Starting phenix.real_space_refine on Tue Aug 4 20:38:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q6b_72265/08_2026/9q6b_72265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q6b_72265/08_2026/9q6b_72265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q6b_72265/08_2026/9q6b_72265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q6b_72265/08_2026/9q6b_72265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q6b_72265/08_2026/9q6b_72265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q6b_72265/08_2026/9q6b_72265.map" } resolution = 2.97 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= 0.018 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 27 5.16 5 C 4114 2.51 5 N 1076 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6505 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "B" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 800 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 810 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1339 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Time building chain proxies: 1.73, per 1000 atoms: 0.27 Number of scatterers: 6505 At special positions: 0 Unit cell: (101.238, 104.11, 71.8, 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 27 16.00 O 1288 8.00 N 1076 7.00 C 4114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 926 " - pdb=" SG CYS G 937 " distance=2.03 Simple disulfide: pdb=" SG CYS G 943 " - pdb=" SG CYS G 956 " distance=2.03 Simple disulfide: pdb=" SG CYS G 950 " - pdb=" SG CYS G 965 " distance=2.03 Simple disulfide: pdb=" SG CYS G 967 " - pdb=" SG CYS G 978 " distance=2.03 Simple disulfide: pdb=" SG CYS G1004 " - pdb=" SG CYS G1074 " 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: 0.55 Conformation dependent library (CDL) restraints added in 456.2 milliseconds 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 21 sheets defined 5.4% alpha, 39.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.506A pdb=" N THR A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.703A pdb=" N GLU D 82 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'G' and resid 941 through 950 removed outlier: 5.250A pdb=" N ASP G 946 " --> pdb=" O CYS G 943 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN G 947 " --> pdb=" O LEU G 944 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.690A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TRP A 34 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.545A pdb=" N VAL B 10 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.545A pdb=" N VAL B 10 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.056A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 112 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.717A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 59 through 61 removed outlier: 4.861A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.840A pdb=" N TRP F 34 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.840A pdb=" N TRP F 34 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 930 through 933 Processing sheet with id=AB9, first strand: chain 'G' and resid 954 through 956 removed outlier: 3.596A pdb=" N THR G 966 " --> pdb=" O GLU G 955 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 971 through 973 Processing sheet with id=AC2, first strand: chain 'G' and resid 987 through 992 removed outlier: 3.781A pdb=" N GLU G 987 " --> pdb=" O ILE G1043 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN G1038 " --> pdb=" O LYS G1057 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS G1057 " --> pdb=" O ASN G1038 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 998 through 1001 removed outlier: 3.621A pdb=" N GLY G1005 " --> pdb=" O LEU G1001 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 576 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: 0.90 Time building geometry restraints manager: 0.75 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: 2019 1.34 - 1.46: 1397 1.46 - 1.58: 3220 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 6667 Sorted by residual: bond pdb=" N ASP A 108 " pdb=" CA ASP A 108 " ideal model delta sigma weight residual 1.462 1.491 -0.029 7.70e-03 1.69e+04 