Starting phenix.real_space_refine on Fri Oct 10 13:21:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6m_41072/10_2025/8t6m_41072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6m_41072/10_2025/8t6m_41072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t6m_41072/10_2025/8t6m_41072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6m_41072/10_2025/8t6m_41072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6m_41072/10_2025/8t6m_41072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6m_41072/10_2025/8t6m_41072.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 22 5.16 5 C 3733 2.51 5 N 1003 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5903 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 945 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1476 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "F" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 801 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 1.64, per 1000 atoms: 0.28 Number of scatterers: 5903 At special positions: 0 Unit cell: (75.24, 111.54, 106.92, 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 22 16.00 O 1145 8.00 N 1003 7.00 C 3733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS B 113 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 112 " distance=2.03 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 81 " distance=2.03 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: 0.50 Conformation dependent library (CDL) restraints added in 227.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 16 sheets defined 14.3% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.840A pdb=" N ILE A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.076A pdb=" N PHE C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'E' and resid 49 through 54 Processing helix chain 'E' and resid 56 through 86 removed outlier: 3.607A pdb=" N TRP E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'E' and resid 151 through 162 removed outlier: 3.649A pdb=" N GLN E 155 " --> pdb=" O HIS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 175 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 23 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.668A pdb=" N TRP B 54 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 68 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 52 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.584A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 109 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.584A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 109 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.625A pdb=" N GLN D 93 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 73 through 75 removed outlier: 6.881A pdb=" N TRP D 52 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR D 66 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP D 50 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR D 49 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS D 111 " --> pdb=" O TRP D 128 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP D 128 " --> pdb=" O CYS D 111 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS D 113 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR D 117 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE D 122 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 73 through 75 removed outlier: 6.881A pdb=" N TRP D 52 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR D 66 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP D 50 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR D 49 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 46 through 47 removed outlier: 5.256A pdb=" N GLN E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 28 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG E 114 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE E 124 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR E 118 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP E 122 " --> pdb=" O TYR E 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 9 through 12 removed outlier: 5.900A pdb=" N PHE F 63 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'F' and resid 37 through 38 276 hydrogen bonds defined for protein. 