Starting phenix.real_space_refine on Tue Feb 3 15:09:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vne_65209/02_2026/9vne_65209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vne_65209/02_2026/9vne_65209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vne_65209/02_2026/9vne_65209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vne_65209/02_2026/9vne_65209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vne_65209/02_2026/9vne_65209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vne_65209/02_2026/9vne_65209.map" } resolution = 3.11 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= 0.002 sd= 0.052 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 2729 2.51 5 N 687 2.21 5 O 776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4216 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 5 Chain: "B" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 764 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain breaks: 2 Chain: "D" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 5 Chain: "E" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 2 Chain: "F" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 718 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 5 Chain: "C" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 659 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain breaks: 5 Time building chain proxies: 0.78, per 1000 atoms: 0.19 Number of scatterers: 4216 At special positions: 0 Unit cell: (94.68, 94.68, 51.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 776 8.00 N 687 7.00 C 2729 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: 0.19 Conformation dependent library (CDL) restraints added in 87.8 milliseconds 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 8.4% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'E' and resid 61 through 70 removed outlier: 3.554A pdb=" N TYR E 65 " --> pdb=" O PRO E 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.631A pdb=" N TYR A 26 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER A 6 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.326A pdb=" N HIS A 117 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A 106 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS A 119 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 104 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 121 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 28 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 51 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU C 28 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA C 59 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN C 30 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 34 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR C 53 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS C 117 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 106 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS C 119 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 104 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE C 121 " --> pdb=" O THR C 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 25 removed outlier: 5.773A pdb=" N LYS B 74 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 33 removed outlier: 6.974A pdb=" N LEU D 28 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA D 59 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN D 30 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N HIS D 117 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE D 106 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS D 119 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 104 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE D 121 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 104 " --> pdb=" O PHE E 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'E' and resid 52 through 54 removed outlier: 3.843A pdb=" N ARG E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LEU F 28 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA F 59 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN F 30 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER F 34 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR F 53 " --> pdb=" O SER F 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS F 117 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE F 106 