Starting phenix.real_space_refine on Wed Aug 5 22:25:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ya_75522/08_2026/10ya_75522.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ya_75522/08_2026/10ya_75522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ya_75522/08_2026/10ya_75522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ya_75522/08_2026/10ya_75522.map" model { file = "/net/cci-nas-00/data/ceres_data/10ya_75522/08_2026/10ya_75522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ya_75522/08_2026/10ya_75522.cif" } resolution = 2.7 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= 0.005 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 294 5.49 5 S 10 5.16 5 C 6625 2.51 5 N 2250 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11998 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1573 Classifications: {'DNA': 76} Link IDs: {'rna3p': 75} Chain: "K" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1459 Classifications: {'DNA': 71} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 70} Time building chain proxies: 2.51, per 1000 atoms: 0.21 Number of scatterers: 11998 At special positions: 0 Unit cell: (74.328, 121.924, 122.576, 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 294 15.00 O 2819 8.00 N 2250 7.00 C 6625 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: 0.80 Conformation dependent library (CDL) restraints added in 239.2 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.4% alpha, 2.7% beta 147 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 55 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 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.629A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.560A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.358A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.502A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.125A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.716A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.559A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.411A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.582A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.169A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.733A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.275A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.002A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.322A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 402 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2323 1.33 - 1.45: 4152 1.45 - 1.57: 5730 1.57 - 1.69: 585 1.69 - 1.81: 20 Bond restraints: 12810 Sorted by residual: bond pdb=" C3' DG K 137 " pdb=" C2' DG K 137 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 bond pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.41e+00 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.38e+00 bond pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.24e+00 bond pdb=" C3' DC I 125 " pdb=" C2' DC I 125 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 ... (remaining 12805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 17704 1.85 - 3.69: 819 3.69 - 5.54: 26 5.54 - 7.39: 7 7.39 - 9.24: 3 Bond angle restraints: 18559 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 111.90 108.12 3.78 8.10e-01 1.52e+00 2.18e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT K 83 " pdb=" C4 DT K 83 " pdb=" O4 DT K 83 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 18554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.53: 5057 28.53 - 57.06: 1729 57.06 - 85.59: 154 85.59 - 114.12: 1 114.12 - 142.65: 3 Dihedral angle restraints: 6944 sinusoidal: 4763 harmonic: 2181 Sorted by residual: dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 77.35 142.65 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DG K 82 " pdb=" C3' DG K 82 " pdb=" O3' DG K 82 " pdb=" P DT K 83 " ideal model delta sinusoidal sigma weight residual 220.00 77.96 142.04 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1755 0.059 - 0.117: 337 0.117 - 0.176: 18 0.176 - 0.235: 1 0.235 - 0.294: 2 Chirality restraints: 2113 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU D 101 " pdb=" CB LEU D 101 " pdb=" CD1 LEU D 101 " pdb=" CD2 LEU D 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2110 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 58 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C THR A 58 " 0.040 2.00e-02 2.50e+03 pdb=" O THR A 58 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C GLU F 63 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU F 63 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN F 64 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.78e+00 pdb=" C LYS F 59 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.011 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 5941 3.02 - 3.49: 11497 3.49 - 3.96: 24618 3.96 - 4.43: 27483 4.43 - 4.90: 35706 Nonbonded interactions: 105245 Sorted by model distance: nonbonded pdb=" O5' DA I 124 " pdb=" O4' DA I 124 " model vdw 2.551 2.432 nonbonded pdb=" N ILE C 79 " pdb=" O ILE C 79 " model vdw 2.586 2.496 nonbonded pdb=" N ILE G 79 " pdb=" O ILE G 79 " model vdw 2.595 2.496 nonbonded pdb=" N1 DG K 120 " pdb=" C4 DG K 120 " model vdw 2.595 2.672 nonbonded pdb=" N1 DG J 67 " pdb=" C4 DG J 67 " model vdw 2.595 2.672 ... (remaining 105240 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' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 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 0.036 12810 Z= 0.520 Angle : 0.773 9.236 18559 Z= 0.686 Chirality : 0.045 0.294 2113 Planarity : 0.005 0.043 1328 Dihedral : 28.410 142.653 5538 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.16 % Allowed : 21.28 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.30), residues: 737 helix: 1.62 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.61 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.012 0.001 TYR D 40 PHE 0.008 0.002 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.52 (12810) covalent geometry : angle 0.77285 / 0.69 (18559) hydrogen bonds : bond 0.10508 / 6.92 ( 778) hydrogen bonds : angle 4.35954 / 3.11 ( 1934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.245 Fit side-chains REVERT: D 108 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8682 (mtmp) REVERT: D 116 LYS cc_start: 0.9266 (ttmm) cc_final: 0.9047 (ttmt) REVERT: G 73 ASN cc_start: 0.8705 (t0) cc_final: 0.8161 (t160) REVERT: G 91 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8719 (pm20) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.8186 