693 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: 1.13 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1875 1.33 - 1.45: 1265 1.45 - 1.57: 2883 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 6053 Sorted by residual: bond pdb=" C PRO D 56 " pdb=" O PRO D 56 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 3.99e+00 bond pdb=" CA ASN F 22 " pdb=" C ASN F 22 " ideal model delta sigma weight residual 1.524 1.500 0.023 1.26e-02 6.30e+03 3.44e+00 bond pdb=" CA ALA E 24 " pdb=" C ALA E 24 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.24e-02 6.50e+03 3.42e+00 bond pdb=" CA GLY E 26 " pdb=" C GLY E 26 " ideal model delta sigma weight residual 1.520 1.507 0.013 7.30e-03 1.88e+04 3.39e+00 bond pdb=" CA SER C 77 " pdb=" C SER C 77 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.30e-02 5.92e+03 3.35e+00 ... (remaining 6048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 6719 1.16 - 2.31: 1235 2.31 - 3.47: 205 3.47 - 4.62: 49 4.62 - 5.78: 14 Bond angle restraints: 8222 Sorted by residual: angle pdb=" C GLY E 56 " pdb=" N PRO E 57 " pdb=" CA PRO E 57 " ideal model delta sigma weight residual 119.05 124.51 -5.46 1.11e+00 8.12e-01 2.42e+01 angle pdb=" C ASP E 119 " pdb=" CA ASP E 119 " pdb=" CB ASP E 119 " ideal model delta sigma weight residual 117.23 111.46 5.77 1.36e+00 5.41e-01 1.80e+01 angle pdb=" O PRO D 56 " pdb=" C PRO D 56 " pdb=" N PRO D 57 " ideal model delta sigma weight residual 121.15 123.10 -1.95 4.70e-01 4.53e+00 1.72e+01 angle pdb=" C LEU A 71 " pdb=" CA LEU A 71 " pdb=" CB LEU A 71 " ideal model delta sigma weight residual 116.54 111.90 4.64 1.15e+00 7.56e-01 1.63e+01 angle pdb=" N SER C 89 " pdb=" CA SER C 89 " pdb=" C SER C 89 " ideal model delta sigma weight residual 108.60 114.10 -5.50 1.46e+00 4.69e-01 1.42e+01 ... (remaining 8217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 3280 16.70 - 33.40: 236 33.40 - 50.10: 46 50.10 - 66.80: 5 66.80 - 83.49: 4 Dihedral angle restraints: 3571 sinusoidal: 1419 harmonic: 2152 Sorted by residual: dihedral pdb=" CA SER C 31 " pdb=" C SER C 31 " pdb=" N PRO C 32 " pdb=" CA PRO C 32 " ideal model delta harmonic sigma weight residual 0.00 -28.90 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CB CYS F 26 " pdb=" SG CYS F 26 " pdb=" SG CYS F 81 " pdb=" CB CYS F 81 " ideal model delta sinusoidal sigma weight residual 93.00 139.09 -46.09 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA GLY D 118 " pdb=" C GLY D 118 " pdb=" N SER D 119 " pdb=" CA SER D 119 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 3568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 662 0.033 - 0.065: 137 0.065 - 0.097: 50 0.097 - 0.130: 25 0.130 - 0.162: 11 Chirality restraints: 885 Sorted by residual: chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE B 55 " pdb=" N ILE B 55 " pdb=" C ILE B 55 " pdb=" CB ILE B 55 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE A 45 " pdb=" N ILE A 45 " pdb=" C ILE A 45 " pdb=" CB ILE A 45 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 882 not shown) Planarity restraints: 1055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 72 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO F 73 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 73 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 73 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 24 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 25 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 90 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO F 91 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 91 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 91 " 0.017 5.00e-02 4.00e+02 ... (remaining 1052 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 966 2.76 - 3.30: 6297 3.30 - 3.83: 10895 3.83 - 4.37: 12918 4.37 - 4.90: 21971 Nonbonded interactions: 53047 Sorted by model distance: nonbonded pdb=" OD1 ASP B 107 " pdb=" N THR B 108 " model vdw 2.226 3.120 nonbonded pdb=" O CYS C 112 " pdb=" N GLY C 123 " model vdw 2.351 3.120 nonbonded pdb=" C ASP B 107 " pdb=" OD1 ASP B 107 " model vdw 2.389 3.270 nonbonded pdb=" OG SER C 84 " pdb=" O GLN E 87 " model vdw 2.446 3.040 nonbonded pdb=" O LYS E 68 " pdb=" OG SER E 71 " model vdw 2.447 3.040 ... (remaining 53042 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.880 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4908 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 : 0.007 0.033 6060 Z= 0.474 Angle : 0.959 5.777 8236 Z= 0.646 Chirality : 0.039 0.162 885 Planarity : 0.004 0.041 1055 Dihedral : 11.951 83.494 2180 