Starting phenix.real_space_refine on Fri Sep 11 20:30:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3z_62034/09_2026/9k3z_62034.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3z_62034/09_2026/9k3z_62034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2026/9k3z_62034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2026/9k3z_62034.map" model { file = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2026/9k3z_62034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2026/9k3z_62034.cif" } resolution = 2.75 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= 0.050 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 289 5.49 5 S 10 5.16 5 C 6565 2.51 5 N 2174 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 11814 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2992 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.43, per 1000 atoms: 0.21 Number of scatterers: 11814 At special positions: 0 Unit cell: (118.992, 78.256, 114.704, 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 10 16.00 P 289 15.00 O 2776 8.00 N 2174 7.00 C 6565 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: 0.93 Conformation dependent library (CDL) restraints added in 222.4 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 75.3% alpha, 2.7% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.507A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 56 through 85 Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 147 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 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 27 through 32 Processing helix chain 'G' and resid 37 through 49 Processing helix chain 'G' and resid 56 through 85 Processing helix chain 'G' and resid 91 through 102 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.876A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.607A pdb=" N ARG C 54 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113 removed outlier: 6.380A pdb=" N THR C 112 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.021A 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 54 through 55 removed outlier: 6.642A pdb=" N ARG G 54 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 90 424 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 688 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.29 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: 1980 1.33 - 1.45: 4258 1.45 - 1.57: 5786 1.57 - 1.69: 577 1.69 - 1.81: 18 Bond restraints: 12619 Sorted by residual: bond pdb=" O3' DG I -26 " pdb=" P DT I -25 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" O3' DA J -46 " pdb=" P DA J -45 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.20e-02 6.94e+03 2.31e+01 bond pdb=" O3' DT I -16 " pdb=" P DC I -15 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.20e-02 6.94e+03 2.09e+01 bond pdb=" O3' DC J -24 " pdb=" P DC J -23 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.20e-02 6.94e+03 1.41e+01 bond pdb=" C3' DT I -69 " pdb=" C2' DT I -69 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 ... (remaining 12614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 15801 1.04 - 2.08: 1780 2.08 - 3.12: 645 3.12 - 4.16: 46 4.16 - 5.20: 13 Bond angle restraints: 18285 Sorted by residual: angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I -54 " pdb=" C4 DT I -54 " pdb=" O4 DT I -54 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J 8 " pdb=" C4 DT J 8 " pdb=" O4 DT J 8 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J -32 " pdb=" C4 DT J -32 " pdb=" O4 DT J -32 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 18280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.95: 4227 18.95 - 37.89: 1269 37.89 - 56.84: 1231 56.84 - 75.79: 182 75.79 - 94.73: 8 Dihedral angle restraints: 6917 sinusoidal: 4771 harmonic: 2146 Sorted by residual: dihedral pdb=" CG ARG E 129 " pdb=" CD ARG E 129 " pdb=" NE ARG E 129 " pdb=" CZ ARG E 129 " ideal model delta sinusoidal sigma weight residual 180.00 -137.26 -42.74 2 1.50e+01 4.44e-03 9.83e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -137.51 -42.49 2 1.50e+01 4.44e-03 9.73e+00 dihedral pdb=" CA ARG F 23 " pdb=" CB ARG F 23 " pdb=" CG ARG F 23 " pdb=" CD ARG F 23 " ideal model delta sinusoidal sigma weight residual 60.00 119.93 -59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1227 0.033 - 0.066: 580 0.066 - 