Starting phenix.real_space_refine on Tue Feb 3 20:00:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jy0_61883/02_2026/9jy0_61883.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jy0_61883/02_2026/9jy0_61883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jy0_61883/02_2026/9jy0_61883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jy0_61883/02_2026/9jy0_61883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jy0_61883/02_2026/9jy0_61883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jy0_61883/02_2026/9jy0_61883.map" } resolution = 3.69 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= 0.013 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 46 5.16 5 C 4204 2.51 5 N 1038 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6521 Number of models: 1 Model: "" Number of chains: 11 Chain: "a" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "b" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 285 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "n" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "f" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "B" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 953 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.29, per 1000 atoms: 0.20 Number of scatterers: 6521 At special positions: 0 Unit cell: (89.816, 120.304, 121.128, 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 46 16.00 O 1233 8.00 N 1038 7.00 C 4204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.02 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 0.49 Conformation dependent library (CDL) restraints added in 147.7 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 13 sheets defined 33.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'a' and resid 31 through 54 removed outlier: 4.012A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 55 removed outlier: 3.590A pdb=" N PHE b 55 " --> pdb=" O LEU b 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 66 Processing helix chain 'd' and resid 100 through 126 Processing helix chain 'e' and resid 126 through 153 Processing helix chain 'm' and resid 256 through 289 removed outlier: 4.222A pdb=" N MET m 261 " --> pdb=" O GLU m 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 252 through 288 removed outlier: 3.527A pdb=" N CYS n 283 " --> pdb=" O ILE n 279 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.853A pdb=" N ALA f 108 " --> pdb=" O PRO f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 Processing helix chain 'g' and resid 76 through 80 Processing helix chain 'g' and resid 111 through 140 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.566A pdb=" N ILE A 83 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.756A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.900A pdb=" N LYS B 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.536A pdb=" N SER B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 70 through 71 removed outlier: 6.039A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.662A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR e 44 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.636A pdb=" N SER f 41 " --> pdb=" O THR f 44 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR f 44 " --> pdb=" O SER f 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 64 through 65 removed outlier: 3.582A pdb=" N TYR f 99 " --> pdb=" O LEU f 58 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY f 94 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU g 97 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.523A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 33 removed outlier: 7.141A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU g 74 " --> pdb=" O VAL g 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.838A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 63 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.675A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.624A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 60 removed outlier: 7.009A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET B 34 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 60 removed outlier: 7.009A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET B 34 " --> pdb=" O LEU B 50 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 