Starting phenix.real_space_refine on Fri Jul 3 01:49:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3z_62034/07_2026/9k3z_62034.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3z_62034/07_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_62034/07_2026/9k3z_62034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3z_62034/07_2026/9k3z_62034.map" model { file = "/net/cci-nas-00/data/ceres_data/9k3z_62034/07_2026/9k3z_62034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3z_62034/07_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-dev-6108/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: 2.07, per 1000 atoms: 0.18 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: 0.78 Conformation dependent library (CDL) restraints added in 195.1 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: 1.20 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: 1.94 Time building geometry restraints manager: 1.11 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 1.50e-02 4.44e+03 1.54e+01 bond pdb=" O3' DA J -46 " pdb=" P DA J -45 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.48e+01 bond pdb=" O3' DT I -16 " pdb=" P DC I -15 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.34e+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 bond pdb=" C3' DT I 49 " pdb=" C2' DT I 49 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 ... (remaining 12614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 15872 1.04 - 2.08: 1717 2.08 - 3.12: 640 3.12 - 4.16: 44 4.16 - 5.20: 12 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: 1.140 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.360 Find NCS groups from input model: 0.110 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- 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= 0.531 Angle : 0.751 5.199 18285 Z= 0.686 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 0.75138 / 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 : 0.296 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: 0.7963 (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: 0.5708 time to fit residues: 134.1767 Evaluate side-chains 173 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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: 0.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 85 GLN E 108 ASN E 125 GLN F 75 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.048517 restraints weight = 37385.053| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.93 r_work: 0.2690 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12619 Z= 0.165 Angle : 0.677 7.041 18285 Z= 0.392 Chirality : 0.047 0.242 2097 Planarity : 0.004 0.031 1296 Dihedral : 31.749 92.710 4072 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.05 % Allowed : 24.92 % 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: 3.03 (0.30), residues: 728 helix: 2.51 (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 0.000 ARG H 105 TYR 0.011 0.001 TYR H 63 PHE 0.006 0.001 PHE H 65 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (12619) covalent geometry : angle 0.67671 / 0.39 (18285) hydrogen bonds : bond 0.05359 / 3.64 ( 770) hydrogen bonds : angle 3.29925 / 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 196 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.345 Fit side-chains REVERT: C 102 ASP cc_start: 0.8766 (t0) cc_final: 0.8488 (t0) REVERT: C 104 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8616 (mm-30) REVERT: D 80 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8691 (mmmm) REVERT: G 48 ARG cc_start: 0.9121 (tpp80) cc_final: 0.8853 (tpp80) REVERT: G 102 ASP cc_start: 0.8735 (t0) cc_final: 0.8525 (t0) REVERT: G 104 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8618 (mm-30) outliers start: 19 outliers final: 3 residues processed: 182 average time/residue: 0.6147 time to fit residues: 119.6004 Evaluate side-chains 167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 D residue 85 MET 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: 0.9980 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.071257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048856 restraints weight = 37770.096| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.92 r_work: 0.2701 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12619 Z= 0.142 Angle : 0.617 6.637 18285 Z= 0.368 Chirality : 0.044 0.232 2097 Planarity : 0.004 0.042 1296 Dihedral : 31.719 89.939 4069 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.05 % Allowed : 24.28 % Favored : 72.67 % 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: 3.34 (0.30), residues: 728 helix: 2.72 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.48 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 105 TYR 0.012 0.001 TYR D 63 PHE 0.007 0.001 PHE H 88 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12619) covalent geometry : angle 0.61722 / 0.37 (18285) hydrogen bonds : bond 0.04858 / 3.34 ( 770) hydrogen bonds : angle 3.08789 / 2.24 ( 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 196 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.336 Fit side-chains REVERT: A 120 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8298 (mtp) REVERT: C 48 ARG cc_start: 0.9044 (tpp80) cc_final: 0.8802 (tpp80) REVERT: C 102 ASP cc_start: 0.8853 (t0) cc_final: 