Starting phenix.real_space_refine on Thu Sep 10 23:51:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygh_72924/09_2026/9ygh_72924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygh_72924/09_2026/9ygh_72924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ygh_72924/09_2026/9ygh_72924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygh_72924/09_2026/9ygh_72924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ygh_72924/09_2026/9ygh_72924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygh_72924/09_2026/9ygh_72924.map" } resolution = 3.83 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= -0.001 sd= 0.064 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 18 5.16 5 C 3499 2.51 5 N 948 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5524 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 187 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 6, 'TRANS': 19} Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 1.41, per 1000 atoms: 0.26 Number of scatterers: 5524 At special positions: 0 Unit cell: (61.573, 94.657, 110.28, 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 18 16.00 O 1059 8.00 N 948 7.00 C 3499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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: 0.44 Conformation dependent library (CDL) restraints added in 218.0 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1282 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 17 sheets defined 6.8% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.791A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 53 through 55 No H-bonds generated for 'chain 'M' and resid 53 through 55' Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 53 through 55 No H-bonds generated for 'chain 'O' and resid 53 through 55' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.520A pdb=" N ASP O 86 " --> pdb=" O ARG O 83 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR O 87 " --> pdb=" O ALA O 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 83 through 87' Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.601A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.358A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.473A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.473A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.738A pdb=" N VAL M 78 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.485A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR M 58 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.138A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.857A pdb=" N GLU N 90 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR N 97 " --> pdb=" O GLU N 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.600A pdb=" N GLY O 10 " --> pdb=" O LEU O 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR O 110 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS O 92 " --> pdb=" O GLY O 104 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY O 106 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR O 90 " --> pdb=" O GLY O 106 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU O 108 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA O 88 " --> pdb=" O LEU O 108 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 18 through 22 Processing sheet with id=AB6, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.661A pdb=" N PHE P 71 " --> pdb=" O CYS P 23 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER P 65 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.518A pdb=" N ALA P 13 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.518A pdb=" N ALA P 13 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU P 90 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR P 97 " --> pdb=" O GLU P 90 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 426 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: 0.86 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1777 1.34 - 1.46: 1502 1.46 - 1.58: 2361 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 5664 Sorted by residual: bond pdb=" N ILE N 29 " pdb=" CA ILE N 29 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.07e-02 8.73e+03 1.13e+01 bond pdb=" N PHE N 28 " pdb=" CA PHE N 28 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.06e+00 bond pdb=" N GLN N 27 " pdb=" CA GLN N 27 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.41e-02 5.03e+03 5.49e+00 bond pdb=" N GLY P 66 " pdb=" CA GLY P 66 " ideal model delta sigma weight residual 1.450 1.477 -0.027 1.19e-02 7.06e+03 