Starting phenix.real_space_refine on Sat May 10 10:11:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6m_41072/05_2025/8t6m_41072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6m_41072/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6m_41072/05_2025/8t6m_41072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6m_41072/05_2025/8t6m_41072.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6m_41072/05_2025/8t6m_41072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6m_41072/05_2025/8t6m_41072.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.57, per 1000 atoms: 0.94 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: 1.56 Conformation dependent library (CDL) restraints added in 919.4 milliseconds 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: 0.94 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: 1.70 Time building geometry restraints manager: 1.79 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: 6.700 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.910 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP B 133 HIS 0.005 0.001 HIS F 32 PHE 0.013 0.002 PHE A 95 TYR 0.015 0.002 TYR E 99 ARG 0.005 0.001 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.19393 ( 247) hydrogen bonds : angle 8.37810 ( 693) SS BOND : bond 0.00356 ( 7) SS BOND : angle 0.75201 ( 14) covalent geometry : bond 0.00650 ( 6053) covalent geometry : angle 0.95938 ( 8222) *********************** 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 : 0.692 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: 0.1960 time to fit residues: 44.0576 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 : 0.656 ------------------------------------------------------------------------------- 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 59 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 D 19 GLN F 3 GLN F 22 ASN F 84 ASN G 4 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114254 restraints weight = 7250.337| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.38 r_work: 0.3236 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6060 Z= 0.205 Angle : 0.661 7.231 8236 Z= 0.355 Chirality : 0.046 0.174 885 Planarity : 0.005 0.035 1055 Dihedral : 6.608 60.170 823 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.69 % Allowed : 11.83 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.31), residues: 732 helix: 2.12 (0.55), residues: 75 sheet: 1.42 (0.32), residues: 302 loop : 0.24 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 52 HIS 0.009 0.002 HIS G 4 PHE 0.016 0.002 PHE C 34 TYR 0.018 0.002 TYR E 27 ARG 0.005 0.001 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 247) hydrogen bonds : angle 6.04152 ( 693) SS BOND : bond 0.01215 ( 7) SS BOND : angle 1.10975 ( 14) covalent geometry : bond 0.00468 ( 6053) covalent geometry : angle 0.66046 ( 8222) *********************** 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 148 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: D 46 GLU cc_start: 0.7838 (tt0) cc_final: 0.7560 (tt0) REVERT: E 138 MET cc_start: 0.4961 (mtt) cc_final: 0.4391 (tmm) REVERT: F 13 ARG cc_start: 0.7033 (ttm-80) cc_final: 0.5268 (tpm170) REVERT: F 60 ASP cc_start: 0.7323 (m-30) cc_final: 0.6920 (t0) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.2162 time to fit residues: 38.7194 Evaluate side-chains 135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain F residue 2 ILE 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 52 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 43 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN C 61 GLN E 86 ASN G 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115908 restraints weight = 7367.944| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.38 r_work: 0.3281 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6060 Z= 0.129 Angle : 0.566 7.755 8236 Z= 0.303 Chirality : 0.043 0.206 885 Planarity : 0.004 0.030 1055 Dihedral : 5.589 57.509 820 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.23 % Allowed : 13.98 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 732 helix: 1.94 (0.55), residues: 75 sheet: 1.37 (0.31), residues: 301 loop : 0.10 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 PHE 0.012 0.001 PHE A 95 TYR 0.015 0.001 TYR E 27 ARG 0.004 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 247) hydrogen bonds : angle 5.45283 ( 693) SS BOND : bond 0.00254 ( 7) SS BOND : angle 1.47448 ( 14) covalent geometry : bond 0.00296 ( 6053) covalent