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS F 119 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 104 " --> pdb=" O LYS F 119 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE F 121 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA F 100 " --> pdb=" O GLN F 123 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 52 through 54 removed outlier: 3.843A pdb=" N ARG E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR F 26 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER F 6 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU F 92 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 8 through 9 removed outlier: 4.341A pdb=" N GLU C 92 " --> pdb=" O ILE C 83 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 954 1.33 - 1.45: 894 1.45 - 1.57: 2400 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4282 Sorted by residual: bond pdb=" N ILE C 120 " pdb=" CA ILE C 120 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.28e+00 bond pdb=" N SER B 104 " pdb=" CA SER B 104 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.24e-02 6.50e+03 6.11e+00 bond pdb=" N ARG B 103 " pdb=" CA ARG B 103 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.23e-02 6.61e+03 5.76e+00 bond pdb=" CA PHE C 7 " pdb=" C PHE C 7 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.26e-02 6.30e+03 5.33e+00 bond pdb=" C ARG B 100 " pdb=" O ARG B 100 " ideal model delta sigma weight residual 1.235 1.209 0.026 1.13e-02 7.83e+03 5.20e+00 ... (remaining 4277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 5577 2.17 - 4.33: 134 4.33 - 6.49: 31 6.49 - 8.66: 9 8.66 - 10.82: 2 Bond angle restraints: 5753 Sorted by residual: angle pdb=" CA GLN A 63 " pdb=" CB GLN A 63 " pdb=" CG GLN A 63 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.52e+01 angle pdb=" C GLY A 60 " pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta sigma weight residual 120.68 126.25 -5.57 1.52e+00 4.33e-01 1.34e+01 angle pdb=" CA GLN C 63 " pdb=" CB GLN C 63 " pdb=" CG GLN C 63 " ideal model delta sigma weight residual 114.10 121.38 -7.28 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CG1 ILE D 81 " pdb=" CB ILE D 81 " pdb=" CG2 ILE D 81 " ideal model delta sigma weight residual 110.70 99.88 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA GLU F 27 " pdb=" CB GLU F 27 " pdb=" CG GLU F 27 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 ... (remaining 5748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 2114 16.05 - 32.09: 294 32.09 - 48.14: 88 48.14 - 64.19: 17 64.19 - 80.23: 6 Dihedral angle restraints: 2519 sinusoidal: 1023 harmonic: 1496 Sorted by residual: dihedral pdb=" CA GLN A 63 " pdb=" C GLN A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta harmonic sigma weight residual -180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PRO B 88 " pdb=" C PRO B 88 " pdb=" N LEU B 89 " pdb=" CA LEU B 89 " ideal model delta harmonic sigma weight residual 180.00 -162.13 -17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CD1 ILE E 51 " ideal model delta sinusoidal sigma weight residual 180.00 120.06 59.94 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 478 0.049 - 0.098: 112 0.098 - 0.147: 57 0.147 - 0.196: 7 0.196 - 0.245: 2 Chirality restraints: 656 Sorted by residual: chirality pdb=" CG LEU C 95 " pdb=" CB LEU C 95 " pdb=" CD1 LEU C 95 " pdb=" CD2 LEU C 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE D 81 " pdb=" CA ILE D 81 " pdb=" CG1 ILE D 81 " pdb=" CG2 ILE D 81 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PHE C 7 " pdb=" N PHE C 7 " pdb=" C PHE C 7 " pdb=" CB PHE C 7 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 653 not shown) Planarity restraints: 709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 61 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO D 62 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 62 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 62 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 72 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO E 73 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 73 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 73 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 63 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" CD GLN D 63 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN D 63 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN D 63 " -0.010 2.00e-02 2.50e+03 ... (remaining 706 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 798 2.78 - 3.31: 3650 3.31 - 3.84: 6634 3.84 - 4.37: 7475 4.37 - 4.90: 13375 Nonbonded interactions: 31932 Sorted by model distance: nonbonded pdb=" O GLY C 60 " pdb=" OG1 THR C 118 " model vdw 2.250 3.040 nonbonded pdb=" O SER C 6 " pdb=" OG SER C 6 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASN B 75 " pdb=" N ASN B 95 " model vdw 2.378 3.120 nonbonded pdb=" O ARG D 9 " pdb=" N ALA D 80 " model vdw 2.380 3.120 nonbonded pdb=" OG SER D 6 " pdb=" N PHE D 7 " model vdw 2.380 3.120 ... (remaining 31927 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' and (resid 6 through 10 or resid 25 through 63 or resid 67 through 72 \ or resid 79 through 85 or resid 90 through 96 or resid 98 through 108 or resid \ 116 through 124)) selection = (chain 'C' and (resid 6 through 10 or resid 25 through 35 or resid 51 through 72 \ or resid 79 through 85 or resid 90 through 96 or resid 98 through 124)) selection = (chain 'D' and (resid 6 through 10 or resid 25 through 63 or resid 67 through 10 \ 8 or resid 116 through 124)) selection = (chain 'F' and (resid 6 through 10 or resid 25 through 35 or resid 51 through 72 \ or resid 79 through 85 or resid 90 through 96 or resid 98 through 124)) } ncs_group { reference = (chain 'B' and (resid 13 through 33 or resid 51 through 80 or resid 88 through 1 \ 24)) selection = (chain 'E' and resid 13 through 124) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.040 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.080 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.004 0.042 4282 Z= 0.212 Angle : 0.866 10.825 5753 Z= 0.456 Chirality : 0.053 0.245 656 Planarity : 0.004 0.054 709 Dihedral : 16.866 80.232 1543 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 37.80 % Favored : 62.20 % 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: -2.32 (0.38), residues: 466 helix: 0.64 (0.89), residues: 39 sheet: -1.52 (0.33), residues: 246 loop : -1.84 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 68 TYR 0.025 0.001 TYR D 26 PHE 0.014 0.001 PHE B 29 TRP 0.010 0.002 TRP F 69 HIS 0.005 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 4282) covalent geometry : angle 0.86639 ( 5753) hydrogen bonds : bond 0.15114 ( 183) hydrogen bonds : angle 9.25077 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.9057 (m) cc_final: 0.8819 (t) REVERT: B 69 MET cc_start: 0.6934 (tmm) cc_final: 0.6498 (tpt) REVERT: D 30 ASN cc_start: 0.8216 (m-40) cc_final: 0.7738 (m-40) REVERT: E 120 ASP cc_start: 0.7840 (t70) cc_final: 0.7615 (t0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0888 time to fit residues: 21.1245 Evaluate side-chains 178 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN E 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.186775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.157912 restraints weight = 6863.460| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.84 r_work: 0.4059 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4282 Z= 0.129 Angle : 0.655 8.556 5753 Z= 0.333 Chirality : 0.047 0.196 656 Planarity : 0.004 0.046 709 Dihedral : 4.423 19.635 539 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 6.26 % Allowed : 35.64 % Favored : 58.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.37), residues: 466 helix: 0.25 (0.77), residues: 45 sheet: -1.41 (0.31), residues: 254 loop : -2.03 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.015 0.001 TYR D 26 PHE 0.013 0.001 PHE C 7 TRP 0.010 0.001 TRP E 16 HIS 0.006 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4282) covalent geometry : angle 0.65491 ( 5753) hydrogen bonds : bond 0.03284 ( 183) hydrogen bonds : angle 7.06334 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8580 (t) REVERT: A 107 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 69 MET cc_start: 0.6950 (tmm) cc_final: 0.6383 (tpt) REVERT: B 103 ARG cc_start: 0.8561 (tpt-90) cc_final: 0.8200 (tpt-90) REVERT: D 30 ASN cc_start: 0.8147 (m-40) cc_final: 0.7632 (m-40) REVERT: E 100 ARG cc_start: 0.8103 (mmp80) cc_final: 0.7814 (mmm-85) REVERT: E 120 ASP cc_start: 0.8021 (t70) cc_final: 0.7757 (t0) outliers start: 29 outliers final: 19 residues processed: 193 average time/residue: 0.0794 time to fit residues: 18.6339 Evaluate side-chains 185 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 GLN E 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.177169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.143443 restraints weight = 7074.475| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.95 r_work: 0.3858 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 4282 Z= 0.442 Angle : 0.942 10.838 5753 Z= 0.462 Chirality : 0.054 0.292 656 Planarity : 0.005 0.051 709 Dihedral : 5.374 21.988 539 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 9.50 % Allowed : 35.21 % Favored : 55.