5.15e+00 bond pdb=" N SER P 67 " pdb=" CA SER P 67 " ideal model delta sigma weight residual 1.461 1.488 -0.027 1.20e-02 6.94e+03 5.14e+00 ... (remaining 5659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 7321 1.34 - 2.68: 280 2.68 - 4.01: 73 4.01 - 5.35: 10 5.35 - 6.69: 2 Bond angle restraints: 7686 Sorted by residual: angle pdb=" CA GLY P 66 " pdb=" C GLY P 66 " pdb=" O GLY P 66 " ideal model delta sigma weight residual 122.56 117.53 5.03 1.03e+00 9.43e-01 2.38e+01 angle pdb=" N ILE N 29 " pdb=" CA ILE N 29 " pdb=" C ILE N 29 " ideal model delta sigma weight residual 113.10 108.79 4.31 9.70e-01 1.06e+00 1.98e+01 angle pdb=" N SER P 67 " pdb=" CA SER P 67 " pdb=" C SER P 67 " ideal model delta sigma weight residual 107.93 114.62 -6.69 1.65e+00 3.67e-01 1.64e+01 angle pdb=" CA SER N 30 " pdb=" C SER N 30 " pdb=" O SER N 30 " ideal model delta sigma weight residual 121.54 117.98 3.56 1.16e+00 7.43e-01 9.40e+00 angle pdb=" CA GLN N 27 " pdb=" C GLN N 27 " pdb=" O GLN N 27 " ideal model delta sigma weight residual 121.40 118.21 3.19 1.11e+00 8.12e-01 8.25e+00 ... (remaining 7681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2877 17.99 - 35.99: 326 35.99 - 53.98: 90 53.98 - 71.98: 15 71.98 - 89.97: 5 Dihedral angle restraints: 3313 sinusoidal: 1295 harmonic: 2018 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 152.96 -59.96 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 59.98 33.02 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 64.80 28.20 1 1.00e+01 1.00e-02 1.14e+01 ... (remaining 3310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 521 0.034 - 0.067: 187 0.067 - 0.101: 53 0.101 - 0.134: 56 0.134 - 0.168: 4 Chirality restraints: 821 Sorted by residual: chirality pdb=" CA ILE N 29 " pdb=" N ILE N 29 " pdb=" C ILE N 29 " pdb=" CB ILE N 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA SER P 67 " pdb=" N SER P 67 " pdb=" C SER P 67 " pdb=" CB SER P 67 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE M 34 " pdb=" N ILE M 34 " pdb=" C ILE M 34 " pdb=" CB ILE M 34 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 818 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 127 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO G 128 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 128 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 128 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP O 98 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" CG ASP O 98 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP O 98 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP O 98 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 107 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO G 108 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " 0.023 5.00e-02 4.00e+02 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 93 2.58 - 3.16: 4600 3.16 - 3.74: 8215 3.74 - 4.32: 11615 4.32 - 4.90: 19408 Nonbonded interactions: 43931 Sorted by model distance: nonbonded pdb=" OD1 ASP N 82 " pdb=" OH TYR N 86 " model vdw 1.998 3.040 nonbonded pdb=" OE1 GLN H 1 " pdb=" OG1 THR P 72 " model vdw 2.080 3.040 nonbonded pdb=" OE2 GLU N 90 " pdb=" OG1 THR N 97 " model vdw 2.089 3.040 nonbonded pdb=" N GLU M 46 " pdb=" OE1 GLU M 46 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP P 17 " pdb=" N ARG P 18 " model vdw 2.113 3.120 ... (remaining 43926 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 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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 group one per residue 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: 3.100 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.003 0.044 5670 Z= 0.173 Angle : 0.630 6.689 7698 Z= 0.355 Chirality : 0.047 0.168 821 Planarity : 0.004 0.051 986 Dihedral : 16.472 89.973 2013 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.38 % Favored : 93.19 % Rotamer: Outliers : 0.17 % Allowed : 27.79 % Favored : 72.05 % 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: 0.11 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.51 (0.32), residues: 279 loop : -0.17 (0.35), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 96 TYR 0.015 0.001 TYR M 32 PHE 0.012 0.001 PHE P 28 TRP 0.013 0.001 TRP M 47 HIS 0.004 0.001 HIS M 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 ( 5664) covalent geometry : angle 0.62966 / 0.35 ( 7686) SS BOND : bond 0.00207 / 0.09 ( 6) SS BOND : angle 0.56278 / 0.38 ( 12) hydrogen bonds : bond 0.26275 / 17.61 ( 176) hydrogen bonds : angle 11.64358 / 8.02 ( 426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: H 21 SER cc_start: 0.7337 (t) cc_final: 0.7070 (p) REVERT: H 36 TRP cc_start: 0.8949 (m100) cc_final: 0.8636 (m100) REVERT: H 56 ASN cc_start: 0.7424 (m-40) cc_final: 0.7202 (t0) REVERT: H 95 ASN cc_start: 0.8878 (t0) cc_final: 0.8005 (t0) REVERT: H 97 TYR cc_start: 0.8373 (m-80) cc_final: 0.7905 (m-80) REVERT: L 4 MET cc_start: 0.8072 (mmm) cc_final: 0.7261 (mmm) REVERT: L 82 ASP cc_start: 0.7328 (t0) cc_final: 0.6969 (t0) REVERT: M 35 HIS cc_start: 0.7826 (m-70) cc_final: 0.7561 (m170) REVERT: M 98 ASP cc_start: 0.8054 (t0) cc_final: 0.7488 (t0) REVERT: N 33 LEU cc_start: 0.8292 (mp) cc_final: 0.8048 (mp) REVERT: N 42 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8115 (tptt) REVERT: N 45 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8082 (tttp) REVERT: P 42 LYS cc_start: 0.8531 (mtpp) cc_final: 0.7932 (mtmt) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.0700 time to fit residues: 23.7448 Evaluate side-chains 196 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 107 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.171636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144426 restraints weight = 8682.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148460 restraints weight = 5030.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150962 restraints weight = 3539.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152632 restraints weight = 2825.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153665 restraints weight = 2421.863| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5670 Z= 0.178 Angle : 0.700 8.385 7698 Z= 0.378 Chirality : 0.049 0.164 821 Planarity : 0.005 0.039 986 Dihedral : 4.555 18.870 775 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.52 % Favored : 93.19 % Rotamer: Outliers : 6.99 % Allowed : 25.62 % Favored : 67.39 % 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: 0.21 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.84 (0.34), residues: 240 loop : -0.22 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 96 TYR 0.017 0.002 TYR N 86 PHE 0.020 0.002 PHE N 71 TRP 0.015 0.002 TRP M 47 HIS 0.005 0.002 HIS O 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 5664) covalent geometry : angle 0.69957 / 0.38 ( 7686) SS BOND : bond 0.00321 / 0.16 ( 6) SS BOND : angle 0.72550 / 0.49 ( 12) hydrogen bonds : bond 0.04218 / 2.87 ( 176) hydrogen bonds : angle 7.54793 / 5.28 ( 426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 113 ASN cc_start: 0.9006 (t0) cc_final: 0.8392 (t0) REVERT: H 81 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: H 95 ASN cc_start: 0.9160 (t0) cc_final: 0.8510 (t0) REVERT: H 96 PHE cc_start: 0.8376 (p90) cc_final: 0.8122 (p90) REVERT: L 4 MET cc_start: 0.7825 (mmm) cc_final: 0.7464 (mmm) REVERT: L 82 ASP cc_start: 0.7138 (t0) cc_final: 0.6653 (t0) REVERT: M 35 HIS cc_start: 0.7753 (m-70) cc_final: 0.7127 (m-70) REVERT: M 90 TYR cc_start: 0.8763 (m-80) cc_final: 0.8244 (m-10) REVERT: M 99 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8516 (tpp80) REVERT: N 42 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8247 (tptt) REVERT: N 45 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8091 (tttp) REVERT: N 50 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7868 (mtpt) REVERT: O 17 SER cc_start: 0.7832 (m) cc_final: 0.7629 (p) REVERT: P 42 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8062 (mtmt) outliers start: 42 outliers final: 27 residues processed: 234 average time/residue: 0.0745 time to fit residues: 22.3412 Evaluate side-chains 227 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 50 LYS Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 HIS P 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143241 restraints weight = 8660.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147085 restraints weight = 5054.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149612 restraints weight = 3593.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151030 restraints weight = 2871.