Starting phenix.real_space_refine on Fri Sep 11 20:40:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6px1_20516/09_2026/6px1_20516.cif Found real_map, /net/cci-nas-00/data/ceres_data/6px1_20516/09_2026/6px1_20516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6px1_20516/09_2026/6px1_20516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6px1_20516/09_2026/6px1_20516.map" model { file = "/net/cci-nas-00/data/ceres_data/6px1_20516/09_2026/6px1_20516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6px1_20516/09_2026/6px1_20516.cif" } resolution = 3.3 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= 0.007 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 290 5.49 5 S 12 5.16 5 C 6594 2.51 5 N 2249 2.21 5 O 2792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11937 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 2.84, per 1000 atoms: 0.24 Number of scatterers: 11937 At special positions: 0 Unit cell: (73.84, 117.52, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 290 15.00 O 2792 8.00 N 2249 7.00 C 6594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 286.0 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 70.9% alpha, 3.2% beta 143 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.672A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.668A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.578A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.613A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.553A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 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 102 through 120 removed outlier: 3.835A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.694A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.339A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.530A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.612A pdb=" N LEU G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.521A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.863A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.765A 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: 6.412A 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: 7.154A 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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.272A 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 78 376 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.31 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: 2040 1.33 - 1.45: 4253 1.45 - 1.57: 5847 1.57 - 1.68: 578 1.68 - 1.80: 22 Bond restraints: 12740 Sorted by residual: bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.435 1.490 -0.055 1.30e-02 5.92e+03 1.78e+01 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.435 1.490 -0.055 1.30e-02 5.92e+03 1.77e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C3' DA I 7 " pdb=" C2' DA I 7 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 ... (remaining 12735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 16935 1.85 - 3.70: 1436 3.70 - 5.55: 52 5.55 - 7.40: 20 7.40 - 9.25: 4 Bond angle restraints: 18447 Sorted by residual: angle pdb=" C GLU G 64 " pdb=" CA GLU G 64 " pdb=" CB GLU G 64 " ideal model delta sigma weight residual 110.90 102.08 8.82 1.58e+00 4.01e-01 3.12e+01 angle pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sigma weight residual 119.70 126.32 -6.62 1.20e+00 6.94e-01 3.04e+01 angle pdb=" O5' DA J 121 " pdb=" C5' DA J 121 " pdb=" C4' DA J 121 " ideal model delta sigma weight residual 109.40 113.69 -4.29 8.00e-01 1.56e+00 2.88e+01 angle pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sigma weight residual 119.70 126.09 -6.39 1.20e+00 6.94e-01 2.84e+01 angle pdb=" O5' DG J 39 " pdb=" C5' DG J 39 " pdb=" C4' DG J 39 " ideal model delta sigma weight residual 109.40 113.64 -4.24 8.00e-01 1.56e+00 2.81e+01 ... (remaining 18442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 5436 35.51 - 71.02: 1476 71.02 - 106.54: 5 106.54 - 142.05: 0 142.05 - 177.56: 3 Dihedral angle restraints: 6920 sinusoidal: 4738 harmonic: 2182 Sorted by residual: dihedral pdb=" CA PRO G 117 " pdb=" C PRO G 117 " pdb=" N LYS G 118 " pdb=" CA LYS G 118 " ideal model delta harmonic sigma weight residual 180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LYS D 31 " pdb=" C LYS D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 37.56 -177.56 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 6917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1559 0.059 - 0.118: 475 0.118 - 0.177: 50 0.177 - 0.236: 11 0.236 - 0.295: 3 Chirality restraints: 2098 Sorted by residual: chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA THR A 45 " pdb=" N THR A 45 " pdb=" C THR A 45 " pdb=" CB THR A 45 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2095 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 68 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C GLU D 68 " 0.076 2.00e-02 2.50e+03 