924 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: 0.70 Time building geometry restraints manager: 0.60 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: 2022 1.34 - 1.46: 1516 1.46 - 1.58: 3052 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 6655 Sorted by residual: bond pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.81e+00 bond pdb=" N GLY A 68 " pdb=" CA GLY A 68 " ideal model delta sigma weight residual 1.464 1.448 0.017 1.12e-02 7.97e+03 2.18e+00 bond pdb=" CD LYS m 286 " pdb=" CE LYS m 286 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" N ASN e 121 " pdb=" CA ASN e 121 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" CB CYS f 119 " pdb=" SG CYS f 119 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.68e+00 ... (remaining 6650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 8921 3.41 - 6.82: 85 6.82 - 10.22: 11 10.22 - 13.63: 3 13.63 - 17.04: 1 Bond angle restraints: 9021 Sorted by residual: angle pdb=" CA MET B 18 " pdb=" CB MET B 18 " pdb=" CG MET B 18 " ideal model delta sigma weight residual 114.10 123.96 -9.86 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CA LEU n 271 " pdb=" CB LEU n 271 " pdb=" CG LEU n 271 " ideal model delta sigma weight residual 116.30 133.34 -17.04 3.50e+00 8.16e-02 2.37e+01 angle pdb=" CB MET m 262 " pdb=" CG MET m 262 " pdb=" SD MET m 262 " ideal model delta sigma weight residual 112.70 125.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CA LEU d 99 " pdb=" CB LEU d 99 " pdb=" CG LEU d 99 " ideal model delta sigma weight residual 116.30 129.67 -13.37 3.50e+00 8.16e-02 1.46e+01 angle pdb=" CA LYS a 54 " pdb=" CB LYS a 54 " pdb=" CG LYS a 54 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.21e+01 ... (remaining 9016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3377 17.93 - 35.87: 490 35.87 - 53.80: 117 53.80 - 71.74: 17 71.74 - 89.67: 4 Dihedral angle restraints: 4005 sinusoidal: 1618 harmonic: 2387 Sorted by residual: dihedral pdb=" CA CYS f 119 " pdb=" C CYS f 119 " pdb=" N GLU f 120 " pdb=" CA GLU f 120 " ideal model delta harmonic sigma weight residual 180.00 147.82 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA VAL d 86 " pdb=" C VAL d 86 " pdb=" N GLN d 87 " pdb=" CA GLN d 87 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CB CYS g 46 " pdb=" SG CYS g 46 " pdb=" SG CYS g 87 " pdb=" CB CYS g 87 " ideal model delta sinusoidal sigma weight residual -86.00 -118.32 32.32 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 4002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 734 0.041 - 0.082: 207 0.082 - 0.122: 85 0.122 - 0.163: 6 0.163 - 0.204: 3 Chirality restraints: 1035 Sorted by residual: chirality pdb=" CB VAL d 109 " pdb=" CA VAL d 109 " pdb=" CG1 VAL d 109 " pdb=" CG2 VAL d 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL g 124 " pdb=" CA VAL g 124 " pdb=" CG1 VAL g 124 " pdb=" CG2 VAL g 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA ASN e 121 " pdb=" N ASN e 121 " pdb=" C ASN e 121 " pdb=" CB ASN e 121 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 1032 not shown) Planarity restraints: 1114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN f 121 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ASN f 121 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN f 121 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS f 122 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU f 120 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C GLU f 120 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU f 120 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN f 121 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP e 107 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C ASP e 107 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP e 107 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA e 108 " 0.010 2.00e-02 2.50e+03 ... (remaining 1111 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 157 2.67 - 3.23: 6323 3.23 - 3.78: 10113 3.78 - 4.34: 13150 4.34 - 4.90: 21510 Nonbonded interactions: 51253 Sorted by model distance: nonbonded pdb=" O GLY f 67 " pdb=" OH TYR B 102 " model vdw 2.109 3.040 nonbonded pdb=" OG SER d 95 " pdb=" OE2 GLU e 124 " model vdw 2.156 3.040 nonbonded pdb=" OE1 GLN A 6 " pdb=" OG1 THR A 102 " model vdw 2.168 3.040 