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.61 % Allowed : 5.99 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 1.36 (0.30), residues: 732 helix: 2.26 (0.54), residues: 75 sheet: 1.45 (0.31), residues: 303 loop : 0.17 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 108 TYR 0.015 0.002 TYR E 99 PHE 0.013 0.002 PHE A 95 TRP 0.010 0.001 TRP B 133 HIS 0.005 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 6053) covalent geometry : angle 0.95938 ( 8222) SS BOND : bond 0.00356 ( 7) SS BOND : angle 0.75201 ( 14) hydrogen bonds : bond 0.19393 ( 247) hydrogen bonds : angle 8.37810 ( 693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.243 Fit side-chains REVERT: B 141 VAL cc_start: 0.4614 (t) cc_final: 0.4409 (t) REVERT: C 109 SER cc_start: 0.6135 (m) cc_final: 0.5875 (t) REVERT: D 91 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6589 (tt0) REVERT: E 132 SER cc_start: 0.6453 (m) cc_final: 0.6138 (m) REVERT: E 138 MET cc_start: 0.3059 (mtt) cc_final: 0.2794 (tmm) REVERT: F 90 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6959 (pt0) outliers start: 17 outliers final: 2 residues processed: 177 average time/residue: 0.0942 time to fit residues: 21.2258 Evaluate side-chains 116 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain D residue 22 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 57 GLN C 61 GLN D 19 GLN E 86 ASN F 3 GLN F 22 ASN F 84 ASN G 4 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117067 restraints weight = 7328.858| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.23 r_work: 0.3282 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6060 Z= 0.189 Angle : 0.657 7.284 8236 Z= 0.352 Chirality : 0.046 0.208 885 Planarity : 0.005 0.034 1055 Dihedral : 6.569 59.508 823 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.53 % Allowed : 11.67 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 1.36 (0.31), residues: 732 helix: 2.12 (0.55), residues: 75 sheet: 1.42 (0.31), residues: 302 loop : 0.25 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 90 TYR 0.019 0.002 TYR E 27 PHE 0.017 0.002 PHE C 34 TRP 0.012 0.002 TRP D 52 HIS 0.011 0.002 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6053) covalent geometry : angle 0.65639 ( 8222) SS BOND : bond 0.00627 ( 7) SS BOND : angle 1.00122 ( 14) hydrogen bonds : bond 0.04755 ( 247) hydrogen bonds : angle 5.96493 ( 693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7843 (ttt-90) cc_final: 0.7353 (ttt-90) REVERT: D 17 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.7028 (pt0) REVERT: D 46 GLU cc_start: 0.7854 (tt0) cc_final: 0.7590 (tt0) REVERT: E 138 MET cc_start: 0.4923 (mtt) cc_final: 0.4462 (tmm) REVERT: F 13 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.5335 (tpm170) REVERT: F 60 ASP cc_start: 0.7207 (m-30) cc_final: 0.6925 (t0) outliers start: 23 outliers final: 13 residues processed: 138 average time/residue: 0.0855 time to fit residues: 15.3645 Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN E 86 ASN G 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113332 restraints weight = 7344.377| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.23 r_work: 0.3227 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6060 Z= 0.185 Angle : 0.607 8.005 8236 Z= 0.325 Chirality : 0.044 0.205 885 Planarity : 0.004 0.034 1055 Dihedral : 5.779 62.184 820 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.76 % Allowed : 13.21 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 1.07 (0.31), residues: 732 helix: 1.78 (0.56), residues: 75 sheet: 1.26 (0.32), residues: 303 loop : 0.03 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 82 TYR 0.015 0.002 TYR E 27 PHE 0.014 0.002 PHE A 95 TRP 0.014 0.002 TRP B 133 HIS 0.006 0.002 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6053) covalent geometry : angle 0.60354 ( 8222) SS BOND : bond 0.00244 ( 7) SS BOND : angle 1.73318 ( 14) hydrogen bonds : bond 0.04492 ( 247) hydrogen bonds : angle 5.58484 ( 693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.287 Fit side-chains REVERT: B 89 LYS cc_start: 0.8367 (tttp) cc_final: 0.8144 (tttt) REVERT: E 103 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7357 (m) REVERT: E 138 MET cc_start: 0.5292 (mtt) cc_final: 0.4539 (tmm) REVERT: F 60 ASP cc_start: 0.7240 (m-30) cc_final: 0.6988 (t0) REVERT: F 84 ASN cc_start: 0.8473 (t0) cc_final: 0.8103 (m-40) outliers start: 31 outliers final: 21 residues processed: 