pdb=" O GLU D 68 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG D 69 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 64 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C ASN F 64 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN F 64 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 65 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 80 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C THR F 80 " -0.051 2.00e-02 2.50e+03 pdb=" O THR F 80 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL F 81 " 0.017 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1790 2.76 - 3.30: 9452 3.30 - 3.83: 23879 3.83 - 4.37: 28890 4.37 - 4.90: 40918 Nonbonded interactions: 104929 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.287 3.040 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 89 " model vdw 2.308 3.120 nonbonded pdb=" OE1 GLN F 93 " pdb=" NH2 ARG F 95 " model vdw 2.319 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.329 3.040 ... (remaining 104924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.040 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.008 0.076 12740 Z= 0.625 Angle : 1.005 9.252 18447 Z= 0.819 Chirality : 0.055 0.295 2098 Planarity : 0.008 0.068 1330 Dihedral : 28.550 177.562 5512 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.24), residues: 736 helix: -1.77 (0.18), residues: 528 sheet: None (None), residues: 0 loop : -2.02 (0.34), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 95 TYR 0.024 0.003 TYR E 41 PHE 0.019 0.003 PHE C 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.63 (12740) covalent geometry : angle 1.00517 / 0.82 (18447) hydrogen bonds : bond 0.09859 / 6.31 ( 744) hydrogen bonds : angle 4.03200 / 2.84 ( 1849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.326 Fit side-chains REVERT: F 25 ASN cc_start: 0.8710 (m-40) cc_final: 0.8489 (m-40) REVERT: F 35 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8052 (mtm110) REVERT: G 42 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.8051 (mtm180) REVERT: G 94 ASN cc_start: 0.8629 (t0) cc_final: 0.8326 (t0) REVERT: H 87 THR cc_start: 0.8363 (p) cc_final: 0.8143 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1818 time to fit residues: 37.4031 Evaluate side-chains 129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.144723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101397 restraints weight = 17048.972| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.48 r_work: 0.3118 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12740 Z= 0.149 Angle : 0.689 9.949 18447 Z= 0.392 Chirality : 0.048 0.322 2098 Planarity : 0.005 0.068 1330 Dihedral : 31.423 174.166 4008 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.79 % Allowed : 10.63 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.29), residues: 736 helix: 0.20 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -1.47 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 72 TYR 0.008 0.001 TYR A 54 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (12740) covalent geometry : angle 0.68904 / 0.39 (18447) hydrogen bonds : bond 0.04378 / 2.92 ( 744) hydrogen bonds : angle 2.95868 / 2.08 ( 1849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.293 Fit side-chains REVERT: B 72 TYR cc_start: 0.8962 (m-80) cc_final: 0.8681 (m-80) REVERT: D 83 ARG cc_start: 0.8461 (mmt-90) cc_final: 0.8243 (mmt90) REVERT: E 59 GLU cc_start: 0.8021 (mp0) cc_final: 0.7781 (mp0) REVERT: E 73 GLU cc_start: 0.7836 (tt0) cc_final: 0.7610 (tt0) REVERT: F 25 ASN cc_start: 0.8800 (m110) cc_final: 0.8586 (m-40) REVERT: G 42 ARG cc_start: 0.8330 (ptp-170) cc_final: 0.7964 (mtm180) outliers start: 5 outliers final: 3 residues processed: 136 average time/residue: 0.1552 time to fit residues: 27.3661 Evaluate side-chains 133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 0.0040 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 25 ASN C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 76 GLN E 113 HIS F 27 GLN G 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102110 restraints weight = 17300.016| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.48 r_work: 0.3124 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12740 Z= 0.129 Angle : 0.603 9.415 18447 Z= 0.355 Chirality : 0.045 0.334 2098 Planarity : 0.004 0.053 1330 Dihedral : 31.258 175.966 4008 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.27 % Allowed : 12.38 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.30), residues: 736 helix: 1.30 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.92 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 76 TYR 0.018 0.001 TYR H 37 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (12740) covalent geometry : angle 0.60334 / 0.35 (18447) hydrogen bonds : bond 0.03949 / 2.64 ( 744) hydrogen bonds : angle 2.69047 / 1.88 ( 1849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.345 Fit side-chains