0.8508 (t0) REVERT: C 104 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8620 (mm-30) REVERT: G 102 ASP cc_start: 0.8691 (t0) cc_final: 0.8349 (t0) REVERT: G 104 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8624 (mm-30) outliers start: 19 outliers final: 7 residues processed: 183 average time/residue: 0.6234 time to fit residues: 122.3298 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain H residue 89 ILE 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: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 73 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.071094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048620 restraints weight = 37775.510| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.96 r_work: 0.2701 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12619 Z= 0.142 Angle : 0.615 6.713 18285 Z= 0.364 Chirality : 0.044 0.227 2097 Planarity : 0.004 0.040 1296 Dihedral : 31.692 88.319 4069 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.73 % Allowed : 24.60 % Favored : 72.67 % 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: 3.42 (0.30), residues: 728 helix: 2.76 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.60 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG G 40 TYR 0.011 0.002 TYR C 62 PHE 0.008 0.001 PHE H 88 HIS 0.002 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (12619) covalent geometry : angle 0.61485 / 0.36 (18285) hydrogen bonds : bond 0.04710 / 3.24 ( 770) hydrogen bonds : angle 3.00626 / 2.18 ( 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 188 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.314 Fit side-chains REVERT: A 59 GLU cc_start: 0.8036 (pt0) cc_final: 0.7635 (pm20) REVERT: C 102 ASP cc_start: 0.8888 (t0) cc_final: 0.8502 (t0) REVERT: C 104 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8599 (mm-30) REVERT: D 80 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8816 (mmmm) REVERT: D 128 GLU cc_start: 0.8575 (tp30) cc_final: 0.8049 (mm-30) REVERT: E 59 GLU cc_start: 0.8023 (pt0) cc_final: 0.7803 (pm20) REVERT: G 46 LYS cc_start: 0.9206 (mtpp) cc_final: 0.8960 (mtpp) REVERT: G 88 LYS cc_start: 0.9354 (mtmt) cc_final: 0.9151 (mtmt) REVERT: G 102 ASP cc_start: 0.8681 (t0) cc_final: 0.8288 (t0) REVERT: H 58 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7500 (mm-30) REVERT: H 99 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8983 (tp30) outliers start: 17 outliers final: 7 residues processed: 177 average time/residue: 0.7167 time to fit residues: 135.2680 Evaluate side-chains 164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 E residue 61 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 LEU 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: 1.9990 chunk 38 optimal weight: 0.8980 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.071566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049171 restraints weight = 37849.029| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.95 r_work: 0.2723 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12619 Z= 0.131 Angle : 0.605 6.636 18285 Z= 0.361 Chirality : 0.043 0.223 2097 Planarity : 0.004 0.035 1296 Dihedral : 31.652 87.420 4069 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.89 % Allowed : 24.28 % 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: 3.45 (0.30), residues: 728 helix: 2.79 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.51 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 105 TYR 0.017 0.002 TYR G 62 PHE 0.007 0.001 PHE H 88 HIS 0.003 0.000 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (12619) covalent geometry : angle 0.60497 / 0.36 (18285) hydrogen bonds : bond 0.04488 / 3.09 ( 770) hydrogen bonds : angle 2.99464 / 2.16 ( 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 191 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.315 Fit side-chains REVERT: A 59 GLU cc_start: 0.8012 (pt0) cc_final: 0.7659 (pm20) REVERT: C 102 ASP cc_start: 0.8876 (t0) cc_final: 0.8430 (t0) REVERT: C 104 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8577 (mm-30) REVERT: D 80 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8794 (mmmm) REVERT: D 128 GLU cc_start: 0.8573 (tp30) cc_final: 0.8373 (tp30) REVERT: E 59 GLU cc_start: 0.8022 (pt0) cc_final: 0.7783 (pm20) REVERT: G 102 ASP cc_start: 0.8641 (t0) cc_final: 0.8218 (t0) outliers start: 18 outliers final: 6 residues processed: 181 average time/residue: 0.6927 time to fit residues: 134.2389 Evaluate side-chains 166 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 E residue 61 LEU Chi-restraints excluded: chain F residue 49 LEU 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: 1.