Starting phenix.real_space_refine on Fri Jul 3 04:22:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ya_75522/07_2026/10ya_75522.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ya_75522/07_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_75522/07_2026/10ya_75522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ya_75522/07_2026/10ya_75522.map" model { file = "/net/cci-nas-00/data/ceres_data/10ya_75522/07_2026/10ya_75522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ya_75522/07_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-dev-6108/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: 2.47, 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: 0.94 Conformation dependent library (CDL) restraints added in 224.1 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: 1.84 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: 2.11 Time building geometry restraints manager: 1.25 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: 17715 1.85 - 3.69: 808 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: 5.380 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.120 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- 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 : 0.765 9.236 18559 Z= 0.680 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 0.76513 / 0.68 (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 : 0.326 Fit side-chains REVERT: D 86 ARG cc_start: 0.9257 (mmt90) cc_final: 0.9051 (mmt90) 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: 0.8295 time to fit residues: 142.9352 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 : 0.309 ------------------------------------------------------------------------------- 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 = 0.103880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074848 restraints weight = 19499.382| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.26 r_work: 0.2897 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.0521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12810 Z= 0.155 Angle : 0.606 8.223 18559 Z= 0.373 Chirality : 0.044 0.217 2113 Planarity : 0.004 0.039 1328 Dihedral : 30.639 144.855 4051 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.60 % Allowed : 19.84 % 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: 2.20 (0.30), residues: 737 helix: 2.11 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.53 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.009 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.16 (12810) covalent geometry : angle 0.60612 / 0.37 (18559) hydrogen bonds : bond 0.04872 / 3.29 ( 778) hydrogen bonds : angle 3.37623 / 2.39 ( 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: 10 poor density : 156 time to evaluate : 0.323 Fit side-chains REVERT: D 71 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: G 73 ASN cc_start: 0.8693 (t0) cc_final: 0.8149 (t160) outliers start: 10 outliers final: 2 residues processed: 161 average time/residue: 0.8249 time to fit residues: 140.1462 Evaluate side-chains 159 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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: 0.8980 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.102221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073801 restraints weight = 19675.024| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.24 r_work: 0.2853 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12810 Z= 0.211 Angle : 0.624 6.884 18559 Z= 0.373 Chirality : 0.045 0.240 2113 Planarity : 0.004 0.044 1328 Dihedral : 31.053 145.315 4051 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.92 % Allowed : 18.88 % Favored : 79.20 % 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: 2.43 (0.30), residues: 737 helix: 2.39 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.61 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.012 0.002 TYR B 51 PHE 0.014 0.002 PHE C 25 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 (12810) covalent geometry : angle 0.62426 / 0.37 (18559) hydrogen bonds : bond 0.04937 / 3.34 ( 778) hydrogen bonds : angle 3.08618 / 2.19 ( 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 167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.307 Fit side-chains REVERT: C 75 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9011 (mmtm) REVERT: D 71 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: G 73 ASN cc_start: 0.8758 (t0) cc_final: 0.8196 (t160) outliers start: 12 outliers final: 6 residues processed: 162 average time/residue: 0.8034 time to fit residues: 137.2443 Evaluate side-chains 162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 C residue 95 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: 0.7980 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 19 optimal weight: 0.0470 chunk 44 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.102686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073460 restraints weight = 19459.922| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.27 r_work: 0.2865 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12810 Z= 0.146 Angle : 0.610 8.087 18559 Z= 0.363 Chirality : 0.045 0.311 2113 Planarity : 0.004 0.041 1328 Dihedral : 31.083 146.198 4051 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.24 % Allowed : 18.56 % Favored : 79.20 % 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: 2.62 (0.30), residues: 737 helix: 2.52 (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 0.006 0.000 ARG D 86 TYR 0.010 0.001 TYR C 57 PHE 0.010 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (12810) covalent geometry : angle 0.60979 / 0.36 (18559) hydrogen