geometry : angle 0.56324 ( 8222) *********************** 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 140 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.604 Fit side-chains REVERT: B 89 LYS cc_start: 0.8289 (tttp) cc_final: 0.8069 (tttt) REVERT: E 27 TYR cc_start: 0.8199 (m-80) cc_final: 0.7985 (m-80) REVERT: E 138 MET cc_start: 0.5044 (mtt) cc_final: 0.4350 (tmm) REVERT: F 60 ASP cc_start: 0.7155 (m-30) cc_final: 0.6915 (t0) REVERT: F 84 ASN cc_start: 0.8434 (t0) cc_final: 0.8010 (t0) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 0.1782 time to fit residues: 29.2695 Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 98 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 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.139997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110375 restraints weight = 7491.153| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.45 r_work: 0.3180 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 6060 Z= 0.195 Angle : 0.608 10.170 8236 Z= 0.323 Chirality : 0.045 0.278 885 Planarity : 0.004 0.035 1055 Dihedral : 5.650 61.826 820 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.45 % Allowed : 14.29 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.31), residues: 732 helix: 1.70 (0.57), residues: 75 sheet: 1.11 (0.31), residues: 301 loop : -0.06 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 133 HIS 0.006 0.002 HIS G 4 PHE 0.014 0.002 PHE A 95 TYR 0.016 0.002 TYR E 27 ARG 0.005 0.001 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 247) hydrogen bonds : angle 5.44403 ( 693) SS BOND : bond 0.00581 ( 7) SS BOND : angle 2.11631 ( 14) covalent geometry : bond 0.00472 ( 6053) covalent geometry : angle 0.60192 ( 8222) *********************** 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 138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.673 Fit side-chains REVERT: A 106 ASP cc_start: 0.7811 (m-30) cc_final: 0.7282 (t0) REVERT: B 27 LEU cc_start: 0.9143 (tp) cc_final: 0.8884 (tp) REVERT: B 89 LYS cc_start: 0.8397 (tttp) cc_final: 0.8137 (tttt) REVERT: C 126 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8327 (t) REVERT: E 138 MET cc_start: 0.5254 (mtt) cc_final: 0.4450 (tmm) REVERT: F 60 ASP cc_start: 0.7280 (m-30) cc_final: 0.7010 (t0) REVERT: F 84 ASN cc_start: 0.8430 (t0) cc_final: 0.8010 (t0) outliers start: 29 outliers final: 19 residues processed: 126 average time/residue: 0.1619 time to fit residues: 27.1034 Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 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 46 THR Chi-restraints excluded: chain C residue 50 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 132 SER 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 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.139981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110973 restraints weight = 7399.614| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.36 r_work: 0.3208 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6060 Z= 0.167 Angle : 0.587 15.220 8236 Z= 0.310 Chirality : 0.044 0.282 885 Planarity : 0.004 0.035 1055 Dihedral : 5.461 60.150 820 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.99 % Allowed : 16.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.31), residues: 732 helix: 1.69 (0.58), residues: 75 sheet: 1.07 (0.31), residues: 300 loop : -0.21 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 133 HIS 0.005 0.001 HIS G 4 PHE 0.013 0.001 PHE A 95 TYR 0.014 0.002 TYR F 64 ARG 0.004 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 247) hydrogen bonds : angle 5.28438 ( 693) SS BOND : bond 0.01032 ( 7) SS BOND : angle 2.39020 ( 14) covalent geometry : bond 0.00403 ( 6053) covalent geometry : angle 0.57872 ( 8222) *********************** 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 131 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.624 Fit side-chains REVERT: A 26 ILE cc_start: 0.8245 (mp) cc_final: 0.8039 (mm) REVERT: A 93 THR cc_start: 0.8721 (p) cc_final: 0.8222 (t) REVERT: B 27 LEU cc_start: 0.9234 (tp) cc_final: 0.8940 (tp) REVERT: B 89 LYS cc_start: 0.8342 (tttp) cc_final: 0.8105 (tttt) REVERT: B 93 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7309 (mp10) REVERT: C 126 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8315 (t) REVERT: D 42 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.8039 (mtm-85) REVERT: E 27 TYR cc_start: 0.8423 (m-80) cc_final: 0.8146 (m-80) REVERT: E 108 