Starting phenix.real_space_refine on Thu Oct 22 23:25:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/33ci_59344/10_2026/33ci_59344.cif Found real_map, /net/cci-nas-00/data/ceres_data/33ci_59344/10_2026/33ci_59344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/33ci_59344/10_2026/33ci_59344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/33ci_59344/10_2026/33ci_59344.map" model { file = "/net/cci-nas-00/data/ceres_data/33ci_59344/10_2026/33ci_59344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/33ci_59344/10_2026/33ci_59344.cif" } resolution = 2.2 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= 0.010 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 29 5.16 5 C 4165 2.51 5 N 1142 2.21 5 O 1306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6642 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2256 Classifications: {'peptide': 277} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "F" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "E" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 913 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 0.88, per 1000 atoms: 0.13 Number of scatterers: 6642 At special positions: 0 Unit cell: (73.0002, 98.6706, 135.572, 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 29 16.00 O 1306 8.00 N 1142 7.00 C 4165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " 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: 0.30 Conformation dependent library (CDL) restraints added in 218.7 milliseconds 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 18 sheets defined 14.1% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 56 through 85 Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.594A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 252 through 255 removed outlier: 4.332A pdb=" N GLN A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.709A pdb=" N THR G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.749A pdb=" N SER D 28 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'E' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 5.393A pdb=" N GLN A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 28 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 34 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 94 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR A 118 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN A 96 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 116 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET A 98 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS A 114 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 100 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY A 112 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP A 102 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N HIS A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.518A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.518A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.640A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.640A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.503A pdb=" N THR F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.645A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.411A pdb=" N ILE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.786A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE G 100 " --> pdb=" O MET G 106 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N MET G 106 " --> pdb=" O PHE G 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.517A pdb=" N VAL D 10 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP D 34 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.517A pdb=" N VAL D 10 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.506A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG E 38 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.790A pdb=" N LEU E 111 " --> pdb=" O LYS E 97 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2160 1.34 - 1.46: 1747 1.46 - 1.58: 2854 1.58 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 6803 Sorted by residual: bond pdb=" N GLY C 1 " pdb=" CA GLY C 1 " ideal model delta sigma weight residual 1.451 1.486 -0.035 1.60e-02 3.91e+03 4.69e+00 bond pdb=" N MET A 0 " pdb=" CA MET A 0 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.22e+00 bond pdb=" N SER D 1 " pdb=" CA SER D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N