135 average time/residue: 0.0775 time to fit residues: 13.9454 Evaluate side-chains 135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 GLN E 86 ASN E 87 GLN G 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112292 restraints weight = 7381.131| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.45 r_work: 0.3206 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 6060 Z= 0.157 Angle : 0.572 10.738 8236 Z= 0.303 Chirality : 0.044 0.258 885 Planarity : 0.004 0.038 1055 Dihedral : 5.508 59.709 820 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.15 % Allowed : 15.51 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.92 (0.31), residues: 732 helix: 1.73 (0.56), residues: 75 sheet: 1.20 (0.32), residues: 300 loop : -0.10 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 42 TYR 0.015 0.002 TYR E 27 PHE 0.012 0.002 PHE A 95 TRP 0.011 0.001 TRP B 133 HIS 0.005 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6053) covalent geometry : angle 0.56288 ( 8222) SS BOND : bond 0.00927 ( 7) SS BOND : angle 2.48074 ( 14) hydrogen bonds : bond 0.03923 ( 247) hydrogen bonds : angle 5.32127 ( 693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.276 Fit side-chains REVERT: B 89 LYS cc_start: 0.8382 (tttp) cc_final: 0.8144 (tttt) REVERT: B 100 MET cc_start: 0.8850 (ttp) cc_final: 0.8642 (mtm) REVERT: C 126 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8293 (t) REVERT: E 103 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7243 (m) REVERT: E 138 MET cc_start: 0.5070 (mtt) cc_final: 0.4261 (tmm) REVERT: F 60 ASP cc_start: 0.7198 (m-30) cc_final: 0.6944 (t0) REVERT: F 84 ASN cc_start: 0.8363 (t0) cc_final: 0.7994 (t0) outliers start: 27 outliers final: 15 residues processed: 113 average time/residue: 0.0805 time to fit residues: 12.1975 Evaluate side-chains 112 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 HIS E 86 ASN E 180 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112731 restraints weight = 7550.384| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.24 r_work: 0.3221 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 6060 Z= 0.158 Angle : 0.584 14.911 8236 Z= 0.307 Chirality : 0.044 0.291 885 Planarity : 0.004 0.035 1055 Dihedral : 5.414 59.068 820 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.45 % Allowed : 15.67 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.81 (0.31), residues: 732 helix: 1.75 (0.57), residues: 75 sheet: 1.13 (0.31), residues: 300 loop : -0.21 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.017 0.002 TYR E 27 PHE 0.013 0.001 PHE A 95 TRP 0.011 0.001 TRP B 133 HIS 0.005 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6053) covalent geometry : angle 0.57369 ( 8222) SS BOND : bond 0.00995 ( 7) SS BOND : angle 2.65521 ( 14) hydrogen bonds : bond 0.03898 ( 247) hydrogen bonds : angle 5.17595 ( 693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.243 Fit side-chains REVERT: A 26 ILE cc_start: 0.8198 (mp) cc_final: 0.7992 (mm) REVERT: A 93 THR cc_start: 0.8690 (p) cc_final: 0.8218 (t) REVERT: B 89 LYS cc_start: 0.8338 (tttp) cc_final: 0.8104 (tttt) REVERT: B 93 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7279 (mp10) REVERT: C 126 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8299 (t) REVERT: E 138 MET cc_start: 0.5259 (mtt) cc_final: 0.4469 (tmm) REVERT: E 158 VAL cc_start: 0.7771 (t) cc_final: 0.7537 (m) REVERT: F 84 ASN cc_start: 0.8336 (t0) cc_final: 0.8028 (t0) outliers start: 29 outliers final: 20 residues processed: 115 average time/residue: 0.0823 time to fit residues: 12.6450 Evaluate side-chains 118 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107285 restraints weight = 7478.921| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.45 r_work: 0.3128 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 6060 Z= 0.250 Angle : 0.647 13.253 8236 Z= 0.344 Chirality : 0.047 0.278 885 Planarity : 0.005 0.040 1055 Dihedral : 5.776 65.665 820 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.22 % Allowed : 15.36 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.45 (0.31), residues: 732 helix: 1.35 (0.58), residues: 75 sheet: 0.83 (0.31), residues: 312 loop : -0.40 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 82 TYR 0.027 0.003 TYR E 59 PHE 0.014 0.002 PHE A 95 TRP 0.015 0.002 TRP B 133 HIS 0.006 0.002 HIS F 52 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 6053) covalent geometry : angle 