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.37), residues: 466 helix: -0.18 (0.82), residues: 41 sheet: -1.74 (0.31), residues: 248 loop : -2.08 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 100 TYR 0.024 0.002 TYR D 26 PHE 0.027 0.003 PHE B 33 TRP 0.011 0.003 TRP E 16 HIS 0.010 0.003 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.01039 ( 4282) covalent geometry : angle 0.94215 ( 5753) hydrogen bonds : bond 0.04515 ( 183) hydrogen bonds : angle 7.72610 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8636 (t) REVERT: A 70 ILE cc_start: 0.7408 (mp) cc_final: 0.7042 (mp) REVERT: B 20 ASP cc_start: 0.8194 (p0) cc_final: 0.7725 (m-30) REVERT: B 33 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: B 64 ILE cc_start: 0.8640 (mt) cc_final: 0.8416 (mt) REVERT: B 69 MET cc_start: 0.6656 (tmm) cc_final: 0.6323 (tpt) REVERT: B 112 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8123 (tm-30) REVERT: D 110 GLN cc_start: 0.8613 (tp40) cc_final: 0.8394 (tp40) REVERT: E 20 ASP cc_start: 0.7910 (p0) cc_final: 0.7663 (p0) REVERT: E 22 GLN cc_start: 0.7392 (tt0) cc_final: 0.7179 (tt0) REVERT: E 26 MET cc_start: 0.8340 (mmt) cc_final: 0.7643 (mmt) REVERT: E 120 ASP cc_start: 0.8265 (t70) cc_final: 0.8032 (t0) outliers start: 44 outliers final: 28 residues processed: 196 average time/residue: 0.0865 time to fit residues: 20.4115 Evaluate side-chains 193 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.182398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.152352 restraints weight = 6748.530| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.85 r_work: 0.3984 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4282 Z= 0.149 Angle : 0.685 9.131 5753 Z= 0.347 Chirality : 0.048 0.190 656 Planarity : 0.004 0.044 709 Dihedral : 4.745 15.498 539 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 7.56 % Allowed : 37.58 % Favored : 54.86 % 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: -2.58 (0.37), residues: 466 helix: -0.15 (0.80), residues: 41 sheet: -1.60 (0.31), residues: 248 loop : -2.01 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 100 TYR 0.016 0.001 TYR D 26 PHE 0.013 0.002 PHE C 7 TRP 0.009 0.001 TRP E 16 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4282) covalent geometry : angle 0.68505 ( 5753) hydrogen bonds : bond 0.03154 ( 183) hydrogen bonds : angle 6.87007 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8616 (t) REVERT: A 107 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 20 ASP cc_start: 0.8061 (p0) cc_final: 0.7548 (m-30) REVERT: B 64 ILE cc_start: 0.8513 (mt) cc_final: 0.8305 (mt) REVERT: B 69 MET cc_start: 0.6562 (tmm) cc_final: 0.6097 (tpt) REVERT: D 55 TYR cc_start: 0.8045 (m-80) cc_final: 0.7495 (m-80) REVERT: E 112 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7735 (tm-30) REVERT: E 115 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8938 (mp) REVERT: E 120 ASP cc_start: 0.8119 (t70) cc_final: 0.7883 (t0) REVERT: F 50 ARG cc_start: 0.7692 (mmp-170) cc_final: 0.7332 (mmp-170) outliers start: 35 outliers final: 19 residues processed: 190 average time/residue: 0.0892 time to fit residues: 20.4010 Evaluate side-chains 183 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.180227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146641 restraints weight = 6990.511| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.82 r_work: 0.3907 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4282 Z= 0.266 Angle : 0.791 9.455 5753 Z= 0.392 Chirality : 0.050 0.205 656 Planarity : 0.004 0.049 709 Dihedral : 4.908 18.854 539 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 8.64 % Allowed : 36.50 % Favored : 54.86 % 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: -2.81 (0.37), residues: 466 helix: -0.46 (0.75), residues: 41 sheet: -1.75 (0.31), residues: 258 loop : -2.11 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.021 