bonds : bond 0.04277 / 2.89 ( 778) hydrogen bonds : angle 3.03266 / 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 171 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.301 Fit side-chains REVERT: B 79 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9003 (mtpp) REVERT: C 75 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9019 (mmtm) REVERT: D 71 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: G 73 ASN cc_start: 0.8765 (t0) cc_final: 0.8203 (t160) outliers start: 14 outliers final: 4 residues processed: 163 average time/residue: 0.8146 time to fit residues: 140.2392 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 : 0.319 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.102580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073381 restraints weight = 19518.417| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.27 r_work: 0.2867 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12810 Z= 0.164 Angle : 0.604 8.051 18559 Z= 0.359 Chirality : 0.044 0.324 2113 Planarity : 0.004 0.042 1328 Dihedral : 31.140 145.795 4051 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.92 % Allowed : 19.04 % Favored : 79.04 % 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: 2.72 (0.30), residues: 737 helix: 2.59 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.47 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.009 0.001 TYR C 57 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12810) covalent geometry : angle 0.60390 / 0.36 (18559) hydrogen bonds : bond 0.04158 / 2.81 ( 778) hydrogen bonds : angle 2.98056 / 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 169 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.324 Fit side-chains REVERT: A 94 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8585 (mm-30) REVERT: C 75 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9017 (mmtm) REVERT: D 71 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: G 73 ASN cc_start: 0.8768 (t0) cc_final: 0.8211 (t160) outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 0.7993 time to fit residues: 136.8792 Evaluate side-chains 165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 C residue 95 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.102578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073351 restraints weight = 19505.508| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.27 r_work: 0.2865 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1037 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= 0.164 Angle : 0.598 8.966 18559 Z= 0.355 Chirality : 0.043 0.263 2113 Planarity : 0.004 0.042 1328 Dihedral : 31.202 145.958 4051 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.08 % Allowed : 19.68 % 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: 2.77 (0.30), residues: 737 helix: 2.63 (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 0.004 0.000 ARG D 99 TYR 0.009 0.001 TYR B 51 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (12810) covalent geometry : angle 0.59785 / 0.36 (18559) hydrogen bonds : bond 0.04113 / 2.78 ( 778) hydrogen bonds : angle 2.93974 / 2.07 ( 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 169 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.236 Fit side-chains REVERT: C 75 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9032 (mmtm) REVERT: D 71 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: G 73 ASN cc_start: 0.8788 (t0) cc_final: 0.8206 (t160) outliers start: 13 outliers final: 6 residues processed: 162 average time/residue: 0.7502 time to fit residues: 128.2891 Evaluate side-chains 162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 C residue 95 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.0030 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4828 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.103209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.074057 restraints weight = 19417.722| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.27 r_work: 0.2881 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12810 Z= 0.134 Angle : 0.600 8.106 18559 Z= 0.356 Chirality : 0.043 0.277 2113 Planarity : 0.004 0.040 1328 Dihedral : 31.204 145.712 4051 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.08 % Allowed : 19.68 % 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: 2.89 (0.30), residues: 737 helix: 2.72 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.009 0.001 TYR H 40 PHE 0.012 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.13 (12810) covalent geometry : angle 0.59991 / 0.36 (18559) hydrogen bonds : bond 0.03900 / 2.64 ( 778) hydrogen bonds : angle 2.93332 / 2.06 ( 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 170 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.292 Fit side-chains REVERT: B 79 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9005 (mtpp) REVERT: C 75 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9078 (mmtm) REVERT: D 71 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: G 56 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8924 (tt0) REVERT: G 73 ASN cc_start: 0.8772 (t0) cc_final: 0.8184 (t160) outliers start: 13 outliers final: 6 residues processed: 164 average time/residue: 0.7800 time to fit residues: 135.1202 Evaluate side-chains 165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 B residue 84 MET 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 G residue 56 GLU 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: 2.9990 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 0.0270 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 5.4048 