time to fit residues: 141.1692 Evaluate side-chains 154 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN G 68 ASN G 104 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074819 restraints weight = 19510.300| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.27 r_work: 0.2895 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12810 Z= 0.153 Angle : 0.623 8.273 18559 Z= 0.378 Chirality : 0.046 0.209 2113 Planarity : 0.004 0.039 1328 Dihedral : 30.594 144.579 4051 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.44 % Allowed : 20.32 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.30), residues: 737 helix: 2.10 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.54 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.009 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.15 (12810) covalent geometry : angle 0.62348 / 0.38 (18559) hydrogen bonds : bond 0.04986 / 3.36 ( 778) hydrogen bonds : angle 3.39081 / 2.40 ( 1934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.318 Fit side-chains REVERT: D 71 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: G 73 ASN cc_start: 0.8693 (t0) cc_final: 0.8149 (t160) outliers start: 9 outliers final: 2 residues processed: 161 average time/residue: 0.7920 time to fit residues: 134.9753 Evaluate side-chains 161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain D residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072775 restraints weight = 19660.743| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.23 r_work: 0.2790 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12810 Z= 0.242 Angle : 0.666 6.819 18559 Z= 0.384 Chirality : 0.047 0.247 2113 Planarity : 0.005 0.044 1328 Dihedral : 31.167 147.626 4051 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.56 % Allowed : 18.72 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.30), residues: 737 helix: 2.38 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 86 TYR 0.014 0.002 TYR F 51 PHE 0.016 0.002 PHE C 25 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (12810) covalent geometry : angle 0.66649 / 0.38 (18559) hydrogen bonds : bond 0.05272 / 3.55 ( 778) hydrogen bonds : angle 3.07715 / 2.18 ( 1934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.338 Fit side-chains REVERT: C 75 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8928 (mmtm) REVERT: D 71 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7956 (mp0) outliers start: 16 outliers final: 5 residues processed: 166 average time/residue: 0.8433 time to fit residues: 147.5712 Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 19 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.102576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074035 restraints weight = 19435.699| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.21 r_work: 0.2863 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12810 Z= 0.149 Angle : 0.639 7.094 18559 Z= 0.370 Chirality : 0.046 0.312 2113 Planarity : 0.004 0.042 1328 Dihedral : 31.207 147.480 4051 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.40 % Allowed : 18.24 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.30), residues: 737 helix: 2.49 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.009 0.001 TYR C 57 PHE 0.009 0.002 PHE A 67 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (12810) covalent geometry : angle 0.63850 / 0.37 (18559) hydrogen bonds : bond 0.04289 / 2.89 ( 778) hydrogen bonds : angle 3.02634 / 2.14 ( 1934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.238 Fit side-chains REVERT: B 79 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.9016 (mtpp) REVERT: C 75 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8980 (mmtm) REVERT: D 71 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7945 (mp0) outliers start: 15 outliers final: 5 residues processed: 167 average time/residue: 0.7577 time to fit residues: 133.6539 Evaluate side-chains 167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 30.0000 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.102353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073192 restraints weight = 19523.669| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.26 r_work: 0.2862 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12810 Z= 0.151 Angle : 0.631 8.603 18559 Z= 0.366 Chirality : 0.044 0.282 2113 Planarity : 0.004 0.043 1328 Dihedral : 31.192 146.729 4051 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.76 % Allowed : 20.00 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.30), residues: 737 helix: 2.59 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.51 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.013 0.001 TYR F 51 PHE 0.011 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12810) covalent geometry : angle 0.63116 / 0.37 (18559) hydrogen bonds : bond 0.04067 / 2.75 ( 778) hydrogen bonds : angle 2.97891 / 2.10 ( 1934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.293 Fit side-chains REVERT: C 75 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9075 (mmtm) REVERT: D 71 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: G 73 ASN cc_start: 0.8769 (t0) cc_final: 0.8201 (t160) outliers start: 11 outliers final: 6 residues processed: 165 average time/residue: 0.7900 time to fit residues: 137.6824 Evaluate side-chains 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.102813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073669 restraints weight = 19513.603| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.27 r_work: 0.2874 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12810 Z= 0.139 Angle : 0.619 8.819 18559 Z= 0.362 Chirality : 0.044 0.334 2113 Planarity : 0.004 0.041 1328 Dihedral : 31.176 146.017 4051 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 20.16 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.30), residues: 737 helix: 2.62 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.45 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.008 0.001 TYR C 57 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (12810) covalent geometry : angle 0.61897 / 0.36 (18559) hydrogen bonds : bond 0.03944 / 2.67 ( 778) hydrogen bonds : angle 2.95614 / 2.08 ( 1934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.264 Fit side-chains REVERT: B 79 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9019 (mtpp) REVERT: C 75 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9030 (mmtm) REVERT: D 71 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: G 73 ASN cc_start: 