REVERT: A 59 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: A 133 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 72 TYR cc_start: 0.8950 (m-80) cc_final: 0.8723 (m-80) REVERT: D 83 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.8162 (mmt90) REVERT: E 59 GLU cc_start: 0.8026 (mp0) cc_final: 0.7816 (mp0) REVERT: E 73 GLU cc_start: 0.7839 (tt0) cc_final: 0.7599 (tt0) REVERT: F 25 ASN cc_start: 0.8817 (m110) cc_final: 0.8552 (m-40) REVERT: G 42 ARG cc_start: 0.8321 (ptp-170) cc_final: 0.7934 (mtm180) REVERT: H 37 TYR cc_start: 0.9132 (m-80) cc_final: 0.8757 (m-80) outliers start: 8 outliers final: 6 residues processed: 126 average time/residue: 0.1458 time to fit residues: 24.0133 Evaluate side-chains 125 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 40.0000 chunk 67 optimal weight: 0.5980 chunk 83 optimal weight: 20.0000 chunk 24 optimal weight: 0.0970 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 76 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.145067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102197 restraints weight = 17291.127| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.50 r_work: 0.3124 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12740 Z= 0.125 Angle : 0.596 9.230 18447 Z= 0.346 Chirality : 0.044 0.341 2098 Planarity : 0.004 0.049 1330 Dihedral : 31.258 179.015 4008 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.59 % Allowed : 13.17 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.31), residues: 736 helix: 1.80 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.81 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 76 TYR 0.009 0.001 TYR D 118 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.13 (12740) covalent geometry : angle 0.59626 / 0.35 (18447) hydrogen bonds : bond 0.03782 / 2.53 ( 744) hydrogen bonds : angle 2.60040 / 1.81 ( 1849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.304 Fit side-chains REVERT: A 59 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: A 133 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7541 (mt-10) REVERT: B 72 TYR cc_start: 0.8946 (m-80) cc_final: 0.8742 (m-80) REVERT: E 73 GLU cc_start: 0.7856 (tt0) cc_final: 0.7632 (tt0) REVERT: F 25 ASN cc_start: 0.8762 (m110) cc_final: 0.8476 (m-40) REVERT: F 85 ASP cc_start: 0.8439 (m-30) cc_final: 0.8091 (m-30) REVERT: G 42 ARG cc_start: 0.8304 (ptp-170) cc_final: 0.7899 (mtm180) outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 0.1541 time to fit residues: 25.0860 Evaluate side-chains 127 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 75 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 75 HIS G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101238 restraints weight = 17327.596| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.50 r_work: 0.3107 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12740 Z= 0.144 Angle : 0.607 9.715 18447 Z= 0.348 Chirality : 0.044 0.352 2098 Planarity : 0.004 0.047 1330 Dihedral : 31.329 179.062 4008 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.11 % Allowed : 13.97 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.31), residues: 736 helix: 1.94 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.73 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 77 TYR 0.016 0.001 TYR D 118 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (12740) covalent geometry : angle 0.60718 / 0.35 (18447) hydrogen bonds : bond 0.03925 / 2.63 ( 744) hydrogen bonds : angle 2.59975 / 1.81 ( 1849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.300 Fit side-chains REVERT: A 56 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8090 (ttpp) REVERT: A 59 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: A 133 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7562 (mt-10) REVERT: E 59 GLU cc_start: 0.8035 (mp0) cc_final: 0.7602 (pm20) REVERT: E 73 GLU cc_start: 0.7874 (tt0) cc_final: 0.7602 (tt0) REVERT: F 25 ASN cc_start: 0.8713 (m110) cc_final: 0.8456 (m-40) REVERT: F 85 ASP cc_start: 0.8394 (m-30) cc_final: 0.8047 (m-30) REVERT: G 42 ARG cc_start: 0.8329 (ptp-170) cc_final: 0.7920 (mtm180) outliers start: 7 outliers final: 6 residues processed: 122 average time/residue: 0.1473 time to fit residues: 23.4075 Evaluate side-chains 127 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 8 optimal weight: 0.0070 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.144877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101904 restraints weight = 17180.649| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.47 r_work: 0.3118 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12740 Z= 0.128 Angle : 0.590 10.759 18447 Z= 0.340 Chirality : 0.043 0.362 2098 Planarity : 0.004 0.048 1330 Dihedral : 31.257 176.381 4008 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.27 % Allowed : 14.60 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.31), residues: 736 helix: 2.19 