nonbonded pdb=" O LEU a 51 " pdb=" OG SER a 56 " model vdw 2.173 3.040 nonbonded pdb=" O GLY b 43 " pdb=" OG1 THR b 47 " model vdw 2.176 3.040 ... (remaining 51248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 27 through 55) selection = chain 'b' } ncs_group { reference = chain 'e' selection = (chain 'f' and resid 33 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 0.043 6664 Z= 0.193 Angle : 0.900 17.038 9039 Z= 0.454 Chirality : 0.044 0.204 1035 Planarity : 0.004 0.045 1114 Dihedral : 17.222 89.674 2454 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.44 % Allowed : 34.57 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.29), residues: 802 helix: 2.00 (0.32), residues: 226 sheet: -0.59 (0.37), residues: 195 loop : -1.31 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG m 270 TYR 0.025 0.002 TYR f 99 PHE 0.019 0.002 PHE b 55 TRP 0.014 0.001 TRP d 43 HIS 0.003 0.001 HIS e 61 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6655) covalent geometry : angle 0.89787 ( 9021) SS BOND : bond 0.00392 ( 9) SS BOND : angle 1.62761 ( 18) hydrogen bonds : bond 0.16696 ( 319) hydrogen bonds : angle 6.75969 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 98 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6448 (mt-10) REVERT: g 122 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 71 TYR cc_start: 0.8122 (m-80) cc_final: 0.7900 (m-80) REVERT: A 82 ASP cc_start: 0.6681 (t70) cc_final: 0.6382 (t0) REVERT: B 18 MET cc_start: 0.7896 (tpt) cc_final: 0.7313 (tpt) outliers start: 25 outliers final: 23 residues processed: 266 average time/residue: 0.0518 time to fit residues: 19.1628 Evaluate side-chains 248 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 47 THR Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 139 CYS Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 269 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 72 ASP Chi-restraints excluded: chain f residue 154 ASN Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 119 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 HIS m 280 ASN A 37 GLN A 38 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112975 restraints weight = 11602.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115354 restraints weight = 7949.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117268 restraints weight = 4880.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117508 restraints weight = 3908.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117867 restraints weight = 3953.012| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6664 Z= 0.148 Angle : 0.714 10.141 9039 Z= 0.351 Chirality : 0.043 0.177 1035 Planarity : 0.004 0.073 1114 Dihedral : 7.235 52.775 987 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.34 % Allowed : 29.34 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.29), residues: 802 helix: 2.42 (0.31), residues: 228 sheet: -0.24 (0.37), residues: 188 loop : -1.21 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG e 117 TYR 0.026 0.002 TYR B 102 PHE 0.018 0.001 PHE b 50 TRP 0.009 0.001 TRP B 36 HIS 0.002 0.001 HIS e 61 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6655) covalent geometry : angle 0.71255 ( 9021) SS BOND : bond 0.00287 ( 9) SS BOND : angle 1.15903 ( 18) hydrogen bonds : bond 0.04001 ( 319) hydrogen bonds : angle 5.01835 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 34 PHE cc_start: 0.6195 (m-80) cc_final: 0.5943 (m-80) REVERT: d 63 ARG cc_start: 0.8585 (mtm110) cc_final: 0.7958 (mtm110) REVERT: d 79 TYR cc_start: 0.7080 (m-10) cc_final: 0.6785 (m-80) REVERT: d 90 TYR cc_start: 0.7812 (m-80) cc_final: 0.7318 (m-80) REVERT: e 111 TYR cc_start: 0.7127 (m-80) cc_final: 0.6859 (m-80) REVERT: f 118 VAL cc_start: 0.8139 (m) cc_final: 0.7877 (p) REVERT: g 108 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7654 (pt) REVERT: A 82 ASP cc_start: 0.7534 (t70) cc_final: 0.6794 (t0) REVERT: B 30 THR cc_start: 0.8999 (p) cc_final: 0.8653 (t) outliers start: 46 outliers final: 29 residues processed: 265 average time/residue: 0.0551 time to fit residues: 20.0756 Evaluate side-chains 254 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain n residue 254 LEU Chi-restraints excluded: chain n residue 269 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 58 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.166015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112959 restraints weight = 11355.