0.63920 ( 8222) SS BOND : bond 0.01011 ( 7) SS BOND : angle 2.50523 ( 14) hydrogen bonds : bond 0.04624 ( 247) hydrogen bonds : angle 5.45164 ( 693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.274 Fit side-chains REVERT: A 93 THR cc_start: 0.8683 (p) cc_final: 0.8209 (t) REVERT: B 93 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7300 (mp10) REVERT: C 126 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8436 (t) REVERT: E 59 TYR cc_start: 0.7503 (t80) cc_final: 0.7230 (t80) REVERT: E 138 MET cc_start: 0.5337 (mtt) cc_final: 0.4529 (tmm) REVERT: E 158 VAL cc_start: 0.7675 (t) cc_final: 0.7395 (m) REVERT: F 84 ASN cc_start: 0.8378 (t0) cc_final: 0.8015 (t0) outliers start: 34 outliers final: 24 residues processed: 123 average time/residue: 0.0800 time to fit residues: 13.2592 Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110175 restraints weight = 7517.427| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.40 r_work: 0.3183 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 6060 Z= 0.172 Angle : 0.592 15.724 8236 Z= 0.313 Chirality : 0.044 0.267 885 Planarity : 0.004 0.039 1055 Dihedral : 5.548 62.201 820 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.30 % Allowed : 16.59 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.47 (0.31), residues: 732 helix: 1.31 (0.57), residues: 75 sheet: 0.90 (0.31), residues: 310 loop : -0.42 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 82 TYR 0.021 0.002 TYR E 59 PHE 0.013 0.001 PHE A 95 TRP 0.012 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6053) covalent geometry : angle 0.58400 ( 8222) SS BOND : bond 0.00973 ( 7) SS BOND : angle 2.42252 ( 14) hydrogen bonds : bond 0.04015 ( 247) hydrogen bonds : angle 5.24187 ( 693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.245 Fit side-chains REVERT: A 93 THR cc_start: 0.8696 (p) cc_final: 0.8279 (t) REVERT: B 93 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7354 (mp10) REVERT: C 126 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8354 (t) REVERT: D 99 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8445 (mtpp) REVERT: E 59 TYR cc_start: 0.7493 (t80) cc_final: 0.7197 (t80) REVERT: E 138 MET cc_start: 0.5315 (mtt) cc_final: 0.4442 (tmm) REVERT: E 158 VAL cc_start: 0.7749 (t) cc_final: 0.7476 (m) REVERT: F 7 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7648 (mttp) REVERT: F 84 ASN cc_start: 0.8386 (t0) cc_final: 0.8027 (t0) outliers start: 28 outliers final: 23 residues processed: 119 average time/residue: 0.0788 time to fit residues: 12.6176 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN G 4 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109908 restraints weight = 7503.584| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.40 r_work: 0.3184 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 6060 Z= 0.173 Angle : 0.596 15.401 8236 Z= 0.315 Chirality : 0.044 0.262 885 Planarity : 0.004 0.038 1055 Dihedral : 5.451 61.212 820 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.45 % Allowed : 16.44 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.38 (0.31), residues: 732 helix: 1.31 (0.58), residues: 75 sheet: 0.80 (0.31), residues: 310 loop : -0.46 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 82 TYR 0.018 0.002 TYR E 59 PHE 0.012 0.001 PHE A 95 TRP 0.012 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6053) covalent geometry : angle 0.58782 ( 8222) SS BOND : bond 0.01061 ( 7) SS BOND : angle 2.48803 ( 14) hydrogen bonds : bond 0.03954 ( 247) hydrogen bonds : angle 5.16034 ( 693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.237 Fit side-chains REVERT: A 93 THR cc_start: 0.8735 (p) cc_final: 0.8329 (t) REVERT: B 93 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7349 (mp10) REVERT: C 126 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8353 (t) REVERT: D 99 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8442 (mtpp) REVERT: E 59 TYR cc_start: 0.7455 (t80) cc_final: 0.7224 (t80) REVERT: E 138 MET cc_start: 0.5331 (mtt) cc_final: 0.4459 (tmm) REVERT: E 158 VAL cc_start: 0.7778 (t) cc_final: 0.7538 (m) REVERT: F 7 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7687 (mttp) REVERT: F 84 ASN cc_start: 0.8392 (t0) cc_final: 0.8026 (t0) outliers start: 29 outliers final: 26 residues processed: 120 average time/residue: 0.0776 time to fit residues: 12.5519 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.137795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109280 