0.8759 (t0) cc_final: 0.8192 (t160) outliers start: 12 outliers final: 6 residues processed: 167 average time/residue: 0.7692 time to fit residues: 135.6406 Evaluate side-chains 169 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074108 restraints weight = 19473.950| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.27 r_work: 0.2881 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12810 Z= 0.145 Angle : 0.605 8.916 18559 Z= 0.356 Chirality : 0.043 0.252 2113 Planarity : 0.004 0.041 1328 Dihedral : 31.166 144.607 4051 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.40 % Allowed : 20.00 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.30), residues: 737 helix: 2.70 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.009 0.001 TYR H 40 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (12810) covalent geometry : angle 0.60527 / 0.36 (18559) hydrogen bonds : bond 0.03879 / 2.63 ( 778) hydrogen bonds : angle 2.88977 / 2.03 ( 1934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.348 Fit side-chains REVERT: B 79 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9030 (mtpp) REVERT: C 75 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9020 (mmtm) REVERT: D 71 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: G 73 ASN cc_start: 0.8769 (t0) cc_final: 0.8203 (t160) outliers start: 15 outliers final: 5 residues processed: 166 average time/residue: 0.7407 time to fit residues: 129.8380 Evaluate side-chains 165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS G 104 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.070036 restraints weight = 19417.893| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.26 r_work: 0.2773 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 12810 Z= 0.414 Angle : 0.791 7.894 18559 Z= 0.431 Chirality : 0.055 0.276 2113 Planarity : 0.006 0.047 1328 Dihedral : 31.739 152.304 4049 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.76 % Allowed : 21.12 % Favored : 77.12 % 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: 2.05 (0.30), residues: 737 helix: 2.05 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.022 0.002 TYR A 54 PHE 0.016 0.003 PHE D 70 HIS 0.006 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.41 (12810) covalent geometry : angle 0.79085 / 0.43 (18559) hydrogen bonds : bond 0.07356 / 4.93 ( 778) hydrogen bonds : angle 3.20012 / 2.27 ( 1934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.263 Fit side-chains REVERT: C 75 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8923 (mmtm) REVERT: D 71 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: G 64 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: G 73 ASN cc_start: 0.8960 (t0) cc_final: 0.8353 (t0) outliers start: 11 outliers final: 2 residues processed: 153 average time/residue: 0.7858 time to fit residues: 126.5422 Evaluate side-chains 150 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.073534 restraints weight = 19340.151| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.21 r_work: 0.2852 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12810 Z= 0.146 Angle : 0.661 7.576 18559 Z= 0.375 Chirality : 0.045 0.240 2113 Planarity : 0.004 0.045 1328 Dihedral : 31.663 148.613 4049 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.64 % Allowed : 22.24 % Favored : 77.12 % 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: 2.60 (0.30), residues: 737 helix: 2.52 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.60 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.009 0.001 TYR C 57 PHE 0.011 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (12810) covalent geometry : angle 0.66108 / 0.38 (18559) hydrogen bonds : bond 0.03932 / 2.66 ( 778) hydrogen bonds : angle 3.00136 / 2.12 ( 1934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.215 Fit side-chains REVERT: C 75 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9015 (mmtm) REVERT: D 71 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: G 73 ASN cc_start: 0.8840 (t0) cc_final: 0.8223 (t0) outliers start: 4 outliers final: 1 residues processed: 155 average time/residue: 0.7819 time to fit residues: 127.5967 Evaluate side-chains 155 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073614 restraints weight = 19578.654| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.27 r_work: 0.2873 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12810 Z= 0.149 Angle : 0.626 9.737 18559 Z= 0.363 Chirality : 0.043 0.258 2113 Planarity : 0.004 0.047 1328 Dihedral : 31.373 144.198 4049 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.80 % Allowed : 22.08 % Favored : 77.12 % 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: 2.82 (0.30), residues: 737 helix: 2.68 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.51 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.009 0.001 TYR D 40 PHE 0.012 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12810) covalent geometry : angle 0.62630 / 0.36 (18559) hydrogen bonds : bond 0.03885 / 2.63 ( 778) hydrogen bonds : angle 2.89532 / 2.03 ( 1934) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.263 Fit side-chains REVERT: C 75 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9020 (mmtm) REVERT: D 71 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: G 56 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: G 73 ASN cc_start: 0.8820 (t0) cc_final: 0.8241 (t0) outliers start: 5 outliers final: 1 residues processed: 157 average time/residue: 0.8146 time to fit residues: 134.9054 Evaluate side-chains 154 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 56 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074140 restraints weight = 19573.834| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.27 r_work: 0.2885 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12810 Z= 0.133 Angle : 0.626 12.264 18559 Z= 0.362 Chirality : 0.043 0.313 2113 Planarity : 0.004 0.047 1328 Dihedral : 31.359 144.194 4049 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.96 % Allowed : 22.40 % Favored : 76.64 % 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: 2.85 (0.30), residues: 737 helix: 2.70 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.010 0.001 TYR D 40 PHE 0.012 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (12810) covalent geometry : angle 0.62641 / 0.36 (18559) hydrogen bonds : bond 0.03714 / 2.52 ( 778) hydrogen bonds : angle 2.90127 / 2.03 ( 1934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4022.94 seconds wall clock time: 68 minutes 51.72 seconds (4131.72 seconds total)