0.099: 202 0.099 - 0.132: 84 0.132 - 0.165: 4 Chirality restraints: 2097 Sorted by residual: chirality pdb=" C3' DG I 7 " pdb=" C4' DG I 7 " pdb=" O3' DG I 7 " pdb=" C2' DG I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2094 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " 0.023 2.00e-02 2.50e+03 1.02e-02 2.84e+00 pdb=" N9 DA I 57 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 17 " -0.019 2.00e-02 2.50e+03 1.00e-02 2.26e+00 pdb=" N1 DC I 17 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC I 17 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 17 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 17 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 17 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 17 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 17 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC I 17 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 32 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.021 5.00e-02 4.00e+02 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1099 2.74 - 3.28: 10207 3.28 - 3.82: 23398 3.82 - 4.36: 28618 4.36 - 4.90: 40527 Nonbonded interactions: 103849 Sorted by model distance: nonbonded pdb=" NH1 ARG G 48 " pdb=" OE1 GLU H 94 " model vdw 2.204 3.120 nonbonded pdb=" NZ LYS F 59 " pdb=" OE2 GLU F 63 " model vdw 2.216 3.120 nonbonded pdb=" OG SER C 29 " pdb=" O PHE C 36 " model vdw 2.216 3.040 nonbonded pdb=" OG SER G 29 " pdb=" O PHE G 36 " model vdw 2.217 3.040 nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.233 3.120 ... (remaining 103844 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=0.00 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: 1.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 11.370 Find NCS groups from input model: 0.080 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12619 Z= 0.535 Angle : 0.760 5.199 18285 Z= 0.693 Chirality : 0.045 0.165 2097 Planarity : 0.003 0.036 1296 Dihedral : 29.151 94.731 5529 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.64 % Allowed : 22.19 % Favored : 77.17 % 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: 2.69 (0.30), residues: 728 helix: 2.34 (0.21), residues: 552 sheet: None (None), residues: 0 loop : 0.00 (0.40), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.009 0.001 TYR D 63 PHE 0.007 0.001 PHE D 88 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.53 (12619) covalent geometry : angle 0.76036 / 0.69 (18285) hydrogen bonds : bond 0.11994 / 7.76 ( 770) hydrogen bonds : angle 4.18541 / 2.93 ( 1936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 0.301 Fit side-chains REVERT: C 48 ARG cc_start: 0.8476 (ttm170) cc_final: 0.8021 (tpp80) REVERT: C 62 TYR cc_start: 0.8840 (t80) cc_final: 0.8450 (t80) REVERT: D 147 SER cc_start: 0.8233 (m) cc_final: 0.7962 (p) REVERT: G 62 TYR cc_start: 0.8809 (t80) cc_final: 0.8601 (t80) outliers start: 4 outliers final: 2 residues processed: 220 average time/residue: 0.6541 time to fit residues: 154.0638 Evaluate side-chains 175 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN A 108 ASN A 113 HIS B 75 HIS D 132 HIS E 39 HIS E 108 ASN E 125 GLN F 75 HIS H 132 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.071495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.048664 restraints weight = 37412.163| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.91 r_work: 0.2691 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12619 Z= 0.156 Angle : 0.692 7.287 18285 Z= 0.397 Chirality : 0.047 0.241 2097 Planarity : 0.004 0.032 1296 Dihedral : 31.634 92.570 4072 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.73 % Allowed : 25.24 % Favored : 72.03 % 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: 2.97 (0.30), residues: 728 helix: 2.46 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.34 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 40 TYR 0.010 0.001 TYR D 63 PHE 0.006 0.001 PHE H 65 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (12619) covalent geometry : angle 0.69248 / 0.40 (18285) hydrogen bonds : bond 0.05467 / 3.71 ( 770) hydrogen bonds : angle 3.31039 / 2.38 ( 1936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.306 Fit side-chains REVERT: C 102 ASP cc_start: 0.8786 (t0) cc_final: 0.8493 (t0) REVERT: C 104 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8626 (mm-30) REVERT: D 80 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8683 (mmmm) REVERT: G 48 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8832 (tpp80) REVERT: G 102 ASP cc_start: 0.8758 (t0) cc_final: 0.8550 (t0) REVERT: G 104 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8611 (mm-30) outliers start: 17 outliers final: 2 residues processed: 182 average time/residue: 0.6655 time to fit residues: 129.5921 Evaluate side-chains 168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 104 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.070535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048045 restraints weight = 37586.940| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.92 r_work: 0.2677 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12619 Z= 0.166 Angle : 0.649 6.748 18285 Z= 0.377 Chirality : 0.045 0.237 2097 Planarity : 0.004 0.041 1296 Dihedral : 31.701 89.882 4069 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.05 % Allowed : 23.47 % Favored : 73.47 % 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: 3.32 (0.30), residues: 728 helix: 2.70 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.49 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 105 TYR 0.011 0.001 TYR G 62 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (12619) covalent geometry : angle 0.64866 / 0.38 (18285) hydrogen bonds : bond 0.05135 / 3.51 ( 770) hydrogen bonds : angle 3.13036 / 2.27 ( 1936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.324 Fit side-chains REVERT: A 59 GLU cc_start: 0.8109 (pt0) cc_final: 0.7723 (pm20) REVERT: A 120 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: C 102 ASP cc_start: 0.8877 (t0) cc_final: 0.8544 (t0) REVERT: C 104 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8635 (mm-30) REVERT: D 128 GLU cc_start: 0.8631 (tp30) cc_final: 0.8192 (mm-30) REVERT: E 59 GLU cc_start: 0.8118 (pt0) cc_final: 0.7895 (pm20) REVERT: G 88 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9209 (mtmt) REVERT: G 102 ASP cc_start: 0.8741 (t0) cc_final: 0.8372 (t0) REVERT: G 104 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8633 (mm-30) REVERT: H 128 GLU cc_start: 0.8607 (tp30) cc_final: 0.8143 (mm-30) outliers start: 19 outliers final: 5 residues processed: 174 average time/residue: 0.6766 time to fit residues: 125.7930 Evaluate side-chains 158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 104 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 20.0000 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 8 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.046649 restraints weight = 37806.002| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.96 r_work: 0.2644 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12619 Z= 0.202 Angle : 0.676 7.065 18285 Z= 0.384 Chirality : 0.046 0.251 2097 Planarity : 0.004 0.030 1296 Dihedral : 31.827 88.846 4069 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.02 % Allowed : 23.15 % Favored : 72.83 % 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: 3.36 (0.30), residues: 728 helix: 2.74 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.41 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 105 TYR 0.015 0.002 TYR D 63 PHE 0.007 0.001 PHE C 36 HIS 0.002 0.000 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (12619) covalent geometry : angle 0.67650 / 0.38 (18285) hydrogen bonds : bond 0.05548 / 3.75 ( 770) hydrogen bonds : angle 3.14560 / 2.26 ( 1936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.350 Fit side-chains REVERT: A 59 GLU cc_start: 0.8397 (pt0) cc_final: 0.8155 (pm20) REVERT: C 102 ASP cc_start: 0.8902 (t0) cc_final: 0.8565 (t0) REVERT: C 104 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8642 (mm-30) REVERT: D 80 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9001 (mmmm) REVERT: E 59 GLU cc_start: 0.8403 (pt0) cc_final: 0.8203 (pm20) REVERT: G 102 ASP cc_start: 0.8720 (t0) cc_final: 0.8356 (t0) REVERT: H 58 GLU cc_start: 0.8259 (tt0) cc_final: 0.8026 (tp30) outliers start: 25 outliers final: 8 residues processed: 162 average time/residue: 0.7108 time to fit residues: 122.7106 Evaluate side-chains 154 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 57 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048252 restraints weight = 37833.926| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.97 r_work: 