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.61 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 77 TYR 0.012 0.001 TYR D 118 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (12740) covalent geometry : angle 0.59047 / 0.34 (18447) hydrogen bonds : bond 0.03839 / 2.58 ( 744) hydrogen bonds : angle 2.54161 / 1.78 ( 1849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.272 Fit side-chains REVERT: A 56 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8120 (ttpp) REVERT: A 59 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: A 133 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7573 (mt-10) REVERT: D 90 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: E 57 SER cc_start: 0.9230 (t) cc_final: 0.8930 (t) REVERT: E 59 GLU cc_start: 0.7987 (mp0) cc_final: 0.7473 (pm20) REVERT: E 73 GLU cc_start: 0.7872 (tt0) cc_final: 0.7592 (tt0) REVERT: F 25 ASN cc_start: 0.8710 (m110) cc_final: 0.8452 (m-40) REVERT: F 85 ASP cc_start: 0.8390 (m-30) cc_final: 0.8022 (m-30) REVERT: G 42 ARG cc_start: 0.8317 (ptp-170) cc_final: 0.7892 (mtm180) REVERT: H 90 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8017 (mp0) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 0.1497 time to fit residues: 23.7039 Evaluate side-chains 122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.145434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102127 restraints weight = 17384.477| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.45 r_work: 0.3134 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12740 Z= 0.125 Angle : 0.590 12.068 18447 Z= 0.337 Chirality : 0.043 0.366 2098 Planarity : 0.004 0.047 1330 Dihedral : 31.224 173.990 4008 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.06 % Allowed : 14.29 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.31), residues: 736 helix: 2.41 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 77 TYR 0.018 0.001 TYR D 118 PHE 0.009 0.001 PHE E 67 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.12 (12740) covalent geometry : angle 0.59048 / 0.34 (18447) hydrogen bonds : bond 0.03855 / 2.59 ( 744) hydrogen bonds : angle 2.52920 / 1.76 ( 1849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.304 Fit side-chains REVERT: A 56 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8138 (ttpp) REVERT: A 59 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: A 133 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 90 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 57 SER cc_start: 0.9292 (t) cc_final: 0.8945 (t) REVERT: E 59 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: E 73 GLU cc_start: 0.7937 (tt0) cc_final: 0.7663 (tt0) REVERT: F 25 ASN cc_start: 0.8714 (m110) cc_final: 0.8406 (m-40) REVERT: F 85 ASP cc_start: 0.8352 (m-30) cc_final: 0.8009 (m-30) REVERT: G 42 ARG cc_start: 0.8319 (ptp-170) cc_final: 0.7907 (mtm180) REVERT: H 54 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8316 (mmtt) REVERT: H 90 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7971 (mp0) outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 0.1480 time to fit residues: 24.0669 Evaluate side-chains 129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.143746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101272 restraints weight = 17677.371| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.42 r_work: 0.3134 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12740 Z= 0.153 Angle : 0.603 11.070 18447 Z= 0.341 Chirality : 0.043 0.370 2098 Planarity : 0.004 0.046 1330 Dihedral : 31.303 172.993 4008 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.06 % Allowed : 14.76 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.31), residues: 736 helix: 2.36 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.59 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.017 0.001 TYR D 118 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (12740) covalent geometry : angle 0.60338 / 0.34 (18447) hydrogen bonds : bond 0.03963 / 2.66 ( 744) hydrogen bonds : angle 2.55832 / 1.79 ( 1849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.271 Fit side-chains REVERT: A 59 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: A 133 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7566 (mt-10) REVERT: D 49 THR cc_start: 0.8985 (m) cc_final: 0.8727 (t) REVERT: D 90 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: E 59 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: E 73 GLU cc_start: 0.7901 (tt0) cc_final: 0.7608 (tt0) REVERT: F 25 ASN cc_start: 0.8721 (m110) cc_final: 0.8429 (m-40) REVERT: F 85 ASP cc_start: 0.8347 (m-30) cc_final: 0.8019 (m-30) REVERT: G 42 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.7944 (mtm180) REVERT: H 54 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8313 (mmtt) REVERT: H 90 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7963 (mp0) outliers start: 13 outliers final: 9 residues processed: 