GLU G 1 " pdb=" CA GLU G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N MET B 0 " pdb=" CA MET B 0 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 ... (remaining 6798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 9001 1.55 - 3.10: 195 3.10 - 4.65: 35 4.65 - 6.21: 1 6.21 - 7.76: 1 Bond angle restraints: 9233 Sorted by residual: angle pdb=" C TYR G 60 " pdb=" CA TYR G 60 " pdb=" CB TYR G 60 " ideal model delta sigma weight residual 109.38 101.62 7.76 2.09e+00 2.29e-01 1.38e+01 angle pdb=" C ARG D 49 " pdb=" N ASP D 50 " pdb=" CA ASP D 50 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA TRP A 244 " pdb=" CB TRP A 244 " pdb=" CG TRP A 244 " ideal model delta sigma weight residual 113.60 117.88 -4.28 1.90e+00 2.77e-01 5.08e+00 angle pdb=" N ASP D 50 " pdb=" CA ASP D 50 " pdb=" C ASP D 50 " ideal model delta sigma weight residual 110.80 115.14 -4.34 2.13e+00 2.20e-01 4.14e+00 angle pdb=" C TYR G 60 " pdb=" N ASP G 61 " pdb=" CA ASP G 61 " ideal model delta sigma weight residual 120.67 117.96 2.71 1.34e+00 5.57e-01 4.08e+00 ... (remaining 9228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3597 17.56 - 35.11: 304 35.11 - 52.67: 76 52.67 - 70.22: 23 70.22 - 87.78: 16 Dihedral angle restraints: 4016 sinusoidal: 1588 harmonic: 2428 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 87 " pdb=" CB CYS D 87 " ideal model delta sinusoidal sigma weight residual 93.00 57.03 35.97 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.10 34.90 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 4013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 523 0.027 - 0.054: 299 0.054 - 0.082: 82 0.082 - 0.109: 46 0.109 - 0.136: 29 Chirality restraints: 979 Sorted by residual: chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL E 4 " pdb=" N VAL E 4 " pdb=" C VAL E 4 " pdb=" CB VAL E 4 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA PRO D 8 " pdb=" N PRO D 8 " pdb=" C PRO D 8 " pdb=" CB PRO D 8 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 976 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 40 " 0.145 9.50e-02 1.11e+02 6.52e-02 2.79e+00 pdb=" NE ARG G 40 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 40 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG G 40 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 40 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 81 " -0.128 9.50e-02 1.11e+02 5.75e-02 2.05e+00 pdb=" NE ARG B 81 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG B 81 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 81 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 81 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 42 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO D 43 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO D 43 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 43 " 0.018 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 643 2.75 - 3.29: 6196 3.29 - 3.82: 11795 3.82 - 4.36: 14618 4.36 - 4.90: 24494 Nonbonded interactions: 57746 Sorted by model distance: nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 2.211 3.040 nonbonded pdb=" N GLU B 74 " pdb=" OE1 GLU B 74 " model vdw 2.215 3.120 nonbonded pdb=" OG SER D 42 " pdb=" O GLY E 113 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU A 58 " pdb=" OH TYR E 32 " model vdw 2.240 3.040 nonbonded pdb=" O SER F 60 " pdb=" NH2 ARG F 76 " model vdw 2.269 3.120 ... (remaining 57741 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: 1.320 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.620 Find NCS groups from input model: 0.020 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:4.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6810 Z= 0.187 Angle : 0.586 7.758 9247 Z= 0.314 Chirality : 0.043 0.136 979 Planarity : 0.005 0.065 1191 Dihedral : 15.518 87.780 2451 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.14 % Allowed : 12.55 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.29), residues: 829 helix: 1.11 (0.58), residues: 80 sheet: 0.98 (0.26), residues: 359 loop : 0.94 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 40 TYR 0.020 0.002 TYR G 103 PHE 0.020 0.002 PHE E 109 TRP 0.017 0.002 TRP G 99 HIS 0.008 0.002 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 6803) covalent geometry : angle 0.58396 / 0.31 ( 9233) SS BOND : bond 0.00900 / 0.45 ( 7) SS BOND : angle 1.40687 / 0.80 ( 14) hydrogen