1.41e+01 bond pdb=" N VAL B 32 " pdb=" CA VAL B 32 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 9.00e+00 bond pdb=" N TYR A 32 " pdb=" CA TYR A 32 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.21e-02 6.83e+03 8.42e+00 bond pdb=" N VAL G1069 " pdb=" CA VAL G1069 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.17e-02 7.31e+03 7.66e+00 ... (remaining 6662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 8941 2.78 - 5.57: 116 5.57 - 8.35: 6 8.35 - 11.13: 0 11.13 - 13.92: 1 Bond angle restraints: 9064 Sorted by residual: angle pdb=" C LYS B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta sigma weight residual 120.97 134.89 -13.92 2.84e+00 1.24e-01 2.40e+01 angle pdb=" N ASP B 29 " pdb=" CA ASP B 29 " pdb=" C ASP B 29 " ideal model delta sigma weight residual 113.20 108.49 4.71 1.21e+00 6.83e-01 1.51e+01 angle pdb=" C LYS G 968 " pdb=" N GLU G 969 " pdb=" CA GLU G 969 " ideal model delta sigma weight residual 120.82 126.23 -5.41 1.50e+00 4.44e-01 1.30e+01 angle pdb=" N PHE E 101 " pdb=" CA PHE E 101 " pdb=" C PHE E 101 " ideal model delta sigma weight residual 110.91 115.09 -4.18 1.17e+00 7.31e-01 1.28e+01 angle pdb=" CA GLN A 99 " pdb=" C GLN A 99 " pdb=" O GLN A 99 " ideal model delta sigma weight residual 122.27 118.15 4.12 1.16e+00 7.43e-01 1.26e+01 ... (remaining 9059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3606 17.24 - 34.49: 250 34.49 - 51.73: 33 51.73 - 68.98: 16 68.98 - 86.22: 2 Dihedral angle restraints: 3907 sinusoidal: 1502 harmonic: 2405 Sorted by residual: dihedral pdb=" CB CYS G1004 " pdb=" SG CYS G1004 " pdb=" SG CYS G1074 " pdb=" CB CYS G1074 " ideal model delta sinusoidal sigma weight residual 93.00 158.23 -65.23 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 138.77 -45.77 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual 93.00 56.25 36.75 1 1.00e+01 1.00e-02 1.91e+01 ... (remaining 3904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 723 0.053 - 0.105: 194 0.105 - 0.157: 51 0.157 - 0.210: 3 0.210 - 0.262: 4 Chirality restraints: 975 Sorted by residual: chirality pdb=" CB ILE G 939 " pdb=" CA ILE G 939 " pdb=" CG1 ILE G 939 " pdb=" CG2 ILE G 939 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA VAL G1069 " pdb=" N VAL G1069 " pdb=" C VAL G1069 " pdb=" CB VAL G1069 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA PHE G1029 " pdb=" N PHE G1029 " pdb=" C PHE G1029 " pdb=" CB PHE G1029 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 972 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 34 " -0.021 2.00e-02 2.50e+03 1.94e-02 7.50e+00 pdb=" CG TYR E 34 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 34 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 34 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR E 34 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 34 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 97 " 0.174 9.50e-02 1.11e+02 7.79e-02 3.74e+00 pdb=" NE ARG C 97 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 97 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 97 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 97 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 101 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C PHE E 101 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE E 101 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL E 102 " 0.011 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2968 2.96 - 3.44: 6173 3.44 - 3.93: 11775 3.93 - 4.41: 13381 4.41 - 4.90: 22080 Nonbonded interactions: 56377 Sorted by model distance: nonbonded pdb=" N ASP A 108 " pdb=" OD1 ASP A 108 " model vdw 2.473 3.120 nonbonded pdb=" O SER A 103 " pdb=" OG SER A 103 " model vdw 2.555 3.040 nonbonded pdb=" N ASN A 52 " pdb=" O ASP A 56 " model vdw 2.593 3.120 nonbonded pdb=" N GLU G1046 " pdb=" O GLU G1046 " model vdw 2.595 2.496 nonbonded pdb=" N SER A 101 " pdb=" O SER A 101 " model vdw 2.604 2.496 ... (remaining 56372 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 'C' and (resid 1 or resid 3 through 34 or resid 36 through 49 or resid 51 \ or resid 53 or resid 55 or resid 57 or resid 59 through 64 or resid 66 through \ 77 or resid 79 through 