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152167 restraints weight = 2500.238| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5670 Z= 0.166 Angle : 0.652 7.963 7698 Z= 0.351 Chirality : 0.049 0.232 821 Planarity : 0.004 0.034 986 Dihedral : 4.595 20.200 775 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.52 % Favored : 93.19 % Rotamer: Outliers : 7.15 % Allowed : 27.29 % Favored : 65.56 % 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: 0.32 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.98 (0.33), residues: 258 loop : -0.24 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 31 TYR 0.018 0.001 TYR M 32 PHE 0.013 0.002 PHE N 71 TRP 0.012 0.001 TRP M 47 HIS 0.004 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 5664) covalent geometry : angle 0.65143 / 0.35 ( 7686) SS BOND : bond 0.00661 / 0.33 ( 6) SS BOND : angle 0.81948 / 0.55 ( 12) hydrogen bonds : bond 0.03481 / 2.35 ( 176) hydrogen bonds : angle 6.75551 / 4.76 ( 426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: H 95 ASN cc_start: 0.9164 (t0) cc_final: 0.8607 (t0) REVERT: L 4 MET cc_start: 0.8019 (mmm) cc_final: 0.7491 (mmm) REVERT: O 17 SER cc_start: 0.7946 (m) cc_final: 0.7736 (p) REVERT: P 4 MET cc_start: 0.8474 (tpp) cc_final: 0.8121 (mmm) outliers start: 43 outliers final: 33 residues processed: 224 average time/residue: 0.0805 time to fit residues: 23.0410 Evaluate side-chains 228 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS M 56 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142090 restraints weight = 8681.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145959 restraints weight = 5064.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148416 restraints weight = 3604.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.150016 restraints weight = 2893.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150845 restraints weight = 2494.983| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5670 Z= 0.168 Angle : 0.641 8.717 7698 Z= 0.344 Chirality : 0.048 0.161 821 Planarity : 0.004 0.040 986 Dihedral : 4.579 19.998 775 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.10 % Favored : 92.61 % Rotamer: Outliers : 8.32 % Allowed : 25.96 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.88 (0.33), residues: 258 loop : -0.31 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.012 0.001 TYR L 94 PHE 0.025 0.002 PHE M 96 TRP 0.024 0.002 TRP H 36 HIS 0.005 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 5664) covalent geometry : angle 0.64028 / 0.34 ( 7686) SS BOND : bond 0.00303 / 0.15 ( 6) SS BOND : angle 0.94518 / 0.56 ( 12) hydrogen bonds : bond 0.03100 / 2.10 ( 176) hydrogen bonds : angle 6.38042 / 4.49 ( 426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: H 95 ASN cc_start: 0.9152 (t0) cc_final: 0.8670 (t0) REVERT: L 4 MET cc_start: 0.8122 (mmm) cc_final: 0.7442 (mmm) REVERT: M 99 ARG cc_start: 0.8661 (tpp80) cc_final: 0.8423 (tpp80) REVERT: N 4 MET cc_start: 0.7361 (mmm) cc_final: 0.7121 (mmt) REVERT: N 6 GLN cc_start: 0.7110 (mp10) cc_final: 0.6630 (mt0) REVERT: N 90 GLU cc_start: 0.7454 (pm20) cc_final: 0.6942 (pm20) REVERT: O 17 SER cc_start: 0.8086 (m) cc_final: 0.7848 (p) REVERT: O 71 ARG cc_start: 0.7401 (tpt-90) cc_final: 0.7036 (tpt170) REVERT: O 72 ASP cc_start: 0.7534 (t0) cc_final: 0.7241 (t0) REVERT: P 4 MET cc_start: 0.8471 (tpp) cc_final: 0.7979 (mmm) REVERT: P 42 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8295 (mtmt) outliers start: 50 outliers final: 41 residues processed: 226 average time/residue: 0.0753 time to fit residues: 22.0287 Evaluate side-chains 239 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** 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 = 0.3978 r_free = 0.3978 target = 0.165621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135919 restraints weight = 8900.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139949 restraints weight = 5182.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142494 restraints weight = 3683.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144068 restraints weight = 2971.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144978 restraints weight = 2585.479| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5670 Z= 0.174 Angle : 0.641 9.421 7698 Z= 0.344 Chirality : 0.048 0.162 821 Planarity : 0.004 0.038 986 Dihedral : 4.575 19.913 775 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.39 % Favored : 92.32 % Rotamer: Outliers : 9.48 % Allowed : 24.96 % Favored : 65.56 % 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: 0.13 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.85 (0.34), residues: 240 loop : -0.33 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.012 0.001 TYR O 91 PHE 0.028 0.002 PHE M 96 TRP 0.013 0.002 TRP M 47 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 5664) covalent geometry : angle 0.63940 / 0.34 ( 7686) SS BOND : bond 0.00193 / 0.10 ( 6) SS BOND : angle 1.15502 / 0.66 ( 12) hydrogen bonds : bond 0.03046 / 2.06 ( 176) hydrogen bonds : angle 6.21420 / 4.40 ( 426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.210 Fit side-chains REVERT: H 81 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: H 95 ASN cc_start: 0.9241 (t0) cc_final: 0.8749 (t0) REVERT: L 4 MET cc_start: 0.8228 (mmm) cc_final: 0.7413 (mmm) REVERT: M 99 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8444 (tpp80) REVERT: N 6 GLN cc_start: 0.7064 (mp10) cc_final: 0.6691 (mt0) REVERT: N 42 LYS cc_start: 0.8530 (ptpt) cc_final: 0.8222 (ptpt) REVERT: O 17 SER cc_start: 0.8093 (m) cc_final: 0.7884 (p) REVERT: P 4 MET cc_start: 0.8566 (tpp) cc_final: 0.8117 (mmm) outliers start: 57 outliers final: 44 residues processed: 233 average time/residue: 0.0760 time to fit residues: 22.8875 Evaluate side-chains 242 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.0470 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136669 restraints weight = 8810.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140730 restraints weight = 5097.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143285 restraints weight = 3612.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144975 restraints weight = 2900.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145795 restraints weight = 2507.559| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5670 Z= 0.145 Angle : 0.642 9.590 7698 Z= 0.344 Chirality : 0.048 0.216 821 Planarity : 0.004 0.051 986 Dihedral : 4.548 20.074 775 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.54 % Favored : 92.17 % Rotamer: Outliers : 7.82 % Allowed : 28.45 % Favored : 63.73 % 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: 0.16 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.89 (0.34), residues: 240 loop : -0.32 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.014 0.001 TYR M 90 PHE 0.031 0.002 PHE M 96 TRP 0.014 0.001 TRP M 47 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5664) covalent geometry : angle 0.63885 / 0.34 ( 7686) SS BOND : bond 0.00278 / 0.13 ( 6) SS BOND : angle 1.71725 / 0.95 ( 12) hydrogen bonds : bond 0.02987 / 2.05 ( 176) hydrogen bonds : angle 6.04786 / 4.27 ( 426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: H 95 ASN cc_start: 0.9204 (t0) cc_final: 0.8634 (t0) REVERT: L 4 MET cc_start: 0.8184 (mmm) cc_final: 0.7300 (mmm) REVERT: M 99 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8431 (tpp80) REVERT: N 6 GLN cc_start: 0.7004 (mp10) cc_final: 0.6562 (mt0) REVERT: N 42 LYS cc_start: 0.8487 (ptpt) cc_final: 0.8207 (ptpt) REVERT: O 17 SER cc_start: 0.8167 (m) cc_final: 0.7936 (p) REVERT: P 4 MET cc_start: 0.8550 (tpp) cc_final: 0.8104 (mmm) outliers start: 47 outliers final: 38 residues processed: 236 average time/residue: 0.0749 time to fit residues: 22.6910 Evaluate side-chains 240 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 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 = 0.3948 r_free = 0.3948 target = 0.163480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134958 restraints weight = 8899.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138795 restraints weight = 5175.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141217 restraints weight = 3677.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142587 restraints weight = 2958.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143689 restraints weight = 2598.740| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5670 Z= 0.162 Angle : 0.658 9.547 7698 Z= 0.352 Chirality : 0.048 0.170 821 Planarity : 0.004 0.040 986 Dihedral : 4.602 19.464 775 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.12 % Favored : 91.59 % Rotamer: Outliers : 7.99 % Allowed : 27.62 % Favored : 64.39 % 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: 0.20 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.92 (0.35), residues: 240 loop : -0.29 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 31 TYR 0.014 0.001 TYR M 90 PHE 0.035 0.003 PHE M 96 TRP 0.036 0.002 TRP M 36 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 5664) covalent geometry : angle 0.65384 / 0.35 ( 7686) SS BOND : bond 0.00582 / 0.29 ( 6) SS BOND : angle 1.97379 / 1.06 ( 12) hydrogen bonds : bond 0.02999 / 2.04 ( 176) hydrogen bonds : angle 6.01614 / 4.24 ( 426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.155 Fit side-chains REVERT: H 95 ASN cc_start: 0.9136 (t0) cc_final: 0.8673 (t0) REVERT: L 4 MET cc_start: 0.8261 (mmm) cc_final: 0.7297 (mmm) REVERT: M 37 VAL cc_start: 0.9065 (t) cc_final: 0.8845 (p) REVERT: M 99 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8431 (tpp80) REVERT: N 6 GLN cc_start: 0.6883 (mp10) cc_final: 0.6553 (mt0) REVERT: N 42 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8209 (ptpt) REVERT: O 17 SER cc_start: 0.8207 (m) cc_final: 0.7984 (p) REVERT: P 4 MET cc_start: 0.8527 (tpp) cc_final: 0.8029 (mmm) outliers start: 48 outliers final: 42 residues processed: 229 average time/residue: 0.0792 time to fit residues: 23.0694 Evaluate side-chains 244 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 13 optimal weight: 0.0000 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 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 = 0.3978 r_free = 0.3978 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137977 restraints weight = 8834.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141888 restraints weight = 5137.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144374 restraints weight = 3636.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145704 restraints weight = 2910.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146898 restraints weight = 2546.930| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5670 Z= 0.137 Angle : 0.655 9.819 7698 Z= 0.350 Chirality : 0.048 0.196 821 Planarity : 0.004 0.042 986 Dihedral : 4.511 17.311 775 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.96 % Favored : 92.75 % Rotamer: Outliers : 7.65 % Allowed : 27.45 % Favored : 64.89 % 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: 0.26 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.99 (0.35), residues: 240 loop : -0.27 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 19 TYR 0.012 0.001 TYR H 102 PHE 0.035 0.002 PHE M 96 TRP 0.029 0.002 TRP M 36 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5664) covalent geometry : angle 0.65084 / 0.35 ( 7686) SS BOND : bond 0.00348 / 0.17 ( 6) SS BOND : angle 1.89294 / 1.09 ( 12) hydrogen bonds : bond 0.02942 / 2.01 ( 176) hydrogen bonds : angle 5.96750 / 4.20 ( 426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: G 119 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: H 81 GLN cc_start: 0.7779 (tt0) cc_final: 0.6529 (tt0) REVERT: H 95 ASN cc_start: 0.9115 (t0) cc_final: 0.8596 (t0) REVERT: L 4 MET cc_start: 0.8260 (mmm) cc_final: 0.7538 (mmm) REVERT: M 37 VAL cc_start: 0.9085 (t) cc_final: 0.8834 (p) REVERT: M 78 VAL cc_start: 0.8674 (m) cc_final: 0.8393 (p) REVERT: M 99 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8416 (tpp80) REVERT: N 6 GLN cc_start: 0.6640 (mp10) cc_final: 0.6331 (mt0) REVERT: O 17 SER cc_start: 0.8235 (m) cc_final: 0.8020 (p) REVERT: O 99 ARG cc_start: 0.6838 (mmm160) cc_final: 0.6606 (mmm-85) REVERT: P 4 MET cc_start: 0.8507 (tpp) cc_final: 0.8084 (mmm) outliers start: 46 outliers final: 34 residues processed: 234 average time/residue: 0.0756 time to fit residues: 22.8317 Evaluate side-chains 243 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135219 restraints weight = 8846.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139047 restraints weight = 5192.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141427 restraints weight = 3721.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142754 restraints weight = 3016.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143880 restraints weight = 2650.803| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5670 Z= 0.175 Angle : 0.692 10.010 7698 Z= 0.366 Chirality : 0.048 0.155 821 Planarity : 0.005 0.041 986 Dihedral : 4.663 17.972 775 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.41 % Favored : 91.30 % Rotamer: Outliers : 6.99 % Allowed : 28.29 % Favored : 64.73 % 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: 0.20 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.94 (0.35), residues: 240 loop : -0.31 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.019 0.002 TYR H 102 PHE 0.043 0.003 PHE M 96 TRP 0.021 0.002 TRP M 36 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 5664) covalent geometry : angle 0.68777 / 0.36 ( 7686) SS BOND : bond 0.00365 / 0.18 ( 6) SS BOND : angle 2.08361 / 1.18 ( 12) hydrogen bonds : bond 0.03010 / 2.05 ( 176) hydrogen bonds : angle 6.05158 / 4.26 ( 426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: G 119 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: H 70 SER cc_start: 0.7615 (t) cc_final: 0.6829 (p) REVERT: H 81 GLN cc_start: 0.7870 (tt0) cc_final: 0.6790 (tt0) REVERT: L 4 MET cc_start: 0.8296 (mmm) cc_final: 0.7460 (mmm) REVERT: M 27 PHE cc_start: 0.8024 (p90) cc_final: 0.7633 (p90) REVERT: M 99 ARG cc_start: 0.8617 (tpp80) cc_final: 0.8391 (tpp80) REVERT: N 6 GLN cc_start: 0.6761 (mp10) cc_final: 0.6515 (mt0) REVERT: O 17 SER cc_start: 0.8231 (m) cc_final: 0.8002 (p) REVERT: O 85 GLU cc_start: 0.8448 (tp30) cc_final: 0.8202 (tp30) REVERT: P 4 MET cc_start: 0.8519 (tpp) cc_final: 0.7958 (mmm) outliers start: 42 outliers final: 37 residues processed: 226 average time/residue: 0.0776 time to fit residues: 22.4126 Evaluate side-chains 240 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139311 restraints weight = 8876.