0.2699 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12619 Z= 0.132 Angle : 0.624 6.746 18285 Z= 0.366 Chirality : 0.043 0.235 2097 Planarity : 0.004 0.031 1296 Dihedral : 31.664 87.689 4069 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.54 % Allowed : 24.12 % Favored : 72.35 % 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: 3.49 (0.30), residues: 728 helix: 2.84 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.45 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 105 TYR 0.012 0.001 TYR C 62 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.13 (12619) covalent geometry : angle 0.62382 / 0.37 (18285) hydrogen bonds : bond 0.04492 / 3.09 ( 770) hydrogen bonds : angle 2.93184 / 2.12 ( 1936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.326 Fit side-chains REVERT: A 59 GLU cc_start: 0.8263 (pt0) cc_final: 0.7879 (pm20) REVERT: B 95 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7283 (mmm160) REVERT: C 46 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9046 (mtpp) REVERT: C 102 ASP cc_start: 0.8952 (t0) cc_final: 0.8556 (t0) REVERT: C 104 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8593 (mm-30) REVERT: D 80 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8867 (mmmm) REVERT: F 95 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7361 (mmm160) REVERT: G 48 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8773 (tpp80) REVERT: G 88 LYS cc_start: 0.9439 (mtmt) cc_final: 0.9228 (mtmt) REVERT: G 102 ASP cc_start: 0.8679 (t0) cc_final: 0.8223 (t0) REVERT: H 58 GLU cc_start: 0.8254 (tt0) cc_final: 0.7957 (tp30) REVERT: H 128 GLU cc_start: 0.8362 (tp30) cc_final: 0.7928 (mm-30) outliers start: 22 outliers final: 4 residues processed: 188 average time/residue: 0.6561 time to fit residues: 132.1725 Evaluate side-chains 168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 86 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 70 GLN H 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.070669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.048274 restraints weight = 37376.201| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.93 r_work: 0.2704 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12619 Z= 0.133 Angle : 0.623 6.587 18285 Z= 0.364 Chirality : 0.044 0.230 2097 Planarity : 0.004 0.037 1296 Dihedral : 31.590 87.418 4069 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.41 % Allowed : 26.69 % Favored : 70.90 % 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: 3.61 (0.30), residues: 728 helix: 2.96 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.47 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 105 TYR 0.016 0.002 TYR G 62 PHE 0.007 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (12619) covalent geometry : angle 0.62307 / 0.36 (18285) hydrogen bonds : bond 0.04470 / 3.06 ( 770) hydrogen bonds : angle 2.91270 / 2.10 ( 1936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.307 Fit side-chains REVERT: A 59 GLU cc_start: 0.8238 (pt0) cc_final: 0.8012 (pm20) REVERT: B 95 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7272 (mmm160) REVERT: C 46 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9048 (mtpp) REVERT: C 102 ASP cc_start: 0.8969 (t0) cc_final: 0.8537 (t0) REVERT: C 104 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8977 (mm-30) REVERT: D 80 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8963 (mmmm) REVERT: D 91 ASP cc_start: 0.9389 (t0) cc_final: 0.8903 (t0) REVERT: D 128 GLU cc_start: 0.8379 (tp30) cc_final: 0.7729 (mm-30) REVERT: F 95 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7388 (mmm160) REVERT: G 102 ASP cc_start: 0.8682 (t0) cc_final: 0.8221 (t0) REVERT: H 58 GLU cc_start: 0.8263 (tt0) cc_final: 0.7968 (tp30) REVERT: H 91 ASP cc_start: 0.9407 (t0) cc_final: 0.8926 (t0) outliers start: 15 outliers final: 2 residues processed: 174 average time/residue: 0.7297 time to fit residues: 135.3100 Evaluate side-chains 164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048248 restraints weight = 37289.128| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.94 r_work: 0.2703 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12619 Z= 0.138 Angle : 0.628 6.332 18285 Z= 0.366 Chirality : 0.043 0.229 2097 Planarity : 0.004 0.038 1296 Dihedral : 31.579 86.014 4069 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.57 % Allowed : 27.01 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.30), residues: 728 helix: 3.00 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.45 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 105 TYR 0.014 0.002 TYR G 62 PHE 0.007 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (12619) covalent geometry : angle 0.62818 / 0.37 (18285) hydrogen bonds : bond 0.04450 / 3.05 ( 770) hydrogen bonds : angle 2.89061 / 2.09 ( 1936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.334 Fit side-chains REVERT: A 59 GLU cc_start: 0.8286 (pt0) cc_final: 0.8007 (pm20) REVERT: B 95 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7278 (mmm160) REVERT: C 46 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9057 (mtpp) REVERT: C 102 ASP cc_start: 0.8967 (t0) cc_final: 0.8531 (t0) REVERT: C 104 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8979 (mm-30) REVERT: D 80 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9005 (mmmm) REVERT: D 91 ASP cc_start: 0.9384 (t0) cc_final: 0.8907 (t0) REVERT: F 95 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7393 (mmm160) REVERT: G 88 LYS cc_start: 0.9452 (mtmt) cc_final: 0.8928 (ptmt) REVERT: G 102 ASP cc_start: 0.8666 (t0) cc_final: 0.8146 (t0) REVERT: H 58 GLU cc_start: 0.8175 (tt0) cc_final: 0.7813 (tp30) REVERT: H 91 ASP cc_start: 0.9417 (t0) cc_final: 0.8948 (t0) REVERT: H 128 GLU cc_start: 0.8150 (tp30) cc_final: 0.7747 (mm-30) outliers start: 16 outliers final: 6 residues processed: 174 average time/residue: 0.7124 time to fit residues: 132.2423 Evaluate side-chains 167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047880 restraints weight = 37467.756| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.95 r_work: 0.2693 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12619 Z= 0.148 Angle : 0.635 6.956 18285 Z= 0.367 Chirality : 0.044 0.239 2097 Planarity : 0.004 0.042 1296 Dihedral : 31.596 86.317 4069 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.93 % Allowed : 28.46 % Favored : 69.61 % 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: 3.66 (0.30), residues: 728 helix: 3.01 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.41 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 105 TYR 0.014 0.002 TYR G 69 PHE 0.006 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12619) covalent geometry : angle 0.63523 / 0.37 (18285) hydrogen bonds : bond 0.04572 / 3.11 ( 770) hydrogen bonds : angle 2.90794 / 2.10 ( 1936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.313 Fit side-chains REVERT: A 59 GLU cc_start: 0.8339 (pt0) cc_final: 0.8031 (pm20) REVERT: B 95 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7276 (mmm160) REVERT: C 46 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9079 (mtpp) REVERT: C 102 ASP cc_start: 0.8974 (t0) cc_final: 0.8515 (t0) REVERT: C 104 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8984 (mm-30) REVERT: D 80 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9060 (mmmm) REVERT: D 91 ASP cc_start: 0.9381 (t0) cc_final: 0.8921 (t0) REVERT: D 128 GLU cc_start: 0.8409 (tp30) cc_final: 0.7804 (mm-30) REVERT: F 95 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7419 (mmm160) REVERT: G 88 LYS cc_start: 0.9441 (mtmt) cc_final: 0.8940 (ptmt) REVERT: G 102 ASP cc_start: 0.8688 (t0) cc_final: 0.8159 (t0) REVERT: H 91 ASP cc_start: 0.9420 (t0) cc_final: 0.8956 (t0) outliers start: 12 outliers final: 5 residues processed: 165 average time/residue: 0.7153 time to fit residues: 125.9826 Evaluate side-chains 164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047245 restraints weight = 37277.709| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.97 r_work: 0.2679 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12619 Z= 0.157 Angle : 0.650 7.608 18285 Z= 0.373 Chirality : 0.044 0.234 2097 Planarity : 0.004 0.037 1296 Dihedral : 31.651 87.730 4069 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.57 % Allowed : 28.14 % Favored : 69.29 % 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: 3.59 (0.30), residues: 728 helix: 2.96 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.41 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 105 TYR 0.016 0.002 TYR C 62 PHE 0.006 0.001 PHE B 61 HIS 0.005 0.001 HIS G 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12619) covalent geometry : angle 