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114507 restraints weight = 7075.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116832 restraints weight = 4946.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116785 restraints weight = 4029.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116933 restraints weight = 3798.949| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6664 Z= 0.149 Angle : 0.694 9.316 9039 Z= 0.344 Chirality : 0.042 0.193 1035 Planarity : 0.004 0.073 1114 Dihedral : 6.626 57.284 967 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 7.99 % Allowed : 29.34 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.29), residues: 802 helix: 2.57 (0.32), residues: 228 sheet: -0.35 (0.35), residues: 216 loop : -1.11 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 117 TYR 0.022 0.002 TYR B 102 PHE 0.020 0.001 PHE a 40 TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6655) covalent geometry : angle 0.69284 ( 9021) SS BOND : bond 0.00273 ( 9) SS BOND : angle 1.25277 ( 18) hydrogen bonds : bond 0.03752 ( 319) hydrogen bonds : angle 4.66891 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4941 (OUTLIER) cc_final: 0.3975 (t80) REVERT: b 53 VAL cc_start: 0.5563 (t) cc_final: 0.5184 (t) REVERT: d 63 ARG cc_start: 0.8653 (mtm110) cc_final: 0.8324 (mtm110) REVERT: d 79 TYR cc_start: 0.7131 (m-80) cc_final: 0.6816 (m-80) REVERT: d 87 GLN cc_start: 0.1888 (mt0) cc_final: 0.1646 (tp40) REVERT: e 36 TYR cc_start: 0.6597 (m-80) cc_final: 0.5462 (m-80) REVERT: f 48 THR cc_start: 0.8915 (m) cc_final: 0.8541 (p) REVERT: g 108 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7764 (pt) REVERT: A 82 ASP cc_start: 0.7504 (t70) cc_final: 0.6709 (t0) REVERT: B 30 THR cc_start: 0.8986 (p) cc_final: 0.8659 (t) outliers start: 58 outliers final: 45 residues processed: 268 average time/residue: 0.0466 time to fit residues: 17.7016 Evaluate side-chains 274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain n residue 269 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.165072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111460 restraints weight = 11392.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113741 restraints weight = 7324.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115854 restraints weight = 4682.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115841 restraints weight = 3783.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116116 restraints weight = 3799.998| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6664 Z= 0.158 Angle : 0.707 11.279 9039 Z= 0.343 Chirality : 0.043 0.174 1035 Planarity : 0.004 0.072 1114 Dihedral : 6.414 59.399 965 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 8.13 % Allowed : 29.61 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.30), residues: 802 helix: 2.63 (0.32), residues: 228 sheet: -0.44 (0.35), residues: 208 loop : -1.09 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 117 TYR 0.021 0.002 TYR d 90 PHE 0.020 0.001 PHE b 50 TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6655) covalent geometry : angle 0.70559 ( 9021) SS BOND : bond 0.00263 ( 9) SS BOND : angle 1.18328 ( 18) hydrogen bonds : bond 0.03676 ( 319) hydrogen bonds : angle 4.58971 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4981 (OUTLIER) cc_final: 0.3982 (t80) REVERT: d 32 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7628 (mtp-110) REVERT: d 34 PHE cc_start: 0.6219 (m-80) cc_final: 0.5671 (t80) REVERT: d 58 LEU cc_start: 0.5898 (tp) cc_final: 0.5458 (tt) REVERT: d 63 ARG cc_start: 0.8816 (mtm110) cc_final: 0.8276 (mtm110) REVERT: d 79 TYR cc_start: 0.7136 (m-80) cc_final: 0.6822 (m-80) REVERT: d 90 TYR cc_start: 0.7511 (m-10) cc_final: 0.7187 (m-10) REVERT: e 34 THR cc_start: 0.4590 (p) cc_final: 0.4318 (m) REVERT: e 110 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4587 (t80) REVERT: m 255 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6215 (t-90) REVERT: f 48 THR cc_start: 0.8921 (m) cc_final: 0.8698 (p) REVERT: f 121 ASN cc_start: 0.8228 (t0) cc_final: 0.7921 (t0) REVERT: f 123 MET cc_start: 0.7654 (tpp) cc_final: 0.7436 (tpp) REVERT: g 108 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7781 (pt) REVERT: g 109 GLU cc_start: 0.8082 (tt0) cc_final: 0.7685 (tt0) REVERT: A 79 GLU cc_start: 0.7904 (mp0) cc_final: 0.7563 (mp0) REVERT: A 82 ASP cc_start: 0.7514 (t70) cc_final: 0.6762 (t0) REVERT: B 30 THR cc_start: 0.9007 (p) cc_final: 0.8703 (t) outliers start: 59 outliers final: 45 residues processed: 269 average time/residue: 0.0477 time to fit residues: 18.2225 Evaluate side-chains 277 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 117 ARG Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.167160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114282 restraints weight = 11392.