU cc_start: 0.9589 (OUTLIER) cc_final: 0.9380 (pp20) REVERT: G 94 ASN cc_start: 0.9442 (t0) cc_final: 0.9086 (t0) REVERT: G 101 THR cc_start: 0.8998 (m) cc_final: 0.8678 (p) REVERT: H 54 LYS cc_start: 0.9730 (mmpt) cc_final: 0.9522 (mmmt) REVERT: H 59 MET cc_start: 0.9802 (mmp) cc_final: 0.9591 (mmm) REVERT: H 64 ASN cc_start: 0.9549 (m-40) cc_final: 0.9323 (m110) REVERT: H 73 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9368 (mt-10) REVERT: H 98 LEU cc_start: 0.9149 (tp) cc_final: 0.8461 (tp) REVERT: H 110 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9239 (mm-30) REVERT: H 113 LYS cc_start: 0.9598 (ptpp) cc_final: 0.9219 (pttp) REVERT: H 117 LYS cc_start: 0.9735 (ptpp) cc_final: 0.9412 (ptmm) REVERT: H 122 LYS cc_start: 0.9116 (tmmt) cc_final: 0.8877 (pttt) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1244 time to fit residues: 30.2464 Evaluate side-chains 133 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 1.9990 chunk 109 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.055776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.043093 restraints weight = 167416.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.043446 restraints weight = 98532.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.043977 restraints weight = 66622.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.044263 restraints weight = 49824.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044433 restraints weight = 40731.666| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15000 Z= 0.172 Angle : 0.644 13.406 21694 Z= 0.375 Chirality : 0.036 0.164 2468 Planarity : 0.004 0.051 1582 Dihedral : 31.925 176.150 4762 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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 aren not related in a simple way. whole: 0.96 (0.27), residues: 882 helix: 0.98 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.17 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.015 0.002 TYR F 72 PHE 0.013 0.002 PHE B 61 TRP 0.012 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00367 (15000) covalent geometry : angle 0.64447 (21694) hydrogen bonds : bond 0.04636 ( 880) hydrogen bonds : angle 3.83461 ( 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 187 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9462 (pp) cc_final: 0.8948 (mp) REVERT: A 62 ILE cc_start: 0.9347 (mm) cc_final: 0.9105 (mm) REVERT: A 81 ASP cc_start: 0.8923 (m-30) cc_final: 0.8656 (m-30) REVERT: A 105 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8644 (tm-30) REVERT: A 109 LEU cc_start: 0.9509 (mt) cc_final: 0.9122 (mt) REVERT: A 115 LYS cc_start: 0.9860 (mmpt) cc_final: 0.9658 (mppt) REVERT: A 126 LEU cc_start: 0.9673 (mm) cc_final: 0.9464 (tt) REVERT: B 63 GLU cc_start: 0.9680 (mt-10) cc_final: 0.9307 (mt-10) REVERT: B 97 LEU cc_start: 0.9445 (tp) cc_final: 0.9209 (tp) REVERT: B 100 PHE cc_start: 0.7467 (m-10) cc_final: 0.7219 (m-10) REVERT: C 25 PHE cc_start: 0.8445 (m-10) cc_final: 0.7992 (m-10) REVERT: C 56 GLU cc_start: 0.9400 (pp20) cc_final: 0.9022 (tt0) REVERT: C 83 LEU cc_start: 0.9695 (mp) cc_final: 0.9420 (mp) REVERT: C 90 ASP cc_start: 0.8642 (t0) cc_final: 0.8361 (t0) REVERT: C 94 ASN cc_start: 0.9689 (t0) cc_final: 0.9240 (t0) REVERT: C 101 THR cc_start: 0.9484 (m) cc_final: 0.9208 (p) REVERT: D 34 TYR cc_start: 0.9515 (m-80) cc_final: 0.8993 (m-80) REVERT: D 56 MET cc_start: 0.9369 (tpt) cc_final: 0.9103 (tpt) REVERT: D 59 MET cc_start: 0.9869 (mmp) cc_final: 0.9185 (mmm) REVERT: D 64 ASN cc_start: 0.9507 (m-40) cc_final: 0.9024 (m110) REVERT: D 65 ASP cc_start: 0.9462 (t70) cc_final: 0.9081 (t0) REVERT: D 67 PHE cc_start: 0.9625 (t80) cc_final: 0.9357 (t80) REVERT: D 79 HIS cc_start: 0.9734 (t-90) cc_final: 0.9391 (t-90) REVERT: D 98 LEU cc_start: 0.9117 (mm) cc_final: 0.8899 (mm) REVERT: D 102 GLU cc_start: 0.9763 (tp30) cc_final: 0.9562 (tm-30) REVERT: D 103 LEU cc_start: 0.9787 (mt) cc_final: 0.9019 (mt) REVERT: F 72 TYR cc_start: 0.9062 (m-80) cc_final: 0.8505 (m-80) REVERT: F 74 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9025 (tm-30) REVERT: G 25 PHE cc_start: 0.8491 (m-10) cc_final: 0.7740 (m-10) REVERT: G 56 GLU cc_start: 0.9070 (tt0) cc_final: 0.7484 (tt0) REVERT: G 73 ASN cc_start: 0.9128 (m110) cc_final: 0.8791 (m110) REVERT: G 94 ASN cc_start: 0.9671 (t0) cc_final: 0.9316 (t0) REVERT: G 101 THR cc_start: 0.9416 (m) cc_final: 0.9073 (p) REVERT: H 34 TYR cc_start: 0.9258 (m-80) cc_final: 0.8862 (m-80) REVERT: H 59 MET cc_start: 0.9813 (mmp) cc_final: 0.9494 (mmm) REVERT: H 64 ASN cc_start: 0.9606 (m-40) cc_final: 0.9348 (m110) REVERT: H 98 LEU cc_start: 0.9462 (tp) cc_final: 0.8851 (tp) REVERT: H 113 LYS cc_start: 0.9390 (ptpp) cc_final: 0.8975 (pttt) REVERT: H 117 LYS cc_start: 0.9651 (ptpp) cc_final: 0.9432 (ptmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1459 time to fit residues: 38.2377 Evaluate side-chains 138 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.055752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.043109 restraints weight = 166982.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.043785 restraints weight = 97324.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044237 restraints weight = 65242.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044503 restraints weight = 49355.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.044664 restraints weight = 39769.828| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15000 Z= 0.174 Angle : 0.644 13.284 21694 Z= 0.374 Chirality : 0.036 0.152 2468 Planarity : 0.005 0.052 1582 Dihedral : 31.752 176.612 4762 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.27), residues: 882 helix: 1.01 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 282 TYR 0.015 0.002 TYR E 99 PHE 0.021 0.002 PHE B 61 TRP 0.011 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00374 (15000) covalent geometry : angle 0.64385 (21694) hydrogen bonds : bond 0.04909 ( 880) hydrogen bonds : angle 3.73881 ( 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 : 0.289 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: A 60 LEU cc_start: 0.9468 (pp) cc_final: 0.9022 (mp) REVERT: A 62 ILE cc_start: 0.9296 (mm) cc_final: 0.8942 (mm) REVERT: A 81 ASP cc_start: 0.8940 (m-30) cc_final: 0.8686 (m-30) REVERT: A 105 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8614 (tm-30) REVERT: A 109 LEU cc_start: 0.9514 (mt) cc_final: 0.9108 (mt) REVERT: B 59 LYS cc_start: 0.9448 (tptp) cc_final: 0.9238 (tppt) REVERT: B 63 GLU cc_start: 0.9663 (mt-10) cc_final: 0.9264 (mt-10) REVERT: C 25 PHE cc_start: 0.8399 (m-10) cc_final: 0.7617 (m-10) REVERT: C 56 GLU cc_start: 0.9390 (pp20) cc_final: 0.9172 (pp20) REVERT: C 83 LEU cc_start: 0.9738 (mp) cc_final: 0.9469 (mp) REVERT: C 90 ASP cc_start: 0.8643 (t0) cc_final: 0.8359 (t0) REVERT: C 94 ASN