98 or resid 100 or resid 105 or resid 108 through 113 or \ resid 115 through 116)) selection = (chain 'E' and (resid 1 or resid 3 through 31 or resid 34 through 36 or resid 38 \ through 51 or resid 53 or resid 55 or resid 57 or resid 59 or resid 61 through \ 66 or resid 68 through 79 or resid 81 through 100 or resid 104 or resid 109 or r \ esid 112 through 117 or resid 119 through 120)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.005 0.052 6678 Z= 0.290 Angle : 0.779 13.919 9086 Z= 0.455 Chirality : 0.052 0.262 975 Planarity : 0.006 0.078 1158 Dihedral : 12.169 86.220 2362 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.14 % Allowed : 0.42 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.28), residues: 824 helix: -4.21 (0.40), residues: 12 sheet: -0.60 (0.26), residues: 351 loop : -0.46 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 90 TYR 0.046 0.002 TYR E 34 PHE 0.030 0.003 PHE E 101 TRP 0.022 0.002 TRP C 34 HIS 0.010 0.003 HIS G1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.29 ( 6667) covalent geometry : angle 0.77724 / 0.45 ( 9064) SS BOND : bond 0.00433 / 0.22 ( 11) SS BOND : angle 1.30581 / 0.92 ( 22) hydrogen bonds : bond 0.21264 / 13.61 ( 235) hydrogen bonds : angle 10.81573 / 7.61 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 ASN cc_start: 0.7554 (m-40) cc_final: 0.7274 (m110) REVERT: E 3 GLN cc_start: 0.7957 (mt0) cc_final: 0.7638 (mt0) REVERT: E 13 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7375 (mmtm) REVERT: G 1040 GLU cc_start: 0.7748 (tt0) cc_final: 0.7342 (mp0) outliers start: 1 outliers final: 2 residues processed: 160 average time/residue: 0.4678 time to fit residues: 79.1084 Evaluate side-chains 129 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain G residue 983 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 41 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN G 964 GLN G 983 ASN G1015 GLN G1022 ASN G1068 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144867 restraints weight = 7399.144| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.64 r_work: 0.3532 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6678 Z= 0.207 Angle : 0.645 6.470 9086 Z= 0.347 Chirality : 0.047 0.160 975 Planarity : 0.005 0.039 1158 Dihedral : 5.165 22.506 922 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.20 % Allowed : 10.01 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.29), residues: 824 helix: -3.80 (0.82), residues: 6 sheet: -0.62 (0.26), residues: 365 loop : -0.01 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.028 0.002 TYR E 34 PHE 0.015 0.002 PHE G1067 TRP 0.020 0.002 TRP A 106 HIS 0.006 0.003 HIS G1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 ( 6667) covalent geometry : angle 0.64319 / 0.35 ( 9064) SS BOND : bond 0.00456 / 0.24 ( 11) SS BOND : angle 1.20642 / 0.80 ( 22) hydrogen bonds : bond 0.03822 / 2.60 ( 235) hydrogen bonds : angle 7.53906 / 5.21 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7975 (ptm160) REVERT: C 56 ASN cc_start: 0.7850 (m-40) cc_final: 0.7498 (m110) REVERT: E 3 GLN cc_start: 0.7730 (mt0) cc_final: 0.7408 (mt0) REVERT: E 13 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7337 (mmtm) REVERT: G 1040 GLU cc_start: 0.7866 (tt0) cc_final: 0.7344 (mp0) outliers start: 23 outliers final: 8 residues processed: 142 average time/residue: 0.4758 time to fit residues: 71.3757 Evaluate side-chains 134 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain G residue 1019 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 41 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 964 GLN G1042 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141233 restraints weight = 7412.203| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.64 r_work: 0.3496 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6678 Z= 0.179 Angle : 0.594 5.799 9086 Z= 0.320 Chirality : 0.046 0.158 975 Planarity : 0.004 0.036 1158 Dihedral : 4.929 18.539 918 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.48 % Allowed : 13.21 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.29), residues: 824 helix: -3.23 (1.32), residues: 6 sheet: -0.43 (0.26), residues: 358 loop : -0.04 