0.002 TYR C 108 PHE 0.019 0.002 PHE C 96 TRP 0.009 0.002 TRP B 16 HIS 0.008 0.002 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 4282) covalent geometry : angle 0.79110 ( 5753) hydrogen bonds : bond 0.03588 ( 183) hydrogen bonds : angle 7.08612 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.7450 (mp) cc_final: 0.7202 (mp) REVERT: A 71 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7330 (mm) REVERT: B 20 ASP cc_start: 0.8045 (p0) cc_final: 0.7500 (m-30) REVERT: B 33 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7052 (m-80) REVERT: B 64 ILE cc_start: 0.8624 (mt) cc_final: 0.8395 (mt) REVERT: B 69 MET cc_start: 0.6728 (tmm) cc_final: 0.6519 (tpt) REVERT: D 93 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8795 (ttmm) REVERT: E 100 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7345 (mmm-85) REVERT: E 112 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7700 (tm-30) REVERT: E 115 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9047 (mp) REVERT: E 120 ASP cc_start: 0.8039 (t70) cc_final: 0.7827 (t0) outliers start: 40 outliers final: 30 residues processed: 194 average time/residue: 0.0803 time to fit residues: 19.0244 Evaluate side-chains 197 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.186280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.153116 restraints weight = 7118.014| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 3.98 r_work: 0.3988 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4282 Z= 0.135 Angle : 0.688 8.443 5753 Z= 0.349 Chirality : 0.048 0.193 656 Planarity : 0.004 0.042 709 Dihedral : 4.506 17.959 539 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.62 % Allowed : 39.74 % Favored : 54.64 % 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: -2.50 (0.38), residues: 466 helix: -0.02 (0.78), residues: 41 sheet: -1.53 (0.31), residues: 263 loop : -1.98 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.019 0.001 TYR C 108 PHE 0.013 0.001 PHE C 7 TRP 0.010 0.001 TRP B 16 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4282) covalent geometry : angle 0.68797 ( 5753) hydrogen bonds : bond 0.02928 ( 183) hydrogen bonds : angle 6.43960 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 20 ASP cc_start: 0.8058 (p0) cc_final: 0.7471 (m-30) REVERT: B 64 ILE cc_start: 0.8563 (mt) cc_final: 0.8347 (mt) REVERT: B 69 MET cc_start: 0.6543 (tmm) cc_final: 0.6042 (tpt) REVERT: D 30 ASN cc_start: 0.8222 (m-40) cc_final: 0.7758 (m-40) REVERT: D 120 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8393 (mt) REVERT: E 20 ASP cc_start: 0.7762 (p0) cc_final: 0.7337 (m-30) REVERT: E 100 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7467 (mmm-85) REVERT: E 112 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7646 (tm-30) REVERT: E 115 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8903 (mp) REVERT: E 120 ASP cc_start: 0.8046 (t70) cc_final: 0.7814 (t0) REVERT: F 50 ARG cc_start: 0.7602 (mmp-170) cc_final: 0.7380 (mmp-170) outliers start: 26 outliers final: 17 residues processed: 191 average time/residue: 0.0790 time to fit residues: 18.3218 Evaluate side-chains 183 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.182638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.149777 restraints weight = 6965.652| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.89 r_work: 0.3951 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4282 Z= 0.194 Angle : 0.751 8.013 5753 Z= 0.381 Chirality : 0.051 0.213 656 Planarity : 0.004 0.045 709 Dihedral : 4.643 17.655 539 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 6.48 % Allowed : 38.23 % Favored : 55.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.38), residues: 466 helix: -0.22 (0.78), residues: 41 sheet: -1.59 (0.31), residues: 265 loop : -1.87 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 100 TYR 0.020 0.001 TYR C 108 PHE 0.014 0.002 PHE B 33 TRP 0.030 0.002 TRP B 16 HIS 0.007 0.002 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 4282) covalent geometry : angle 0.75141 ( 5753) hydrogen bonds : bond 0.03204 ( 183) hydrogen bonds : angle 6.71293 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 20 ASP cc_start: 0.8065 (p0) cc_final: 0.7445 (m-30) REVERT: B 26 MET cc_start: 0.7955 (mmt) cc_final: 0.7747 (mmt) REVERT: B 64 ILE cc_start: 0.8541 (mt) cc_final: 0.8293 (mt) REVERT: B 69 MET cc_start: 0.6647 (tmm) cc_final: 