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116363 restraints weight = 6627.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117308 restraints weight = 4905.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119389 restraints weight = 4009.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119211 restraints weight = 4067.608| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6664 Z= 0.129 Angle : 0.704 10.943 9039 Z= 0.341 Chirality : 0.043 0.218 1035 Planarity : 0.004 0.070 1114 Dihedral : 6.074 59.871 962 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.89 % Allowed : 31.40 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 802 helix: 2.66 (0.31), residues: 224 sheet: -0.36 (0.36), residues: 202 loop : -0.94 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 117 TYR 0.015 0.001 TYR n 266 PHE 0.012 0.001 PHE n 277 TRP 0.007 0.001 TRP B 47 HIS 0.002 0.000 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6655) covalent geometry : angle 0.70311 ( 9021) SS BOND : bond 0.00233 ( 9) SS BOND : angle 1.21380 ( 18) hydrogen bonds : bond 0.03596 ( 319) hydrogen bonds : angle 4.39002 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4959 (OUTLIER) cc_final: 0.4049 (t80) REVERT: a 54 LYS cc_start: 0.8259 (mttt) cc_final: 0.8047 (mmtp) REVERT: b 53 VAL cc_start: 0.5748 (t) cc_final: 0.5447 (t) REVERT: d 32 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7723 (mtp-110) REVERT: d 34 PHE cc_start: 0.6051 (m-80) cc_final: 0.5840 (m-80) REVERT: d 63 ARG cc_start: 0.8845 (mtm110) cc_final: 0.8339 (mtm110) REVERT: d 70 ILE cc_start: 0.6858 (mm) cc_final: 0.6456 (mt) REVERT: d 79 TYR cc_start: 0.7166 (m-80) cc_final: 0.6812 (m-80) REVERT: d 90 TYR cc_start: 0.7602 (m-10) cc_final: 0.7165 (m-10) REVERT: e 110 PHE cc_start: 0.4966 (OUTLIER) cc_final: 0.4554 (t80) REVERT: e 111 TYR cc_start: 0.6921 (m-80) cc_final: 0.6665 (m-80) REVERT: m 255 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.6247 (t-90) REVERT: m 286 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7920 (tppt) REVERT: f 123 MET cc_start: 0.7510 (tpp) cc_final: 0.7277 (tpp) REVERT: g 108 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7804 (pt) REVERT: g 118 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: B 18 MET cc_start: 0.8526 (tpp) cc_final: 0.8277 (tpp) REVERT: B 30 THR cc_start: 0.8946 (p) cc_final: 0.8634 (t) REVERT: B 43 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7868 (mtmm) outliers start: 50 outliers final: 34 residues processed: 266 average time/residue: 0.0489 time to fit residues: 18.0767 Evaluate side-chains 265 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 118 PHE Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 45 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117285 restraints weight = 11256.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118471 restraints weight = 6287.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120735 restraints weight = 4737.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120612 restraints weight = 4103.