122 average time/residue: 0.1563 time to fit residues: 24.7204 Evaluate side-chains 132 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100936 restraints weight = 17679.654| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.42 r_work: 0.3127 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12740 Z= 0.156 Angle : 0.610 11.320 18447 Z= 0.342 Chirality : 0.043 0.372 2098 Planarity : 0.004 0.045 1330 Dihedral : 31.353 172.222 4008 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.06 % Allowed : 15.40 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.31), residues: 736 helix: 2.34 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.56 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.017 0.001 TYR D 118 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (12740) covalent geometry : angle 0.60967 / 0.34 (18447) hydrogen bonds : bond 0.03993 / 2.68 ( 744) hydrogen bonds : angle 2.57519 / 1.81 ( 1849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.315 Fit side-chains REVERT: A 56 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8231 (ttpp) REVERT: A 59 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: A 133 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7564 (mt-10) REVERT: D 90 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: E 59 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: E 73 GLU cc_start: 0.7905 (tt0) cc_final: 0.7603 (tt0) REVERT: F 25 ASN cc_start: 0.8693 (m110) cc_final: 0.8401 (m-40) REVERT: F 85 ASP cc_start: 0.8342 (m-30) cc_final: 0.8014 (m-30) REVERT: G 42 ARG cc_start: 0.8345 (ptp-170) cc_final: 0.7955 (mtm180) REVERT: H 54 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8309 (mmtt) REVERT: H 90 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7966 (mp0) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.1705 time to fit residues: 27.1917 Evaluate side-chains 129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.144645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102349 restraints weight = 17602.377| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.41 r_work: 0.3158 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12740 Z= 0.122 Angle : 0.587 12.197 18447 Z= 0.334 Chirality : 0.042 0.369 2098 Planarity : 0.004 0.046 1330 Dihedral : 31.217 170.458 4008 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.90 % Allowed : 15.71 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.31), residues: 736 helix: 2.52 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.46 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 76 TYR 0.015 0.001 TYR D 118 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.12 (12740) covalent geometry : angle 0.58720 / 0.33 (18447) hydrogen bonds : bond 0.03812 / 2.56 ( 744) hydrogen bonds : angle 2.53596 / 1.78 ( 1849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.336 Fit side-chains REVERT: A 56 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8204 (ttpp) REVERT: A 59 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: D 37 TYR cc_start: 0.9238 (m-80) cc_final: 0.8846 (m-80) REVERT: D 90 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: E 59 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: E 73 GLU cc_start: 0.7867 (tt0) cc_final: 0.7568 (tt0) REVERT: F 25 ASN cc_start: 0.8677 (m110) cc_final: 0.8381 (m-40) REVERT: F 85 ASP cc_start: 0.8285 (m-30) cc_final: 0.7963 (m-30) REVERT: G 42 ARG cc_start: 0.8311 (ptp-170) cc_final: 0.7914 (mtm180) REVERT: H 54 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8261 (mmtt) REVERT: H 90 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7951 (mp0) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 0.1497 time to fit residues: 24.0441 Evaluate side-chains 126 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 0.0570 chunk 76 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 85 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 9 optimal weight: 0.3980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102461 restraints weight = 17783.983| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.44 r_work: 0.3152 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12740 Z= 0.118 Angle : 0.582 11.752 18447 Z= 0.333 Chirality : 0.042 0.366 2098 Planarity : 0.004 0.046 1330 Dihedral : 31.186 169.950 4008 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.75 % Allowed : 16.03 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.31), residues: 736 helix: 2.59 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.39 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 39 TYR 0.018 0.001 TYR D 118 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.12 (12740) covalent geometry : angle 0.58209 / 0.33 (18447) hydrogen bonds : bond 0.03797 / 2.55 ( 744) hydrogen bonds : angle 2.52316 / 1.77 ( 1849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.57 seconds wall clock time: 37 minutes 11.73 seconds (2231.73 seconds total)