cc_start: 0.9676 (t0) cc_final: 0.9222 (t0) REVERT: C 101 THR cc_start: 0.9420 (m) cc_final: 0.9160 (p) REVERT: D 56 MET cc_start: 0.9374 (tpt) cc_final: 0.9144 (tpt) REVERT: D 59 MET cc_start: 0.9851 (mmp) cc_final: 0.9243 (mmm) REVERT: D 64 ASN cc_start: 0.9510 (m-40) cc_final: 0.9008 (m-40) REVERT: D 65 ASP cc_start: 0.9478 (t70) cc_final: 0.9098 (t0) REVERT: D 67 PHE cc_start: 0.9621 (t80) cc_final: 0.9314 (t80) REVERT: D 79 HIS cc_start: 0.9718 (t-90) cc_final: 0.9371 (t-90) REVERT: D 86 ILE cc_start: 0.9224 (mt) cc_final: 0.8904 (mm) REVERT: D 103 LEU cc_start: 0.9797 (mt) cc_final: 0.9039 (mt) REVERT: F 61 PHE cc_start: 0.9604 (t80) cc_final: 0.9399 (t80) REVERT: F 68 ASP cc_start: 0.9492 (m-30) cc_final: 0.9203 (m-30) REVERT: F 72 TYR cc_start: 0.9063 (m-80) cc_final: 0.8493 (m-80) REVERT: F 74 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9130 (tm-30) REVERT: G 25 PHE cc_start: 0.8449 (m-10) cc_final: 0.7672 (m-10) REVERT: G 41 GLU cc_start: 0.8843 (pm20) cc_final: 0.8445 (pp20) REVERT: G 56 GLU cc_start: 0.9017 (tt0) cc_final: 0.7427 (tt0) REVERT: G 73 ASN cc_start: 0.9119 (m110) cc_final: 0.8777 (m110) REVERT: G 94 ASN cc_start: 0.9649 (t0) cc_final: 0.9317 (t0) REVERT: G 101 THR cc_start: 0.9407 (m) cc_final: 0.9087 (p) REVERT: H 34 TYR cc_start: 0.9289 (m-80) cc_final: 0.8940 (m-80) REVERT: H 59 MET cc_start: 0.9823 (mmp) cc_final: 0.9465 (mmm) REVERT: H 64 ASN cc_start: 0.9596 (m-40) cc_final: 0.9335 (m110) REVERT: H 76 ARG cc_start: 0.9728 (mtm110) cc_final: 0.9276 (ptt90) REVERT: H 103 LEU cc_start: 0.9692 (mt) cc_final: 0.9029 (mt) REVERT: H 106 HIS cc_start: 0.9518 (m90) cc_final: 0.9034 (m90) REVERT: H 110 GLU cc_start: 0.9608 (tp30) cc_final: 0.9322 (tp30) REVERT: H 113 LYS cc_start: 0.9538 (ptpp) cc_final: 0.9131 (pttm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1490 time to fit residues: 37.9384 Evaluate side-chains 139 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.055311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.042591 restraints weight = 171060.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042943 restraints weight = 102350.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.043480 restraints weight = 68200.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.043841 restraints weight = 50902.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.043985 restraints weight = 40692.682| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15000 Z= 0.186 Angle : 0.651 12.650 21694 Z= 0.378 Chirality : 0.035 0.152 2468 Planarity : 0.005 0.054 1582 Dihedral : 31.766 176.673 4762 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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 aren not related in a simple way. whole: 0.95 (0.27), residues: 882 helix: 1.01 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.29 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 76 TYR 0.018 0.002 TYR A 99 PHE 0.010 0.001 PHE X 278 TRP 0.012 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00400 (15000) covalent geometry : angle 0.65057 (21694) hydrogen bonds : bond 0.05417 ( 880) hydrogen bonds : angle 3.80501 ( 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 178 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.409 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: A 81 ASP cc_start: 0.9514 (m-30) cc_final: 0.9296 (m-30) REVERT: A 109 LEU cc_start: 0.9447 (mt) cc_final: 