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120771 restraints weight = 3630.158| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6664 Z= 0.135 Angle : 0.716 11.924 9039 Z= 0.345 Chirality : 0.043 0.215 1035 Planarity : 0.004 0.071 1114 Dihedral : 5.602 57.991 960 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 6.89 % Allowed : 32.78 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 802 helix: 2.73 (0.32), residues: 224 sheet: -0.17 (0.36), residues: 200 loop : -0.92 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 82 TYR 0.022 0.002 TYR B 102 PHE 0.025 0.001 PHE b 50 TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS e 81 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6655) covalent geometry : angle 0.71515 ( 9021) SS BOND : bond 0.00232 ( 9) SS BOND : angle 1.16224 ( 18) hydrogen bonds : bond 0.03504 ( 319) hydrogen bonds : angle 4.33773 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.4054 (t80) REVERT: d 32 ARG cc_start: 0.8276 (ptp-110) cc_final: 0.7819 (mtp-110) REVERT: d 34 PHE cc_start: 0.6116 (m-80) cc_final: 0.5859 (m-80) REVERT: d 63 ARG cc_start: 0.8842 (mtm110) cc_final: 0.8333 (mtm110) REVERT: d 70 ILE cc_start: 0.6897 (mm) cc_final: 0.6520 (mt) REVERT: d 79 TYR cc_start: 0.7080 (m-80) cc_final: 0.6727 (m-80) REVERT: d 90 TYR cc_start: 0.7538 (m-10) cc_final: 0.7268 (m-10) REVERT: d 112 VAL cc_start: 0.8685 (m) cc_final: 0.8439 (m) REVERT: d 116 LEU cc_start: 0.8375 (mm) cc_final: 0.8050 (mm) REVERT: e 110 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4699 (t80) REVERT: m 255 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6355 (t-90) REVERT: m 286 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7922 (tppt) REVERT: g 108 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7779 (pt) REVERT: g 109 GLU cc_start: 0.8102 (tt0) cc_final: 0.7818 (tt0) REVERT: B 30 THR cc_start: 0.8938 (p) cc_final: 0.8639 (t) REVERT: B 43 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7893 (mtmm) outliers start: 50 outliers final: 40 residues processed: 257 average time/residue: 0.0528 time to fit residues: 18.9253 Evaluate side-chains 261 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114122 restraints weight = 11319.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115275 restraints weight = 6910.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116753 restraints weight = 5013.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116605 restraints weight = 4289.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116875 restraints weight = 4113.733| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6664 Z= 0.161 Angle : 0.731 12.374 9039 Z= 0.356 Chirality : 0.043 0.186 1035 Planarity : 0.004 0.068 1114 Dihedral : 5.651 55.108 959 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 8.13 % Allowed : 30.99 % Favored : 60.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.30), residues: 802 helix: 2.76 (0.32), residues: 224 sheet: -0.19 (0.37), residues: 192 loop : -0.89 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 117 TYR 0.021 0.002 TYR B 102 PHE 0.013 0.001 PHE n 277 TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS e 81 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6655) covalent geometry : angle 0.73027 ( 9021) SS BOND : bond 0.00264 ( 9) SS BOND : angle 1.10345 ( 18) hydrogen bonds : bond 0.03562 ( 319) hydrogen bonds : angle 4.38684 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4937 (OUTLIER) cc_final: 0.4059 (t80) REVERT: d 32 ARG cc_start: 0.8287 (ptp-110) cc_final: 0.7858 (mtp-110) REVERT: d 34 PHE cc_start: 0.6100 (m-80) cc_final: 0.5871 (m-80) REVERT: d 63 ARG cc_start: 0.8822 (mtm110) cc_final: 0.8239 (mtm110) REVERT: d 70 ILE cc_start: 0.7008 (mm) cc_final: 0.6644 (mt) REVERT: d 79 TYR cc_start: 0.7026 (m-80) cc_final: 0.6704 (m-80) REVERT: d 90 TYR cc_start: 0.7466 (m-10) cc_final: 0.7229 (m-10) REVERT: d 116 LEU cc_start: 0.8332 (mm) cc_final: 0.8042 (mm) REVERT: e 110 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.4992 (t80) REVERT: m 255 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.6345 (t-90) REVERT: m 286 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7924 (tppt) REVERT: f 120 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7690 (tm-30) REVERT: g 108 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7934 (pt) REVERT: B 43 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7844 (mtmm) outliers start: 59 outliers final: 47 residues processed: 256 average time/residue: 0.0535 time to fit residues: 19.1909 Evaluate side-chains 270 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.164346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112114 restraints weight = 11377.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113268 restraints weight = 6739.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114586 restraints weight = 5122.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114420 restraints weight = 4462.