0.6103 (tpt) REVERT: B 112 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 115 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8990 (mp) REVERT: D 30 ASN cc_start: 0.8255 (m-40) cc_final: 0.7792 (m-40) REVERT: D 93 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8566 (ttmt) REVERT: D 120 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8462 (mt) REVERT: E 20 ASP cc_start: 0.7814 (p0) cc_final: 0.7476 (m-30) REVERT: E 100 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7314 (mmm-85) REVERT: E 112 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7689 (tm-30) REVERT: E 115 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9015 (mp) REVERT: E 120 ASP cc_start: 0.8084 (t70) cc_final: 0.7847 (t0) outliers start: 30 outliers final: 24 residues processed: 186 average time/residue: 0.0856 time to fit residues: 19.3128 Evaluate side-chains 190 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.0060 chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.184940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.155980 restraints weight = 6798.215| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.75 r_work: 0.4041 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4282 Z= 0.143 Angle : 0.723 7.580 5753 Z= 0.371 Chirality : 0.049 0.179 656 Planarity : 0.004 0.040 709 Dihedral : 4.490 17.917 539 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.83 % Allowed : 39.74 % Favored : 54.43 % 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 (0.38), residues: 466 helix: -0.15 (0.77), residues: 41 sheet: -1.46 (0.31), residues: 264 loop : -1.90 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 100 TYR 0.010 0.001 TYR E 97 PHE 0.015 0.001 PHE C 7 TRP 0.014 0.002 TRP B 16 HIS 0.005 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4282) covalent geometry : angle 0.72344 ( 5753) hydrogen bonds : bond 0.02986 ( 183) hydrogen bonds : angle 6.38871 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7256 (tm-30) REVERT: A 107 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 120 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8251 (mp) REVERT: B 20 ASP cc_start: 0.7949 (p0) cc_final: 0.7314 (m-30) REVERT: B 22 GLN cc_start: 0.6889 (tt0) cc_final: 0.6614 (tt0) REVERT: B 64 ILE cc_start: 0.8510 (mt) cc_final: 0.8284 (mt) REVERT: B 69 MET cc_start: 0.6510 (tmm) cc_final: 0.6041 (tpt) REVERT: B 112 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7719 (tm-30) REVERT: B 115 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8957 (mp) REVERT: D 93 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8647 (ttmm) REVERT: E 20 ASP cc_start: 0.7705 (p0) cc_final: 0.7376 (m-30) REVERT: E 100 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7389 (mmm-85) REVERT: E 112 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7697 (tm-30) REVERT: E 115 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8903 (mp) REVERT: E 120 ASP cc_start: 0.8032 (t70) cc_final: 0.7814 (t0) REVERT: F 50 ARG cc_start: 0.7583 (mmp-170) cc_final: 0.7352 (mmp-170) outliers start: 27 outliers final: 21 residues processed: 188 average time/residue: 0.0871 time to fit residues: 19.7640 Evaluate side-chains 187 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.183232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150046 restraints weight = 7224.826| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.93 r_work: 0.3961 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4282 Z= 0.199 Angle : 0.808 11.493 5753 Z= 0.406 Chirality : 0.051 0.232 656 Planarity : 0.004 0.056 709 Dihedral : 4.638 18.655 539 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 6.26 % Allowed : 40.17 % Favored : 53.56 % 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: -2.41 (0.38), residues: 466 helix: -0.32 (0.77), residues: 41 sheet: -1.45 (0.31), residues: 265 loop : -1.88 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 103 TYR 0.009 0.001 TYR A 58 PHE 0.016 0.002 PHE F 7 TRP 0.023 0.002 TRP B 16 HIS 0.007 0.002 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4282) covalent geometry : angle 0.80794 ( 5753) hydrogen bonds : bond 0.03211 ( 183) hydrogen bonds : angle 6.54955 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 107 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8205 (tm-30) REVERT: B 20 ASP cc_start: 0.7909 (p0) cc_final: 0.7219 (m-30) REVERT: B 22 GLN cc_start: 0.6963 (tt0) cc_final: 0.6665 (tt0) REVERT: B 64 ILE cc_start: 0.8527 (mt) cc_final: 0.8294 (mt) REVERT: B 69 MET cc_start: 0.6645 (tmm) cc_final: 0.6100 (tpt) REVERT: B 112 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 115 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8987 (mp) REVERT: D 93 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8710 (tppt) REVERT: D 120 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8423 (mt) REVERT: E 90 LYS cc_start: 0.6393 (mptt) cc_final: 0.6090 (mmtm) REVERT: E 100 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7413 (mmm-85) REVERT: E 115 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9029 (mt) REVERT: E 120 ASP cc_start: 0.8038 (t70) cc_final: 0.7812 (t0) REVERT: F 50 ARG cc_start: 0.7603 (mmp-170) cc_final: 0.7384 (mmp-170) outliers start: 29 outliers final: 23 residues processed: 183 average time/residue: 0.0918 time to fit residues: 20.2081 Evaluate side-chains 189 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.185079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.152113 restraints weight = 7036.380| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.88 r_work: 0.3978 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4282 Z= 0.181 Angle : 0.816 11.647 5753 Z= 0.411 Chirality : 0.051 0.251 656 Planarity : 0.004 0.056 709 Dihedral : 4.668 19.187 539 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.18 % Allowed : 41.90 % Favored : 52.92 % 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: -2.42 (0.38), residues: 466 helix: -0.27 (0.78), residues: 41 sheet: -1.48 (0.31), residues: 264 loop : -1.87 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 103 TYR 0.009 0.001 TYR A 58 PHE 0.015 0.002 PHE C 7 TRP 0.013 0.002 TRP E 16 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 4282) covalent geometry : angle 0.81604 ( 5753) hydrogen bonds : bond 0.03125 ( 183) hydrogen bonds : angle 6.45523 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7275 (tm-30) REVERT: A 107 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 20 ASP cc_start: 0.7901 (p0) cc_final: 0.7181 (m-30) REVERT: B 22 GLN cc_start: 0.6928 (tt0) cc_final: 0.6630 (tt0) REVERT: B 64 ILE cc_start: 0.8525 (mt) cc_final: 0.8280 (mt) REVERT: B 65 TYR cc_start: 0.8843 (m-80) cc_final: 0.8416 (m-80) REVERT: B 69 MET cc_start: 0.6614 (tmm) cc_final: 0.6082 (tpt) REVERT: B 81 LYS cc_start: 0.6445 (tptt) cc_final: 0.6197 (pttt) REVERT: B 112 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 115 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8954 (mt) REVERT: D 93 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8682 (tppt) REVERT: D 120 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8462 (mt) REVERT: D 127 ILE cc_start: 0.7351 (mt) cc_final: 0.7119 (mp) REVERT: E 90 LYS cc_start: 0.6407 (mptt) cc_final: 0.6090 (mmtm) REVERT: E 100 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7407 (mmm-85) REVERT: E 115 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8984 (mp) REVERT: E 120 ASP cc_start: 0.8040 (t70) cc_final: 0.7808 (t0) REVERT: F 50 ARG cc_start: 0.7575 (mmp-170) cc_final: 0.7349 (mmp-170) outliers start: 24 outliers final: 20 residues processed: 178 average time/residue: 0.0850 time to fit residues: 18.2946 Evaluate side-chains 185 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.182292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.153998 restraints weight = 6789.775| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 3.68 r_work: 0.4030 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4282 Z= 0.165 Angle : 0.797 10.857 5753 Z= 0.403 Chirality : 0.050 0.231 656 Planarity : 0.004 0.051 709 Dihedral : 4.583 19.325 539 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.75 % Allowed : 41.90 % Favored : 53.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.38), residues: 466 helix: -0.23 (0.78), residues: 41 sheet: -1.47 (0.31), residues: 265 loop : -1.83 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 100 TYR 0.008 0.001 TYR F 55 PHE 0.016 0.002 PHE C 7 TRP 0.012 0.002 TRP E 16 HIS 0.006 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 4282) covalent geometry : angle 0.79672 ( 5753) hydrogen bonds : bond 0.03045 ( 183) hydrogen bonds : angle 6.35911 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1322.83 seconds wall clock time: 23 minutes 21.71 seconds (1401.71 seconds total)