0.9189 (mt) REVERT: A 110 CYS cc_start: 0.9876 (m) cc_final: 0.9516 (t) REVERT: B 97 LEU cc_start: 0.9533 (tp) cc_final: 0.9329 (tp) REVERT: C 25 PHE cc_start: 0.8318 (m-10) cc_final: 0.7356 (m-10) REVERT: C 56 GLU cc_start: 0.9353 (pp20) cc_final: 0.9140 (pp20) REVERT: C 83 LEU cc_start: 0.9584 (mp) cc_final: 0.9279 (mp) REVERT: C 94 ASN cc_start: 0.9358 (t0) cc_final: 0.8989 (t0) REVERT: C 101 THR cc_start: 0.8918 (m) cc_final: 0.8668 (p) REVERT: D 56 MET cc_start: 0.9566 (tpt) cc_final: 0.9361 (tpt) REVERT: D 59 MET cc_start: 0.9818 (mmp) cc_final: 0.9360 (mmm) REVERT: D 64 ASN cc_start: 0.9310 (m-40) cc_final: 0.9052 (m-40) REVERT: D 79 HIS cc_start: 0.9781 (t-90) cc_final: 0.9570 (t-90) REVERT: D 98 LEU cc_start: 0.8530 (mm) cc_final: 0.8325 (mm) REVERT: D 103 LEU cc_start: 0.9784 (mt) cc_final: 0.9584 (mt) REVERT: E 99 TYR cc_start: 0.9530 (t80) cc_final: 0.9247 (t80) REVERT: F 74 GLU cc_start: 0.9523 (tm-30) cc_final: 0.9298 (tm-30) REVERT: G 25 PHE cc_start: 0.8816 (m-10) cc_final: 0.7742 (m-10) REVERT: G 56 GLU cc_start: 0.8702 (tt0) cc_final: 0.7574 (tt0) REVERT: G 73 ASN cc_start: 0.8671 (m110) cc_final: 0.8425 (m110) REVERT: G 94 ASN cc_start: 0.9555 (t0) cc_final: 0.9279 (t0) REVERT: G 101 THR cc_start: 0.9042 (m) cc_final: 0.8746 (p) REVERT: H 34 TYR cc_start: 0.9288 (m-80) cc_final: 0.8953 (m-80) REVERT: H 59 MET cc_start: 0.9775 (mmp) cc_final: 0.9564 (mmm) REVERT: H 64 ASN cc_start: 0.9497 (m-40) cc_final: 0.9265 (m-40) REVERT: H 76 ARG cc_start: 0.9741 (mtm110) cc_final: 0.9453 (mtm110) REVERT: H 102 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8736 (tm-30) REVERT: H 103 LEU cc_start: 0.9670 (mt) cc_final: 0.9435 (mt) REVERT: H 110 GLU cc_start: 0.9815 (tp30) cc_final: 0.9522 (tp30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1467 time to fit residues: 36.6575 Evaluate side-chains 122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 3.9990 chunk 88 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.053272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.040798 restraints weight = 175208.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.041540 restraints weight = 101812.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041951 restraints weight = 69045.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042214 restraints weight = 52810.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.042345 restraints weight = 43278.660| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15000 Z= 0.252 Angle : 0.693 15.061 21694 Z= 0.403 Chirality : 0.037 0.153 2468 Planarity : 0.005 0.052 1582 Dihedral : 32.162 177.098 4762 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 aren not related in a simple way. whole: 0.77 (0.27), residues: 882 helix: 0.89 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 282 TYR 0.024 0.002 TYR A 99 PHE 0.025 0.002 PHE B 61 TRP 0.016 0.003 TRP X 207 HIS 0.013 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00545 (15000) covalent geometry : angle 0.69346 (21694) hydrogen bonds : bond 0.07845 ( 880) hydrogen bonds : angle 4.10078 ( 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 168 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.417 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: A 105 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 106 ASP cc_start: 0.9217 (p0) cc_final: 0.8961 (p0) REVERT: A 109 LEU cc_start: 0.9503 (mt) cc_final: 