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115075 restraints weight = 4115.520| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6664 Z= 0.198 Angle : 0.777 12.372 9039 Z= 0.375 Chirality : 0.045 0.185 1035 Planarity : 0.004 0.068 1114 Dihedral : 5.838 57.900 959 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 7.71 % Allowed : 31.96 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 802 helix: 2.59 (0.32), residues: 229 sheet: -0.33 (0.37), residues: 204 loop : -1.05 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG f 117 TYR 0.023 0.002 TYR B 102 PHE 0.016 0.001 PHE n 277 TRP 0.010 0.001 TRP B 47 HIS 0.002 0.001 HIS e 81 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6655) covalent geometry : angle 0.77612 ( 9021) SS BOND : bond 0.00260 ( 9) SS BOND : angle 1.29407 ( 18) hydrogen bonds : bond 0.03701 ( 319) hydrogen bonds : angle 4.54543 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4961 (OUTLIER) cc_final: 0.4071 (t80) REVERT: a 54 LYS cc_start: 0.8027 (mttt) cc_final: 0.7801 (mmtp) REVERT: d 32 ARG cc_start: 0.8357 (ptp-110) cc_final: 0.7903 (mtp-110) REVERT: d 34 PHE cc_start: 0.6150 (m-80) cc_final: 0.5915 (m-80) REVERT: d 63 ARG cc_start: 0.8892 (mtm110) cc_final: 0.8085 (mtm110) REVERT: d 70 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6698 (mt) REVERT: d 79 TYR cc_start: 0.6974 (m-80) cc_final: 0.6680 (m-80) REVERT: d 90 TYR cc_start: 0.7500 (m-10) cc_final: 0.7205 (m-10) REVERT: d 116 LEU cc_start: 0.8321 (mm) cc_final: 0.8041 (mm) REVERT: m 255 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6414 (t-90) REVERT: m 286 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7925 (tppt) REVERT: g 108 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7949 (pt) REVERT: B 43 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7999 (mtpp) outliers start: 56 outliers final: 45 residues processed: 254 average time/residue: 0.0545 time to fit residues: 19.3923 Evaluate side-chains 267 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 117 ARG Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.165338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113442 restraints weight = 11428.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114553 restraints weight = 6741.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116022 restraints weight = 5066.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115864 restraints weight = 4322.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116246 restraints weight = 4101.588| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6664 Z= 0.162 Angle : 0.780 12.593 9039 Z= 0.372 Chirality : 0.044 0.189 1035 Planarity : 0.004 0.068 1114 Dihedral : 5.835 58.859 959 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 7.44 % Allowed : 31.54 % Favored : 61.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.30), residues: 802 helix: 2.56 (0.31), residues: 225 sheet: -0.32 (0.36), residues: 203 loop : -0.97 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 117 TYR 0.029 0.002 TYR n 263 PHE 0.018 0.001 PHE n 277 TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS e 81 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6655) covalent geometry : angle 0.77812 ( 9021) SS BOND : bond 0.00358 ( 9) SS BOND : angle 1.33312 ( 18) hydrogen bonds : bond 0.03737 ( 319) hydrogen bonds : angle 4.46534 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4894 (OUTLIER) cc_final: 0.3945 (t80) REVERT: a 54 LYS cc_start: 0.8014 (mttt) cc_final: 0.7789 (mmtp) REVERT: d 32 ARG cc_start: 0.8305 (ptp-110) cc_final: 0.7842 (mtp-110) REVERT: d 34 PHE cc_start: 0.6073 (m-80) cc_final: 0.5775 (m-80) REVERT: d 63 ARG cc_start: 0.8861 (mtm110) cc_final: 0.8127 (mtm110) REVERT: d 70 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6891 (mt) REVERT: d 79 TYR cc_start: 0.6952 (m-80) cc_final: 0.6671 (m-80) REVERT: d 90 TYR cc_start: 0.7445 (m-10) cc_final: 0.7196 (m-10) REVERT: d 116 LEU cc_start: 0.8248 (mm) cc_final: 0.7966 (mm) REVERT: m 255 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6313 (t-90) REVERT: m 286 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7930 (tppt) REVERT: n 276 TYR cc_start: 0.8404 (t80) cc_final: 0.8167 (t80) REVERT: B 43 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8001 (mtpp) outliers start: 54 outliers final: 44 residues processed: 253 average time/residue: 0.0579 time to fit residues: 20.6428 Evaluate side-chains 264 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 117 ARG Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.165402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113119 restraints weight = 11268.