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.071337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.048995 restraints weight = 37722.428| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.94 r_work: 0.2721 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12619 Z= 0.134 Angle : 0.604 6.509 18285 Z= 0.359 Chirality : 0.043 0.224 2097 Planarity : 0.004 0.043 1296 Dihedral : 31.615 86.247 4069 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.93 % Allowed : 27.49 % Favored : 70.58 % 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: 3.56 (0.30), residues: 728 helix: 2.88 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.52 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 105 TYR 0.012 0.002 TYR C 62 PHE 0.006 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (12619) covalent geometry : angle 0.60405 / 0.36 (18285) hydrogen bonds : bond 0.04477 / 3.07 ( 770) hydrogen bonds : angle 2.94393 / 2.12 ( 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 178 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.323 Fit side-chains REVERT: A 59 GLU cc_start: 0.8049 (pt0) cc_final: 0.7707 (pm20) REVERT: C 102 ASP cc_start: 0.8906 (t0) cc_final: 0.8462 (t0) REVERT: C 104 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8990 (mm-30) REVERT: E 59 GLU cc_start: 0.8066 (pt0) cc_final: 0.7831 (pm20) REVERT: G 46 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8995 (mtpp) REVERT: G 88 LYS cc_start: 0.9403 (mtmt) cc_final: 0.8789 (ptmt) REVERT: G 102 ASP cc_start: 0.8654 (t0) cc_final: 0.8179 (t0) REVERT: H 128 GLU cc_start: 0.8297 (tp30) cc_final: 0.8041 (tp30) outliers start: 12 outliers final: 5 residues processed: 171 average time/residue: 0.7107 time to fit residues: 129.8875 Evaluate side-chains 159 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain E residue 61 LEU 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: 0.5980 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN H 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.070125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.047768 restraints weight = 37519.999| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.95 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: 0.8729 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12619 Z= 0.169 Angle : 0.633 6.345 18285 Z= 0.369 Chirality : 0.044 0.234 2097 Planarity : 0.004 0.037 1296 Dihedral : 31.766 86.436 4069 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.93 % Allowed : 26.69 % Favored : 71.38 % 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: 3.57 (0.30), residues: 728 helix: 2.90 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.49 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 105 TYR 0.015 0.002 TYR G 69 PHE 0.007 0.001 PHE E 67 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (12619) covalent geometry : angle 0.63333 / 0.37 (18285) hydrogen bonds : bond 0.05130 / 3.47 ( 770) hydrogen bonds : angle 3.02671 / 2.17 ( 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 169 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.326 Fit side-chains REVERT: A 59 GLU cc_start: 0.8305 (pt0) cc_final: 0.8024 (pm20) REVERT: C 102 ASP cc_start: 0.8958 (t0) cc_final: 0.8534 (t0) REVERT: C 104 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8975 (mm-30) REVERT: D 80 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9013 (mmmm) REVERT: D 91 ASP cc_start: 0.9417 (t0) cc_final: 0.8914 (t0) REVERT: D 128 GLU cc_start: 0.8487 (tp30) cc_final: 0.7894 (mm-30) REVERT: G 88 LYS cc_start: 0.9379 (mtmt) cc_final: 0.8864 (ptmt) REVERT: G 102 ASP cc_start: 0.8730 (t0) cc_final: 0.8246 (t0) outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 0.7028 time to fit residues: 121.4387 Evaluate side-chains 154 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 103 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.070230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047719 restraints weight = 37458.220| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.96 r_work: 0.2688 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12619 Z= 0.155 Angle : 0.624 6.876 18285 Z= 0.364 Chirality : 0.043 0.230 2097 Planarity : 0.004 0.042 1296 Dihedral : 31.757 86.427 4069 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.45 % Allowed : 28.78 % Favored : 69.77 % 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: 3.64 (0.30), residues: 728 helix: 3.01 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.38 (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 C 62 PHE 0.006 0.001 PHE B 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12619) covalent geometry : angle 0.62376 / 0.36 (18285) hydrogen bonds : bond 0.04564 / 3.10 ( 770) hydrogen bonds : angle 2.93061 / 2.11 ( 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 166 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.319 Fit side-chains REVERT: A 59 GLU cc_start: 0.8321 (pt0) cc_final: 0.8027 (pm20) REVERT: C 102 ASP cc_start: 0.8961 (t0) cc_final: 0.8522 (t0) REVERT: C 104 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8983 (mm-30) REVERT: D 80 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9016 (mmmm) REVERT: D 91 ASP cc_start: 0.9415 (t0) cc_final: 0.8928 (t0) REVERT: G 46 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8987 (mtpp) REVERT: G 102 ASP cc_start: 0.8736 (t0) cc_final: 0.8217 (t0) REVERT: G 104 GLU cc_start: 0.9286 (mm-30) cc_final: 0.9079 (mm-30) REVERT: H 91 ASP cc_start: 0.9440 (t0) cc_final: 0.8967 (t0) REVERT: H 128 GLU cc_start: 0.8226 (tp30) cc_final: 0.7992 (tp30) outliers start: 9 outliers final: 5 residues processed: 160 average time/residue: 0.7440 time to fit residues: 126.8844 Evaluate side-chains 156 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 50 ILE Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.071039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048705 restraints weight = 