bonds : bond 0.18765 / 12.84 ( 286) hydrogen bonds : angle 7.64065 / 5.42 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.151 Fit side-chains REVERT: A 68 LYS cc_start: 0.8440 (mttt) cc_final: 0.8216 (mttm) REVERT: A 127 LYS cc_start: 0.8290 (mttp) cc_final: 0.7931 (mttt) REVERT: D 105 LYS cc_start: 0.8220 (tttt) cc_final: 0.7648 (tptm) REVERT: E 19 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7311 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.4826 time to fit residues: 65.6740 Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.1312 > 50:) chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS B 31 HIS D 16 GLN D 68 ASN D 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125530 restraints weight = 5598.924| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.54 r_work: 0.3205 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6810 Z= 0.153 Angle : 0.582 6.747 9247 Z= 0.316 Chirality : 0.043 0.144 979 Planarity : 0.005 0.045 1191 Dihedral : 5.079 28.880 930 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.09 % Allowed : 11.85 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.29), residues: 829 helix: 1.98 (0.60), residues: 75 sheet: 1.06 (0.26), residues: 350 loop : 0.91 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 53 TYR 0.019 0.002 TYR A 116 PHE 0.018 0.002 PHE E 109 TRP 0.018 0.002 TRP A 60 HIS 0.004 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6803) covalent geometry : angle 0.58024 / 0.32 ( 9233) SS BOND : bond 0.00747 / 0.37 ( 7) SS BOND : angle 1.30070 / 0.78 ( 14) hydrogen bonds : bond 0.05289 / 3.62 ( 286) hydrogen bonds : angle 5.42895 / 3.85 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.258 Fit side-chains REVERT: A 54 GLN cc_start: 0.7597 (mp10) cc_final: 0.7338 (mp10) REVERT: A 75 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7647 (mtm180) REVERT: A 97 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8488 (ttm110) REVERT: A 218 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.5393 (mp10) REVERT: B 48 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7038 (mmtt) REVERT: B 69 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7939 (tp30) REVERT: F 45 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8358 (mm-40) REVERT: F 76 ARG cc_start: 0.6551 (mtm-85) cc_final: 0.5870 (ptt90) REVERT: G 63 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7916 (pptt) REVERT: D 105 LYS cc_start: 0.8454 (tttt) cc_final: 0.7901 (tptm) REVERT: E 19 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7458 (ttp-170) REVERT: E 119 THR cc_start: 0.8007 (m) cc_final: 0.7743 (p) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 0.6979 time to fit residues: 97.2886 Evaluate side-chains 129 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [4, 25, 36, 71, 26, 33, 7, 65, 46, 49, 16] chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 11 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125699 restraints weight = 5583.941| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.55 r_work: 0.3214 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6810 Z= 0.143 Angle : 0.562 6.451 9247 Z= 0.304 Chirality : 0.042 0.140 979 Planarity : 0.005 0.045 1191 Dihedral : 5.005 27.552 930 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.23 % Allowed : 13.53 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 829 helix: 1.78 (0.59), residues: 75 sheet: 1.05 (0.26), residues: 348 loop : 0.86 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.015 0.002 TYR A 116 PHE 0.018 0.002 PHE E 109 TRP 0.020 0.002 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6803) covalent geometry : angle 0.56013 / 0.30 ( 9233) SS BOND : bond 0.00745 / 0.37 ( 7) SS BOND : angle 1.24911 / 0.75 ( 14) hydrogen bonds : bond 0.04855 / 3.30 ( 286) hydrogen bonds : angle 5.24172 / 3.70 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.264 Fit side-chains REVERT: A 54 GLN cc_start: 0.7663 (mp10) cc_final: 0.7346 (mp10) REVERT: A 75 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7504 (mtt180) REVERT: A 218 GLN cc_start: 0.6606 (OUTLIER) cc_final: 0.5417 (mp10) REVERT: B 48 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7067 (mmtt) REVERT: F 76 ARG cc_start: 0.6532 (mtm-85) cc_final: 0.5894 (ptt90) REVERT: G 27 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6323 (p90) REVERT: G 63 LYS cc_start: 0.8237 (ptmm) cc_final: 0.7951 (pptt) REVERT: D 105 LYS cc_start: 0.8397 (tttt) cc_final: 0.7862 (tptm) REVERT: E 19 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7407 (ttp-170) REVERT: E 119 THR cc_start: 0.8006 (m) cc_final: 0.7742 (p) outliers start: 16 outliers final: 5 residues processed: 130 average time/residue: 0.7234 time to fit residues: 97.6183 Evaluate side-chains 132 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [5, 22, 66, 80, 38, 79, 74, 23, 32, 30, 3] chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 0.0270 chunk 80 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS F 11 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126298 restraints weight = 5568.222| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.53 r_work: 0.3219 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6810 Z= 0.135 Angle : 0.551 6.249 9247 Z= 0.298 Chirality : 0.042 0.140 979 Planarity : 0.004 0.043 1191 Dihedral : 4.912 26.932 930 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.95 % Allowed : 14.09 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.29), residues: 829 helix: 1.76 (0.59), residues: 75 sheet: 1.04 (0.26), residues: 350 loop : 0.88 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 40 TYR 0.014 0.002 TYR A 99 PHE 0.017 0.002 PHE E 109 TRP 0.020 0.002 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 6803) covalent geometry : angle 0.54908 / 0.30 ( 9233) SS BOND : bond 0.00713 / 0.35 ( 7) SS BOND : angle 1.19364 / 0.73 ( 14) hydrogen bonds : bond 0.04587 / 3.11 ( 286) hydrogen bonds : angle 5.14030 / 3.62 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.176 Fit side-chains REVERT: A 54 GLN cc_start: 0.7618 (mp10) cc_final: 0.7376 (mp10) REVERT: A 75 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7510 (mtm180) REVERT: A 127 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8079 (mttm) REVERT: A 173 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: A 218 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5385 (mp10) REVERT: A 260 HIS cc_start: 0.7549 (m-70) cc_final: 0.6851 (m90) REVERT: A 262 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6452 (mt0) REVERT: B 48 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7003 (mmtt) REVERT: F 76 ARG cc_start: 0.6386 (mtm-85) cc_final: 0.5806 (ptt90) REVERT: G 27 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6224 (p90) REVERT: D 105 LYS cc_start: 0.8350 (tttt) cc_final: 0.7782 (tptm) REVERT: E 19 ARG cc_start: 0.7692 (ttp-170) cc_final: 0.7401 (ttp-170) REVERT: E 119 THR cc_start: 0.7941 (m) cc_final: 0.7682 (p) outliers start: 14 outliers final: 4 residues processed: 134 average time/residue: 0.7294 time to fit residues: 101.5230 Evaluate side-chains 134 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [41, 21, 44, 30, 5, 72, 51, 48, 12, 14, 74] chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 68 ASN E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.165217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129408 restraints weight = 5669.748| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.42 r_work: 0.3229 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6810 Z= 0.118 Angle : 0.525 6.152 9247 Z= 0.284 Chirality : 0.041 0.139 979 Planarity : 0.004 0.038 1191 Dihedral : 4.751 25.298 930 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.39 % Allowed : 15.06 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.29), residues: 829 helix: 1.87 (0.59), residues: 75 sheet: 1.07 (0.26), residues: 350 loop : 0.92 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 40 TYR 0.014 0.002 TYR A 116 PHE 0.015 0.002 PHE E 109 TRP 0.021 0.001 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 6803) covalent geometry : angle 0.52386 / 0.28 ( 9233) SS BOND : bond 0.00635 / 0.31 ( 7) SS BOND : angle 1.12362 / 0.69 ( 14) hydrogen bonds : bond 0.04268 / 2.90 ( 286) hydrogen bonds : angle 4.97726 / 3.51 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.253 Fit side-chains REVERT: A 54 GLN cc_start: 0.7626 (mp10) cc_final: 0.7376 (mp10) REVERT: A 75 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7500 (mtm180) REVERT: A 121 LYS cc_start: 0.8582 (pttm) cc_final: 0.8173 (tttm) REVERT: A 127 LYS cc_start: 0.8287 (mtmm) cc_final: 0.8073 (mttm) REVERT: A 173 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: A 260 HIS cc_start: 0.7469 (m-70) cc_final: 0.7218 (m90) REVERT: A 262 