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143108 restraints weight = 5134.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145345 restraints weight = 3661.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147146 restraints weight = 2973.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148051 restraints weight = 2558.415| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5670 Z= 0.140 Angle : 0.694 10.885 7698 Z= 0.366 Chirality : 0.048 0.154 821 Planarity : 0.005 0.068 986 Dihedral : 4.603 18.553 775 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.25 % Favored : 92.46 % Rotamer: Outliers : 5.99 % Allowed : 29.45 % Favored : 64.56 % 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: 0.17 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.97 (0.35), residues: 240 loop : -0.37 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 19 TYR 0.021 0.001 TYR H 102 PHE 0.044 0.002 PHE M 96 TRP 0.026 0.002 TRP M 36 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5664) covalent geometry : angle 0.69010 / 0.36 ( 7686) SS BOND : bond 0.00346 / 0.16 ( 6) SS BOND : angle 2.01988 / 1.15 ( 12) hydrogen bonds : bond 0.02928 / 2.00 ( 176) hydrogen bonds : angle 5.96695 / 4.19 ( 426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: G 119 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: H 70 SER cc_start: 0.7560 (t) cc_final: 0.6762 (p) REVERT: H 81 GLN cc_start: 0.7796 (tt0) cc_final: 0.6877 (tt0) REVERT: H 95 ASN cc_start: 0.9113 (t0) cc_final: 0.8574 (t0) REVERT: H 102 TYR cc_start: 0.5924 (m-10) cc_final: 0.5398 (m-10) REVERT: L 4 MET cc_start: 0.8253 (mmm) cc_final: 0.7496 (mmm) REVERT: L 36 TYR cc_start: 0.9285 (m-80) cc_final: 0.9034 (m-80) REVERT: M 99 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8379 (tpp80) REVERT: N 6 GLN cc_start: 0.6736 (mp10) cc_final: 0.6533 (mt0) REVERT: O 17 SER cc_start: 0.8161 (m) cc_final: 0.7944 (p) REVERT: P 4 MET cc_start: 0.8482 (tpp) cc_final: 0.7858 (mmm) outliers start: 36 outliers final: 33 residues processed: 227 average time/residue: 0.0810 time to fit residues: 23.3317 Evaluate side-chains 236 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 93 HIS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 0.0030 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 38 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 overall best weight: 0.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 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 = 0.4044 r_free = 0.4044 target = 0.172105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144484 restraints weight = 8918.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148308 restraints weight = 5262.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150868 restraints weight = 3778.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152467 restraints weight = 3033.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153216 restraints weight = 2624.532| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5670 Z= 0.132 Angle : 0.687 8.716 7698 Z= 0.364 Chirality : 0.048 0.169 821 Planarity : 0.005 0.076 986 Dihedral : 4.506 18.004 775 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.03 % Rotamer: Outliers : 5.49 % Allowed : 29.45 % Favored : 65.06 % 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: 0.17 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.96 (0.35), residues: 240 loop : -0.36 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 19 TYR 0.018 0.001 TYR P 49 PHE 0.041 0.002 PHE M 96 TRP 0.026 0.002 TRP M 36 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 5664) covalent geometry : angle 0.68240 / 0.36 ( 7686) SS BOND : bond 0.00308 / 0.15 ( 6) SS BOND : angle 2.04508 / 1.17 ( 12) hydrogen bonds : bond 0.02820 / 1.94 ( 176) hydrogen bonds : angle 5.86876 / 4.12 ( 426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1200.21 seconds wall clock time: 21 minutes 29.86 seconds (1289.86 seconds total)