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8114 (ptt180) REVERT: E 138 MET cc_start: 0.5201 (mtt) cc_final: 0.4393 (tmm) REVERT: E 158 VAL cc_start: 0.7795 (t) cc_final: 0.7594 (m) REVERT: F 84 ASN cc_start: 0.8412 (t0) cc_final: 0.8050 (t0) outliers start: 26 outliers final: 19 residues processed: 119 average time/residue: 0.1781 time to fit residues: 28.1825 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 46 THR 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 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 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 178 THR 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 50 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111209 restraints weight = 7388.978| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.39 r_work: 0.3206 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6060 Z= 0.159 Angle : 0.574 12.646 8236 Z= 0.304 Chirality : 0.043 0.255 885 Planarity : 0.004 0.036 1055 Dihedral : 5.324 59.240 820 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.92 % Allowed : 15.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.31), residues: 732 helix: 1.73 (0.58), residues: 75 sheet: 1.01 (0.31), residues: 298 loop : -0.30 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.005 0.001 HIS G 4 PHE 0.013 0.001 PHE A 95 TYR 0.016 0.002 TYR F 64 ARG 0.004 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 247) hydrogen bonds : angle 5.07082 ( 693) SS BOND : bond 0.00899 ( 7) SS BOND : angle 2.40339 ( 14) covalent geometry : bond 0.00385 ( 6053) covalent geometry : angle 0.56630 ( 8222) *********************** 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: 32 poor density : 103 time to evaluate : 0.628 Fit side-chains REVERT: A 93 THR cc_start: 0.8756 (p) cc_final: 0.8284 (t) REVERT: B 27 LEU cc_start: 0.9292 (tp) cc_final: 0.8970 (tp) REVERT: B 89 LYS cc_start: 0.8372 (tttp) cc_final: 0.8135 (tttt) REVERT: B 93 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7317 (mp10) REVERT: C 126 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8269 (t) REVERT: D 99 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8373 (mtpp) REVERT: E 108 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8192 (ptt180) REVERT: E 138 MET cc_start: 0.5248 (mtt) cc_final: 0.4400 (tmm) REVERT: E 158 VAL cc_start: 0.7795 (t) cc_final: 0.7554 (m) REVERT: F 7 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7652 (mttp) REVERT: F 84 ASN cc_start: 0.8434 (t0) cc_final: 0.8094 (t0) outliers start: 32 outliers final: 20 residues processed: 121 average time/residue: 0.1795 time to fit residues: 28.8438 Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 121 THR 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 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 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 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.0000 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4702 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.140465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113729 restraints weight = 7383.131| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.21 r_work: 0.3220 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 6060 Z= 0.132 Angle : 0.556 15.457 8236 Z= 0.293 Chirality : 0.043 0.248 885 Planarity : 0.004 0.038 1055 Dihedral : 5.208 56.763 820 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.99 % Allowed : 15.82 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.31), residues: 732 helix: 1.81 (0.59), residues: 75 sheet: 1.00 (0.31), residues: 300 loop : -0.30 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 133 HIS 0.005 0.001 HIS G 4 PHE 0.012 0.001 PHE A 95 TYR 0.017 0.001 TYR E 27 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 247) hydrogen bonds : angle 4.96491 ( 693) SS BOND : bond 0.00971 ( 7) SS BOND : angle 2.29737 ( 14) covalent geometry : bond 0.00316 ( 6053) covalent geometry : angle 0.54791 ( 8222) *********************** 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 132 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.660 Fit side-chains REVERT: A 93 THR cc_start: 0.8739 (p) cc_final: 0.8299 (t) REVERT: B 27 LEU cc_start: 0.9309 (tp) cc_final: 0.9003 (tp) REVERT: B 89 LYS cc_start: 0.8350 (tttp) cc_final: 0.8118 (tttt) REVERT: B 93 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7294 (mp10) REVERT: C 126 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8242 (t) REVERT: D 99 