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113942 restraints weight = 7362.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115084 restraints weight = 5327.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115460 restraints weight = 4362.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115754 restraints weight = 4174.714| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6664 Z= 0.166 Angle : 0.809 13.330 9039 Z= 0.382 Chirality : 0.045 0.192 1035 Planarity : 0.004 0.069 1114 Dihedral : 5.857 59.308 959 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.75 % Allowed : 32.92 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.30), residues: 802 helix: 2.55 (0.31), residues: 225 sheet: -0.26 (0.37), residues: 203 loop : -1.00 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 117 TYR 0.030 0.002 TYR n 263 PHE 0.028 0.001 PHE b 50 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS e 81 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6655) covalent geometry : angle 0.80793 ( 9021) SS BOND : bond 0.00406 ( 9) SS BOND : angle 1.18397 ( 18) hydrogen bonds : bond 0.03686 ( 319) hydrogen bonds : angle 4.49831 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: a 42 TYR cc_start: 0.4888 (OUTLIER) cc_final: 0.3963 (t80) REVERT: a 54 LYS cc_start: 0.8050 (mttt) cc_final: 0.7815 (mmtp) REVERT: d 32 ARG cc_start: 0.8366 (ptp-110) cc_final: 0.7895 (mtp-110) REVERT: d 34 PHE cc_start: 0.6297 (m-80) cc_final: 0.6073 (m-80) REVERT: d 63 ARG cc_start: 0.8903 (mtm110) cc_final: 0.8132 (mtm110) REVERT: d 70 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6886 (mt) REVERT: d 79 TYR cc_start: 0.6984 (m-80) cc_final: 0.6719 (m-80) REVERT: d 90 TYR cc_start: 0.7532 (m-10) cc_final: 0.7222 (m-10) REVERT: d 116 LEU cc_start: 0.8238 (mm) cc_final: 0.7977 (mm) REVERT: m 255 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.6221 (t-90) REVERT: m 286 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7930 (tppt) REVERT: n 276 TYR cc_start: 0.8329 (t80) cc_final: 0.8128 (t80) REVERT: A 82 ASP cc_start: 0.7630 (t70) cc_final: 0.6735 (t0) REVERT: B 43 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8030 (mtpp) outliers start: 49 outliers final: 43 residues processed: 250 average time/residue: 0.0624 time to fit residues: 21.7406 Evaluate side-chains 265 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 117 ARG Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain n residue 270 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 HIS m 280 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.165469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112293 restraints weight = 11364.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113728 restraints weight = 7612.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114950 restraints weight = 5339.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115210 restraints weight = 4298.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115495 restraints weight = 4282.077| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6664 Z= 0.164 Angle : 0.820 13.311 9039 Z= 0.386 Chirality : 0.045 0.180 1035 Planarity : 0.004 0.069 1114 Dihedral : 5.850 56.899 959 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.89 % Allowed : 33.33 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 802 helix: 2.55 (0.31), residues: 225 sheet: -0.34 (0.36), residues: 203 loop : -0.99 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 117 TYR 0.034 0.002 TYR n 263 PHE 0.027 0.001 PHE b 50 TRP 0.009 0.001 TRP B 47 HIS 0.007 0.001 HIS e 81 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6655) covalent geometry : angle 0.81529 ( 9021) SS BOND : bond 0.00313 ( 9) SS BOND : angle 2.19605 ( 18) hydrogen bonds : bond 0.03715 ( 319) hydrogen bonds : angle 4.48532 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.27 seconds wall clock time: 23 minutes 56.72 seconds (1436.72 seconds total)