37062.895| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.93 r_work: 0.2715 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12619 Z= 0.133 Angle : 0.615 7.436 18285 Z= 0.362 Chirality : 0.043 0.225 2097 Planarity : 0.004 0.040 1296 Dihedral : 31.643 85.705 4069 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.45 % Allowed : 29.10 % Favored : 69.45 % 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: 3.72 (0.30), residues: 728 helix: 3.06 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.44 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 105 TYR 0.015 0.002 TYR G 62 PHE 0.006 0.001 PHE B 61 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (12619) covalent geometry : angle 0.61462 / 0.36 (18285) hydrogen bonds : bond 0.04335 / 2.96 ( 770) hydrogen bonds : angle 2.85687 / 2.06 ( 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 178 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.300 Fit side-chains REVERT: A 59 GLU cc_start: 0.8297 (pt0) cc_final: 0.8030 (pm20) REVERT: C 88 LYS cc_start: 0.9221 (mttp) cc_final: 0.8888 (mtmt) REVERT: C 102 ASP cc_start: 0.8993 (t0) cc_final: 0.8565 (t0) REVERT: C 104 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8962 (mm-30) REVERT: D 80 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9023 (mmmm) REVERT: D 91 ASP cc_start: 0.9387 (t0) cc_final: 0.8918 (t0) REVERT: D 128 GLU cc_start: 0.8411 (tp30) cc_final: 0.7780 (mm-30) REVERT: G 46 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8951 (mtpp) REVERT: G 88 LYS cc_start: 0.9425 (mtmt) cc_final: 0.8939 (ptmm) REVERT: G 102 ASP cc_start: 0.8697 (t0) cc_final: 0.8157 (t0) REVERT: G 104 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9071 (mm-30) REVERT: H 57 VAL cc_start: 0.9316 (t) cc_final: 0.9093 (p) REVERT: H 91 ASP cc_start: 0.9414 (t0) cc_final: 0.8958 (t0) REVERT: H 128 GLU cc_start: 0.8161 (tp30) cc_final: 0.7931 (tp30) outliers start: 9 outliers final: 5 residues processed: 172 average time/residue: 0.7016 time to fit residues: 129.0475 Evaluate side-chains 162 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU 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 F residue 63 GLU 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: 0.7980 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 overall best weight: 1.8382 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.069850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047052 restraints weight = 37773.989| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.97 r_work: 0.2673 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12619 Z= 0.177 Angle : 0.642 7.304 18285 Z= 0.372 Chirality : 0.043 0.230 2097 Planarity : 0.004 0.036 1296 Dihedral : 31.746 85.798 4069 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.13 % Allowed : 30.71 % Favored : 68.17 % 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: 3.65 (0.30), residues: 728 helix: 3.01 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.38 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 40 TYR 0.017 0.002 TYR C 62 PHE 0.007 0.001 PHE C 36 HIS 0.002 0.000 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (12619) covalent geometry : angle 0.64191 / 0.37 (18285) hydrogen bonds : bond 0.05011 / 3.38 ( 770) hydrogen bonds : angle 2.97874 / 2.13 ( 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 155 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.319 Fit side-chains REVERT: A 59 GLU cc_start: 0.8350 (pt0) cc_final: 0.8065 (pm20) REVERT: C 102 ASP cc_start: 0.8977 (t0) cc_final: 0.8559 (t0) REVERT: C 104 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8993 (mm-30) REVERT: D 91 ASP cc_start: 0.9413 (t0) cc_final: 0.8948 (t0) REVERT: D 128 GLU cc_start: 0.8398 (tp30) cc_final: 0.8091 (tp30) REVERT: G 46 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8968 (mtpp) REVERT: G 88 LYS cc_start: 0.9411 (mtmt) cc_final: 0.8958 (pttt) REVERT: G 102 ASP cc_start: 0.8748 (t0) cc_final: 0.8204 (t0) REVERT: G 104 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9078 (mm-30) REVERT: H 91 ASP cc_start: 0.9460 (t0) cc_final: 0.8995 (t0) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 0.7667 time to fit residues: 123.8936 Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 57 VAL 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 94 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.070013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.047498 restraints weight = 37419.404| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.95 r_work: 0.2686 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12619 Z= 0.150 Angle : 0.632 6.972 18285 Z= 0.368 Chirality : 0.043 0.229 2097 Planarity : 0.004 0.038 1296 Dihedral : 31.759 85.912 4069 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 3.64 (0.30), residues: 728 helix: 3.01 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.37 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 40 TYR 0.018 0.002 TYR G 69 PHE 0.013 0.001 PHE H 88 HIS 0.005 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (12619) covalent geometry : angle 0.63194 / 0.37 (18285) hydrogen bonds : bond 0.04715 / 3.19 ( 770) hydrogen bonds : angle 2.93913 / 2.12 ( 1936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.79 seconds wall clock time: 66 minutes 17.98 seconds (3977.98 seconds total)