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.098100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068621 restraints weight = 19471.353| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.40 r_work: 0.2762 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.087 12810 Z= 0.453 Angle : 0.791 7.803 18559 Z= 0.432 Chirality : 0.055 0.252 2113 Planarity : 0.006 0.048 1328 Dihedral : 31.793 153.283 4051 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.56 % Allowed : 19.36 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.30), residues: 737 helix: 2.05 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.023 0.003 TYR A 54 PHE 0.016 0.004 PHE D 70 HIS 0.006 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.45 (12810) covalent geometry : angle 0.79053 / 0.43 (18559) hydrogen bonds : bond 0.07621 / 5.11 ( 778) hydrogen bonds : angle 3.21836 / 2.29 ( 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 161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.273 Fit side-chains REVERT: C 75 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8964 (mmtm) REVERT: D 71 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: G 56 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.9030 (tt0) REVERT: G 64 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: G 73 ASN cc_start: 0.8973 (t0) cc_final: 0.8357 (t0) outliers start: 16 outliers final: 2 residues processed: 155 average time/residue: 0.8375 time to fit residues: 136.7400 Evaluate side-chains 152 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 56 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: 0.9980 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.100862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.071644 restraints weight = 19307.284| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.25 r_work: 0.2827 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 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 0.046 12810 Z= 0.152 Angle : 0.671 9.801 18559 Z= 0.380 Chirality : 0.047 0.283 2113 Planarity : 0.004 0.047 1328 Dihedral : 31.792 151.938 4049 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.12 % Allowed : 20.64 % 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: 2.38 (0.30), residues: 737 helix: 2.35 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.64 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.012 0.002 TYR B 51 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (12810) covalent geometry : angle 0.67104 / 0.38 (18559) hydrogen bonds : bond 0.04308 / 2.91 ( 778) hydrogen bonds : angle 3.06789 / 2.17 ( 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 160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.262 Fit side-chains REVERT: C 75 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9028 (mmtm) REVERT: D 71 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: G 73 ASN cc_start: 0.8898 (t0) cc_final: 0.8297 (t0) outliers start: 7 outliers final: 2 residues processed: 156 average time/residue: 0.8343 time to fit residues: 137.0233 Evaluate side-chains 152 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 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: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.101551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072294 restraints weight = 19531.914| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.26 r_work: 0.2842 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12810 Z= 0.148 Angle : 0.650 10.651 18559 Z= 0.374 Chirality : 0.044 0.297 2113 Planarity : 0.004 0.047 1328 Dihedral : 31.698 148.317 4049 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.64 % Allowed : 21.60 % Favored : 77.76 % 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: 2.62 (0.30), residues: 737 helix: 2.53 (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 0.000 ARG D 86 TYR 0.010 0.001 TYR H 40 PHE 0.012 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12810) covalent geometry : angle 0.65048 / 0.37 (18559) hydrogen bonds : bond 0.04022 / 2.72 ( 778) hydrogen bonds : angle 3.01985 / 2.13 ( 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 152 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.216 Fit side-chains REVERT: C 75 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8976 (mmtm) REVERT: D 71 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: G 73 ASN cc_start: 0.8869 (t0) cc_final: 0.8237 (t0) outliers start: 4 outliers final: 2 residues processed: 151 average time/residue: 0.7739 time to fit residues: 123.1147 Evaluate side-chains 153 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 10.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.0040 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.4870 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.101997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.072820 restraints weight = 19548.903| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.26 r_work: 0.2813 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12810 Z= 0.134 Angle : 0.634 8.880 18559 Z= 0.367 Chirality : 0.044 0.266 2113 Planarity : 0.004 0.048 1328 Dihedral : 31.649 148.084 4049 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 2.69 (0.30), residues: 737 helix: 2.57 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.49 (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 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (12810) covalent geometry : angle 0.63449 / 0.37 (18559) hydrogen bonds : bond 0.03872 / 2.61 ( 778) hydrogen bonds : angle 2.98648 / 2.10 ( 1934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.99 seconds wall clock time: 71 minutes 28.68 seconds (4288.68 seconds total)