restraints weight = 7520.021| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.33 r_work: 0.3186 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 6060 Z= 0.172 Angle : 0.587 15.147 8236 Z= 0.310 Chirality : 0.044 0.260 885 Planarity : 0.005 0.041 1055 Dihedral : 5.429 60.776 820 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.15 % Allowed : 16.74 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.35 (0.31), residues: 732 helix: 1.32 (0.58), residues: 75 sheet: 0.79 (0.31), residues: 310 loop : -0.49 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 82 TYR 0.017 0.002 TYR F 64 PHE 0.011 0.001 PHE A 95 TRP 0.011 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6053) covalent geometry : angle 0.57914 ( 8222) SS BOND : bond 0.01047 ( 7) SS BOND : angle 2.39541 ( 14) hydrogen bonds : bond 0.03899 ( 247) hydrogen bonds : angle 5.14386 ( 693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.267 Fit side-chains REVERT: A 93 THR cc_start: 0.8740 (p) cc_final: 0.8353 (t) REVERT: C 126 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8358 (t) REVERT: D 99 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8452 (mtpp) REVERT: E 138 MET cc_start: 0.5299 (mtt) cc_final: 0.4447 (tmm) REVERT: E 158 VAL cc_start: 0.7742 (t) cc_final: 0.7518 (m) REVERT: F 7 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7671 (mttp) REVERT: F 84 ASN cc_start: 0.8392 (t0) cc_final: 0.8020 (t0) outliers start: 27 outliers final: 26 residues processed: 114 average time/residue: 0.0793 time to fit residues: 12.1134 Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107118 restraints weight = 7620.002| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.40 r_work: 0.3142 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 6060 Z= 0.269 Angle : 0.668 15.479 8236 Z= 0.353 Chirality : 0.047 0.274 885 Planarity : 0.005 0.041 1055 Dihedral : 5.775 65.249 820 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.99 % Allowed : 17.36 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.08 (0.31), residues: 732 helix: 0.99 (0.57), residues: 75 sheet: 0.56 (0.31), residues: 314 loop : -0.59 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 82 TYR 0.048 0.003 TYR E 59 PHE 0.012 0.002 PHE E 8 TRP 0.016 0.002 TRP B 133 HIS 0.007 0.002 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 6053) covalent geometry : angle 0.66087 ( 8222) SS BOND : bond 0.01157 ( 7) SS BOND : angle 2.50315 ( 14) hydrogen bonds : bond 0.04575 ( 247) hydrogen bonds : angle 5.40267 ( 693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.236 Fit side-chains REVERT: A 93 THR cc_start: 0.8753 (p) cc_final: 0.8370 (t) REVERT: C 126 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8439 (t) REVERT: D 93 GLN cc_start: 0.8573 (mt0) cc_final: 0.8246 (mm-40) REVERT: E 45 MET cc_start: 0.8767 (tpp) cc_final: 0.8375 (tpt) REVERT: E 138 MET cc_start: 0.5515 (mtt) cc_final: 0.4666 (tmm) REVERT: F 1 MET cc_start: 0.6899 (mpp) cc_final: 0.4819 (ttt) REVERT: F 7 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7735 (mttp) REVERT: F 84 ASN cc_start: 0.8452 (t0) cc_final: 0.8175 (t0) outliers start: 26 outliers final: 24 residues processed: 107 average time/residue: 0.0756 time to fit residues: 11.0063 Evaluate side-chains 117 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109901 restraints weight = 7535.393| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.38 r_work: 0.3182 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6060 Z= 0.169 Angle : 0.593 14.964 8236 Z= 0.314 Chirality : 0.044 0.260 885 Planarity : 0.005 0.041 1055 Dihedral : 5.515 61.422 820 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.84 % Allowed : 17.36 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 aren not related in a simple way. whole: 0.14 (0.31), residues: 732 helix: 1.12 (0.57), residues: 75 sheet: 0.63 (0.31), residues: 312 loop : -0.61 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 82 TYR 0.046 0.002 TYR E 59 PHE 0.010 0.001 PHE A 95 TRP 0.011 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6053) covalent geometry : angle 0.58514 ( 8222) SS BOND : bond 0.01035 ( 7) SS BOND : angle 2.36638 ( 14) hydrogen bonds : bond 0.03884 ( 247) hydrogen bonds : angle 5.17855 ( 693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.47 seconds wall clock time: 37 minutes 46.08 seconds (2266.08 seconds total)