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8370 (mtpp) REVERT: E 108 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8196 (ptt180) REVERT: E 138 MET cc_start: 0.5180 (mtt) cc_final: 0.4346 (tmm) REVERT: E 158 VAL cc_start: 0.7789 (t) cc_final: 0.7543 (m) REVERT: F 1 MET cc_start: 0.6605 (mpp) cc_final: 0.4434 (tpp) REVERT: F 7 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7608 (mttp) REVERT: F 84 ASN cc_start: 0.8432 (t0) cc_final: 0.8072 (t0) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 0.1683 time to fit residues: 27.0967 Evaluate side-chains 122 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 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 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.0030 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.140448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111263 restraints weight = 7366.356| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.38 r_work: 0.3201 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5124 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= 0.159 Angle : 0.578 15.588 8236 Z= 0.304 Chirality : 0.044 0.251 885 Planarity : 0.004 0.041 1055 Dihedral : 5.263 58.002 820 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.84 % Allowed : 16.59 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.31), residues: 732 helix: 1.72 (0.58), residues: 75 sheet: 0.97 (0.31), residues: 298 loop : -0.40 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 PHE 0.012 0.001 PHE A 95 TYR 0.016 0.002 TYR E 27 ARG 0.003 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 247) hydrogen bonds : angle 5.00305 ( 693) SS BOND : bond 0.01050 ( 7) SS BOND : angle 2.43197 ( 14) covalent geometry : bond 0.00387 ( 6053) covalent geometry : angle 0.56961 ( 8222) *********************** 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 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.627 Fit side-chains REVERT: A 93 THR cc_start: 0.8772 (p) cc_final: 0.8348 (t) REVERT: B 27 LEU cc_start: 0.9316 (tp) cc_final: 0.9010 (tp) REVERT: B 89 LYS cc_start: 0.8401 (tttp) cc_final: 0.8178 (tttt) REVERT: C 117 ASP cc_start: 0.8740 (t70) cc_final: 0.8369 (t0) REVERT: C 126 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8267 (t) REVERT: D 99 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8409 (mtpp) REVERT: E 108 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8174 (ptt180) REVERT: E 138 MET cc_start: 0.5262 (mtt) cc_final: 0.4432 (tmm) REVERT: E 158 VAL cc_start: 0.7808 (t) cc_final: 0.7551 (m) REVERT: F 1 MET cc_start: 0.6624 (mpp) cc_final: 0.4433 (tpp) REVERT: F 7 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7634 (mttp) REVERT: F 84 ASN cc_start: 0.8412 (t0) cc_final: 0.8049 (t0) outliers start: 25 outliers final: 22 residues processed: 117 average time/residue: 0.1675 time to fit residues: 25.8305 Evaluate side-chains 127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 46 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 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 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.138234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111444 restraints weight = 7414.196| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.20 r_work: 0.3198 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5176 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= 0.178 Angle : 0.591 15.430 8236 Z= 0.312 Chirality : 0.044 0.258 885 Planarity : 0.004 0.044 1055 Dihedral : 5.376 59.468 820 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.84 % Allowed : 16.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.31), residues: 732 helix: 1.58 (0.58), residues: 75 sheet: 0.87 (0.31), residues: 300 loop : -0.42 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.007 0.001 HIS G 4 PHE 0.012 0.001 PHE A 95 TYR 0.038 0.002 TYR E 59 ARG 0.004 0.001 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 247) hydrogen bonds : angle 5.04620 ( 693) SS BOND : bond 0.01068 ( 7) SS BOND : angle 2.37284 ( 14) covalent geometry : bond 0.00435 ( 6053) covalent geometry : angle 0.58321 ( 8222) *********************** 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: 25 poor density : 101 time to evaluate : 0.602 Fit side-chains REVERT: A 93 THR cc_start: 0.8762 (p) cc_final: 0.8350 (t) REVERT: B 27 LEU cc_start: 0.9331 (tp) cc_final: 0.9028 (tp) REVERT: B 89 LYS cc_start: 0.8315 (tttp) cc_final: 0.8079 (tttt) REVERT: C 117 ASP cc_start: 0.8700 (t70) cc_final: 0.8332 (t0) REVERT: C 126 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8296 (t) REVERT: D 93 GLN cc_start: 0.8495 (mt0) cc_final: 0.8184 (mm-40) REVERT: D 99 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8435 (mtpp) REVERT: E 108 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8146 (ptt180) REVERT: E 138 MET cc_start: 0.5285 (mtt) cc_final: 0.4492 (tmm) REVERT: E 158 VAL cc_start: 0.7805 (t) cc_final: 0.7553 (m) REVERT: F 7 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7636 (mttp) REVERT: F 84 ASN cc_start: 0.8418 (t0) cc_final: 0.8068 (t0) outliers start: 25 outliers final: 22 residues processed: 115 average time/residue: 0.1693 time to fit residues: 25.8477 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 : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 46 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 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 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 180 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 = 0.3653 r_free = 0.3653 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107903 restraints weight = 7478.827| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.37 r_work: 0.3152 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 6060 Z= 0.248 Angle : 0.648 15.687 8236 Z= 0.343 Chirality : 0.046 0.269 885 Planarity : 0.005 0.046 1055 Dihedral : 5.664 64.126 820 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.84 % Allowed : 17.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.31), residues: 732 helix: 1.24 (0.57), residues: 75 sheet: 0.60 (0.31), residues: 312 loop : -0.48 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 133 HIS 0.006 0.002 HIS G 4 PHE 0.013 0.002 PHE A 95 TYR 0.044 0.003 TYR E 59 ARG 0.005 0.001 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 247) hydrogen bonds : angle 5.29361 ( 693) SS BOND : bond 0.01144 ( 7) SS BOND : angle 2.46015 ( 14) covalent geometry : bond 0.00607 ( 6053) covalent geometry : angle 0.64093 ( 8222) ********************** 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 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.658 Fit side-chains REVERT: A 93 THR cc_start: 0.8776 (p) cc_final: 0.8364 (t) REVERT: B 27 LEU cc_start: 0.9342 (tp) cc_final: 0.9034 (tp) REVERT: B 89 LYS cc_start: 0.8397 (tttp) cc_final: 0.8161 (tttt) REVERT: C 117 ASP cc_start: 0.8749 (t70) cc_final: 0.8350 (t0) REVERT: C 126 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8438 (t) REVERT: D 93 GLN cc_start: 0.8561 (mt0) cc_final: 0.8198 (mm-40) REVERT: D 99 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8463 (mtpp) REVERT: E 108 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8241 (ptt180) REVERT: E 138 MET cc_start: 0.5434 (mtt) cc_final: 0.4615 (tmm) REVERT: F 7 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7716 (mttp) REVERT: F 84 ASN cc_start: 0.8459 (t0) cc_final: 0.8069 (t0) outliers start: 25 outliers final: 23 residues processed: 116 average time/residue: 0.1769 time to fit residues: 26.8806 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 46 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 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 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.0000 chunk 4 optimal weight: 0.9980 overall best weight: 0.4462 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.139801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113169 restraints weight = 7504.755| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.19 r_work: 0.3222 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6060 Z= 0.130 Angle : 0.559 14.995 8236 Z= 0.296 Chirality : 0.043 0.251 885 Planarity : 0.004 0.049 1055 Dihedral : 5.265 57.266 820 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.84 % Allowed : 16.90 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.31), residues: 732 helix: 1.44 (0.58), residues: 75 sheet: 0.87 (0.31), residues: 298 loop : -0.51 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 51 HIS 0.007 0.001 HIS G 4 PHE 0.010 0.001 PHE E 33 TYR 0.039 0.002 TYR E 59 ARG 0.003 0.001 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 247) hydrogen bonds : angle 4.95839 ( 693) SS BOND : bond 0.00983 ( 7) SS BOND : angle 2.30214 ( 14) covalent geometry : bond 0.00310 ( 6053) covalent geometry : angle 0.55142 ( 8222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4015.59 seconds wall clock time: 70 minutes 17.68 seconds (4217.68 seconds total)