0.9068 (mt) REVERT: A 110 CYS cc_start: 0.9730 (m) cc_final: 0.9426 (t) REVERT: B 97 LEU cc_start: 0.9492 (tp) cc_final: 0.9286 (tp) REVERT: C 25 PHE cc_start: 0.8257 (m-10) cc_final: 0.7589 (m-10) REVERT: C 56 GLU cc_start: 0.9290 (pp20) cc_final: 0.9076 (pp20) REVERT: C 83 LEU cc_start: 0.9691 (mp) cc_final: 0.9364 (mp) REVERT: C 90 ASP cc_start: 0.8873 (t0) cc_final: 0.8605 (t70) REVERT: C 94 ASN cc_start: 0.9708 (t0) cc_final: 0.9255 (t0) REVERT: C 101 THR cc_start: 0.9495 (m) cc_final: 0.9236 (p) REVERT: D 59 MET cc_start: 0.9808 (mmp) cc_final: 0.9155 (mmm) REVERT: D 64 ASN cc_start: 0.9459 (m-40) cc_final: 0.9045 (m-40) REVERT: D 67 PHE cc_start: 0.9576 (t80) cc_final: 0.9236 (t80) REVERT: D 79 HIS cc_start: 0.9608 (t-90) cc_final: 0.9261 (t-90) REVERT: D 98 LEU cc_start: 0.9271 (mm) cc_final: 0.8631 (mm) REVERT: D 103 LEU cc_start: 0.9549 (mt) cc_final: 0.9293 (mt) REVERT: F 72 TYR cc_start: 0.8952 (m-80) cc_final: 0.8723 (m-10) REVERT: F 74 GLU cc_start: 0.9355 (tm-30) cc_final: 0.9140 (tm-30) REVERT: F 96 THR cc_start: 0.9436 (p) cc_final: 0.9172 (t) REVERT: G 25 PHE cc_start: 0.8413 (m-10) cc_final: 0.7607 (m-10) REVERT: G 41 GLU cc_start: 0.8762 (pm20) cc_final: 0.8337 (pp20) REVERT: G 56 GLU cc_start: 0.9023 (tt0) cc_final: 0.6568 (tt0) REVERT: G 94 ASN cc_start: 0.9651 (t0) cc_final: 0.9259 (t0) REVERT: G 101 THR cc_start: 0.9479 (m) cc_final: 0.9152 (p) REVERT: H 34 TYR cc_start: 0.9164 (m-80) cc_final: 0.8797 (m-80) REVERT: H 59 MET cc_start: 0.9786 (mmp) cc_final: 0.9446 (mmm) REVERT: H 64 ASN cc_start: 0.9584 (m-40) cc_final: 0.9334 (m-40) REVERT: H 76 ARG cc_start: 0.9689 (mtm110) cc_final: 0.9405 (mtm110) REVERT: H 97 LEU cc_start: 0.9171 (tp) cc_final: 0.8969 (mm) REVERT: H 102 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8277 (tm-30) REVERT: H 103 LEU cc_start: 0.9369 (mt) cc_final: 0.8912 (mt) REVERT: H 110 GLU cc_start: 0.9348 (tp30) cc_final: 0.9100 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1434 time to fit residues: 33.7693 Evaluate side-chains 122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 7.9990 chunk 46 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.054762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042334 restraints weight = 170785.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043049 restraints weight = 99225.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.043505 restraints weight = 66375.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.043790 restraints weight = 49491.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043959 restraints weight = 40868.206| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.8030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15000 Z= 0.178 Angle : 0.663 15.206 21694 Z= 0.384 Chirality : 0.036 0.144 2468 Planarity : 0.005 0.053 1582 Dihedral : 31.781 176.321 4762 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.95 (0.28), residues: 882 helix: 1.01 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 35 TYR 0.021 0.002 TYR A 99 PHE 0.021 0.002 PHE B 61 TRP 0.015 0.003 TRP X 207 HIS 0.007 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00380 (15000) covalent geometry : angle 0.66289 (21694) hydrogen bonds : bond 0.04970 ( 880) hydrogen bonds : angle 3.85617 ( 2227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.59 seconds wall clock time: 41 minutes 12.65 seconds (2472.65 seconds total)