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6439 (mt0) REVERT: B 48 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7000 (mmtt) REVERT: F 76 ARG cc_start: 0.6354 (mtm-85) cc_final: 0.5830 (ptt90) REVERT: G 27 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.5967 (p90) REVERT: G 82 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7922 (tp-100) REVERT: D 105 LYS cc_start: 0.8295 (tttt) cc_final: 0.7715 (tptm) REVERT: E 5 LEU cc_start: 0.8408 (tt) cc_final: 0.8043 (tm) REVERT: E 19 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7377 (ttp-170) REVERT: E 119 THR cc_start: 0.7951 (m) cc_final: 0.7689 (p) outliers start: 10 outliers final: 5 residues processed: 130 average time/residue: 0.7508 time to fit residues: 101.2469 Evaluate side-chains 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [46, 24, 80, 17, 56, 52, 26, 5, 58, 43, 62] chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN C 8 HIS F 11 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125201 restraints weight = 5538.224| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.41 r_work: 0.3175 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 6810 Z= 0.227 Angle : 0.654 7.317 9247 Z= 0.353 Chirality : 0.045 0.136 979 Planarity : 0.006 0.065 1191 Dihedral : 5.366 32.545 930 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.65 % Allowed : 14.37 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.29), residues: 829 helix: 1.71 (0.58), residues: 75 sheet: 1.06 (0.26), residues: 350 loop : 0.81 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.016 0.003 TYR E 93 PHE 0.025 0.003 PHE E 109 TRP 0.022 0.003 TRP A 60 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 6803) covalent geometry : angle 0.65175 / 0.35 ( 9233) SS BOND : bond 0.01026 / 0.51 ( 7) SS BOND : angle 1.52902 / 0.92 ( 14) hydrogen bonds : bond 0.05530 / 3.75 ( 286) hydrogen bonds : angle 5.36538 / 3.79 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.256 Fit side-chains REVERT: A 54 GLN cc_start: 0.7549 (mp10) cc_final: 0.7211 (mp10) REVERT: A 121 LYS cc_start: 0.8597 (pttm) cc_final: 0.8152 (tttm) REVERT: A 127 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8088 (mttm) REVERT: A 262 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6445 (mt0) REVERT: B 48 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7027 (mmtt) REVERT: F 76 ARG cc_start: 0.6481 (mtm-85) cc_final: 0.5847 (ptt90) REVERT: G 27 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6183 (p90) REVERT: D 78 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6907 (mt0) REVERT: D 105 LYS cc_start: 0.8495 (tttt) cc_final: 0.7834 (tptm) REVERT: E 19 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7386 (ttp-170) outliers start: 19 outliers final: 7 residues processed: 134 average time/residue: 0.7478 time to fit residues: 103.8571 Evaluate side-chains 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [47, 10, 21, 69, 9, 35, 54, 50, 68, 32, 6] chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 3 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123813 restraints weight = 5485.285| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.57 r_work: 0.3214 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6810 Z= 0.142 Angle : 0.563 6.311 9247 Z= 0.305 Chirality : 0.042 0.140 979 Planarity : 0.005 0.046 1191 Dihedral : 5.004 28.000 930 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.81 % Allowed : 15.48 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.29), residues: 829 helix: 1.78 (0.59), residues: 75 sheet: 1.11 (0.27), residues: 343 loop : 0.82 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 40 TYR 0.015 0.002 TYR G 108 PHE 0.018 0.002 PHE E 109 TRP 0.025 0.002 TRP A 244 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 6803) covalent geometry : angle 0.56165 / 0.30 ( 9233) SS BOND : bond 0.00743 / 0.37 ( 7) SS BOND : angle 1.27352 / 0.79 ( 14) hydrogen bonds : bond 0.04620 / 3.14 ( 286) hydrogen bonds : angle 5.11186 / 3.60 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.259 Fit side-chains REVERT: A 54 GLN cc_start: 0.7612 (mp10) cc_final: 0.7307 (mp10) REVERT: A 75 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7563 (mtm180) REVERT: A 121 LYS cc_start: 0.8587 (pttm) cc_final: 0.8183 (tttm) REVERT: A 127 LYS cc_start: 0.8298 (mtmm) cc_final: 0.8095 (mttm) REVERT: A 173 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: A 262 