0.65003 / 0.37 (18285) hydrogen bonds : bond 0.04676 / 3.18 ( 770) hydrogen bonds : angle 2.93109 / 2.11 ( 1936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.293 Fit side-chains REVERT: B 95 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7311 (mmm160) REVERT: C 46 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9078 (mtpp) REVERT: C 102 ASP cc_start: 0.8954 (t0) cc_final: 0.8532 (t0) REVERT: C 104 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8954 (mm-30) REVERT: D 91 ASP cc_start: 0.9373 (t0) cc_final: 0.8932 (t0) REVERT: D 128 GLU cc_start: 0.8381 (tp30) cc_final: 0.7805 (mm-30) REVERT: E 59 GLU cc_start: 0.8215 (pm20) cc_final: 0.7994 (pm20) REVERT: F 95 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7440 (mmm160) REVERT: G 88 LYS cc_start: 0.9421 (mtmt) cc_final: 0.8924 (ptmt) REVERT: G 102 ASP cc_start: 0.8720 (t0) cc_final: 0.8147 (t0) REVERT: H 91 ASP cc_start: 0.9418 (t0) cc_final: 0.8972 (t0) REVERT: H 128 GLU cc_start: 0.8147 (tp30) cc_final: 0.7909 (mm-30) outliers start: 16 outliers final: 5 residues processed: 159 average time/residue: 0.7782 time to fit residues: 131.5660 Evaluate side-chains 159 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 98 GLN E 68 GLN H 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047859 restraints weight = 37652.633| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.95 r_work: 0.2694 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12619 Z= 0.139 Angle : 0.639 9.285 18285 Z= 0.368 Chirality : 0.044 0.307 2097 Planarity : 0.004 0.043 1296 Dihedral : 31.596 86.067 4069 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.61 % Allowed : 29.90 % Favored : 68.49 % 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 are not related in a simple way. whole: 3.65 (0.30), residues: 728 helix: 2.99 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.47 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 105 TYR 0.014 0.001 TYR C 62 PHE 0.006 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (12619) covalent geometry : angle 0.63881 / 0.37 (18285) hydrogen bonds : bond 0.04399 / 3.00 ( 770) hydrogen bonds : angle 2.91309 / 2.09 ( 1936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.311 Fit side-chains REVERT: A 59 GLU cc_start: 0.8345 (pm20) cc_final: 0.8108 (pm20) REVERT: B 95 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7322 (mmm160) REVERT: C 46 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9079 (mtpp) REVERT: C 102 ASP cc_start: 0.8988 (t0) cc_final: 0.8555 (t0) REVERT: C 104 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8971 (mm-30) REVERT: D 91 ASP cc_start: 0.9376 (t0) cc_final: 0.8944 (t0) REVERT: E 59 GLU cc_start: 0.8190 (pm20) cc_final: 0.7983 (pm20) REVERT: F 95 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7393 (mmm160) REVERT: G 88 LYS cc_start: 0.9424 (mtmt) cc_final: 0.8970 (ptmt) REVERT: G 102 ASP cc_start: 0.8716 (t0) cc_final: 0.8182 (t0) REVERT: H 91 ASP cc_start: 0.9408 (t0) cc_final: 0.8967 (t0) REVERT: H 128 GLU cc_start: 0.8244 (tp30) cc_final: 0.7690 (mm-30) outliers start: 10 outliers final: 4 residues processed: 161 average time/residue: 0.7359 time to fit residues: 126.1441 Evaluate side-chains 162 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.069975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.047443 restraints weight = 37475.103| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.96 r_work: 0.2683 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 12619 Z= 0.151 Angle : 0.646 8.687 18285 Z= 0.371 Chirality : 0.044 0.303 2097 Planarity : 0.004 0.037 1296 Dihedral : 31.607 87.402 4069 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.45 % Allowed : 30.06 % Favored : 68.49 % 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 are not related in a simple way. whole: 3.69 (0.30), residues: 728 helix: 3.01 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.49 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 105 TYR 0.016 0.002 TYR G 62 PHE 0.006 0.001 PHE E 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (12619) covalent geometry : angle 0.64643 / 0.37 (18285) hydrogen bonds : bond 0.04575 / 3.11 ( 770) hydrogen bonds : angle 2.93890 / 2.11 ( 1936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3691.98 seconds wall clock time: 63 minutes 36.06 seconds (3816.06 seconds total)