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6442 (mt0) REVERT: B 48 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7045 (mmtt) REVERT: F 76 ARG cc_start: 0.6399 (mtm-85) cc_final: 0.5878 (ptt90) REVERT: G 27 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6032 (p90) REVERT: G 82 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7836 (tp-100) REVERT: D 78 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6859 (mt0) REVERT: D 105 LYS cc_start: 0.8427 (tttt) cc_final: 0.7784 (tptm) REVERT: E 5 LEU cc_start: 0.8425 (tt) cc_final: 0.8038 (tm) REVERT: E 19 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7370 (ttp-170) outliers start: 13 outliers final: 6 residues processed: 131 average time/residue: 0.7204 time to fit residues: 98.0471 Evaluate side-chains 138 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [72, 0, 2, 76, 35, 12, 28, 31, 39, 34, 27] chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122602 restraints weight = 5567.204| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.58 r_work: 0.3198 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6810 Z= 0.171 Angle : 0.604 6.747 9247 Z= 0.326 Chirality : 0.043 0.145 979 Planarity : 0.005 0.053 1191 Dihedral : 5.159 29.777 930 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.09 % Allowed : 14.92 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.29), residues: 829 helix: 1.70 (0.58), residues: 75 sheet: 1.11 (0.26), residues: 349 loop : 0.82 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 21 TYR 0.017 0.002 TYR A 116 PHE 0.021 0.002 PHE E 109 TRP 0.024 0.002 TRP A 244 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 6803) covalent geometry : angle 0.60242 / 0.32 ( 9233) SS BOND : bond 0.00860 / 0.42 ( 7) SS BOND : angle 1.37122 / 0.82 ( 14) hydrogen bonds : bond 0.04988 / 3.38 ( 286) hydrogen bonds : angle 5.22213 / 3.69 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.289 Fit side-chains REVERT: A 54 GLN cc_start: 0.7597 (mp10) cc_final: 0.7271 (mp10) REVERT: A 75 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7575 (mtm180) REVERT: A 121 LYS cc_start: 0.8607 (pttm) cc_final: 0.8196 (tttm) REVERT: A 127 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8095 (mttm) REVERT: A 173 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: A 262 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6453 (mt0) REVERT: B 48 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7042 (mmtt) REVERT: F 76 ARG cc_start: 0.6446 (mtm-85) cc_final: 0.5888 (ptt90) REVERT: G 27 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6061 (p90) REVERT: G 82 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7804 (tp-100) REVERT: D 78 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: D 105 LYS cc_start: 0.8434 (tttt) cc_final: 0.7785 (tptm) REVERT: E 19 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.7388 (ttp-170) outliers start: 15 outliers final: 8 residues processed: 134 average time/residue: 0.6963 time to fit residues: 96.9676 Evaluate side-chains 140 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [51, 31, 71, 63, 22, 76, 77, 45, 64, 54, 30] chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 11 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.161433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125352 restraints weight = 5522.014| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.41 r_work: 0.3173 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 6810 Z= 0.225 Angle : 0.668 7.252 9247 Z= 0.360 Chirality : 0.046 0.148 979 Planarity : 0.006 0.065 1191 Dihedral : 5.422 33.039 930 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.23 % Allowed : 15.06 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.29), residues: 829 helix: 1.68 (0.58), residues: 75 sheet: 0.98 (0.26), residues: 361 loop : 0.85 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.023 0.003 TYR G 108 PHE 0.024 0.003 PHE E 109 TRP 0.023 0.003 TRP A 244 HIS 0.005 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 ( 6803) covalent geometry : angle 0.66534 / 0.36 ( 9233) SS BOND : bond 0.01045 / 0.52 ( 7) SS BOND : angle 1.58145 / 0.94 ( 14) hydrogen bonds : bond 0.05522 / 3.75 ( 286) hydrogen bonds : angle 5.39874 / 3.82 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.189 Fit side-chains REVERT: A 54 GLN cc_start: 0.7531 (mp10) cc_final: 0.7298 (mp10) REVERT: A 121 LYS cc_start: 0.8595 (pttm) cc_final: 0.8157 (tttm) REVERT: A 127 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8086 (mttm) REVERT: A 173 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: A 262 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6507 (mt0) REVERT: B 48 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6999 (mmtt) REVERT: F 76 ARG cc_start: 0.6458 (mtm-85) cc_final: 0.5839 (ptt90) REVERT: G 27 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6183 (p90) REVERT: G 82 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7784 (tp-100) REVERT: D 78 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6837 (mt0) REVERT: D 105 LYS cc_start: 0.8490 (tttt) cc_final: 0.7802 (tptm) REVERT: E 19 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7377 (ttp-170) outliers start: 16 outliers final: 8 residues processed: 131 average time/residue: 0.7414 time to fit residues: 100.8067 Evaluate side-chains 136 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [67, 80, 64, 66, 6, 61, 57, 33, 20, 1, 10] chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122533 restraints weight = 5505.395| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.57 r_work: 0.3198 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6810 Z= 0.178 Angle : 0.620 6.814 9247 Z= 0.334 Chirality : 0.044 0.143 979 Planarity : 0.005 0.055 1191 Dihedral : 5.241 30.665 930 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.09 % Allowed : 15.34 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.29), residues: 829 helix: 1.69 (0.58), residues: 75 sheet: 0.96 (0.26), residues: 355 loop : 0.86 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 75 TYR 0.022 0.002 TYR G 108 PHE 0.021 0.002 PHE E 109 TRP 0.028 0.002 TRP A 244 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 6803) covalent geometry : angle 0.61752 / 0.33 ( 9233) SS BOND : bond 0.00889 / 0.44 ( 7) SS BOND : angle 1.41908 / 0.86 ( 14) hydrogen bonds : bond 0.05029 / 3.41 ( 286) hydrogen bonds : angle 5.27126 / 3.73 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.257 Fit side-chains REVERT: A 54 GLN cc_start: 0.7586 (mp10) cc_final: 0.7249 (mp10) REVERT: A 75 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7537 (mtm110) REVERT: A 121 LYS cc_start: 0.8613 (pttm) cc_final: 0.8196 (tttm) REVERT: A 127 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8095 (mttm) REVERT: A 173 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: A 262 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6525 (mt0) REVERT: B 48 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7025 (mmtt) REVERT: F 76 ARG cc_start: 0.6421 (mtm-85) cc_final: 0.5909 (ptt90) REVERT: G 27 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6158 (p90) REVERT: G 82 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7771 (tp-100) REVERT: D 78 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6835 (mt0) REVERT: D 105 LYS cc_start: 0.8448 (tttt) cc_final: 0.7809 (tptm) REVERT: E 19 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7394 (ttp-170) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.7175 time to fit residues: 100.7034 Evaluate side-chains 139 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [1, 77, 66, 55, 72, 29, 0, 63, 67, 25, 35] chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 11 GLN D 68 ASN E 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123494 restraints weight = 5537.117| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.58 r_work: 0.3211 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6810 Z= 0.152 Angle : 0.590 6.416 9247 Z= 0.318 Chirality : 0.043 0.140 979 Planarity : 0.005 0.048 1191 Dihedral : 5.095 28.733 930 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.09 % Allowed : 15.48 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.29), residues: 829 helix: 1.73 (0.58), residues: 75 sheet: 0.99 (0.26), residues: 356 loop : 0.88 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.018 0.002 TYR G 108 PHE 0.019 0.002 PHE E 109 TRP 0.030 0.002 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6803) covalent geometry : angle 0.58841 / 0.32 ( 9233) SS BOND : bond 0.00786 / 0.39 ( 7) SS BOND : angle 1.30491 / 0.79 ( 14) hydrogen bonds : bond 0.04732 / 3.21 ( 286) hydrogen bonds : angle 5.16882 / 3.65 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3616.86 seconds wall clock time: 62 minutes 9.94 seconds (3729.94 seconds total)