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 97 TYR 0.022 0.002 TYR E 34 PHE 0.018 0.002 PHE C 104 TRP 0.014 0.002 TRP C 47 HIS 0.006 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 6667) covalent geometry : angle 0.59180 / 0.32 ( 9064) SS BOND : bond 0.00426 / 0.24 ( 11) SS BOND : angle 1.13041 / 0.74 ( 22) hydrogen bonds : bond 0.03608 / 2.42 ( 235) hydrogen bonds : angle 6.98400 / 4.85 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.180 Fit side-chains REVERT: A 66 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8066 (ptm160) REVERT: C 56 ASN cc_start: 0.7959 (m-40) cc_final: 0.7609 (m110) REVERT: E 3 GLN cc_start: 0.7880 (mt0) cc_final: 0.7565 (mt0) REVERT: E 13 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7313 (mmtm) REVERT: G 1040 GLU cc_start: 0.7864 (tt0) cc_final: 0.7335 (mp0) outliers start: 25 outliers final: 12 residues processed: 132 average time/residue: 0.4732 time to fit residues: 65.9535 Evaluate side-chains 131 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 1020 ILE Chi-restraints excluded: chain G residue 1028 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 41 GLN G 964 GLN G 992 GLN G1042 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135438 restraints weight = 7554.526| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.68 r_work: 0.3400 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6678 Z= 0.251 Angle : 0.651 6.271 9086 Z= 0.350 Chirality : 0.047 0.161 975 Planarity : 0.005 0.038 1158 Dihedral : 5.118 18.869 918 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.17 % Allowed : 14.74 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.29), residues: 824 helix: -2.72 (1.81), residues: 6 sheet: -0.42 (0.28), residues: 336 loop : -0.05 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 19 TYR 0.021 0.002 TYR G1027 PHE 0.018 0.003 PHE D 48 TRP 0.016 0.002 TRP A 110 HIS 0.006 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 ( 6667) covalent geometry : angle 0.64675 / 0.35 ( 9064) SS BOND : bond 0.00713 / 0.40 ( 11) SS BOND : angle 1.70748 / 1.16 ( 22) hydrogen bonds : bond 0.03763 / 2.54 ( 235) hydrogen bonds : angle 6.96359 / 4.82 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.181 Fit side-chains REVERT: A 63 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 66 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8114 (ptm160) REVERT: A 68 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7779 (p) REVERT: C 56 ASN cc_start: 0.8132 (m-40) cc_final: 0.7731 (m110) REVERT: E 3 GLN cc_start: 0.8084 (mt0) cc_final: 0.7779 (mt0) REVERT: E 13 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7357 (mmtm) REVERT: G 1040 GLU cc_start: 0.7935 (tt0) cc_final: 0.7395 (mp0) REVERT: G 1042 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8558 (tt0) outliers start: 30 outliers final: 20 residues processed: 132 average time/residue: 0.4705 time to fit residues: 65.6684 Evaluate side-chains 137 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain G residue 927 THR Chi-restraints excluded: chain G residue 974 LYS Chi-restraints excluded: chain G residue 1020 ILE Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1042 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN F 16 GLN G 992 GLN ** G1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135751 restraints weight = 7615.627| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.69 r_work: 0.3424 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6678 Z= 0.213 Angle : 0.616 6.255 9086 Z= 0.332 Chirality : 0.046 0.158 975 Planarity : 0.005 0.040 1158 Dihedral : 5.073 18.995 918 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.73 % Allowed : 15.16 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.29), residues: 824 helix: -2.69 (1.85), residues: 6 sheet: -0.36 (0.28), residues: 336 loop : -0.10 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 952 TYR 0.019 0.002 TYR E 34 PHE 0.020 0.002 PHE D 48 TRP 0.015 0.002 TRP C 47 HIS 0.006 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 6667) covalent geometry : angle 0.61277 / 0.33 ( 9064) SS BOND : bond 0.00570 / 0.33 ( 11) SS BOND : angle 1.41325 / 0.96 ( 22) hydrogen bonds : bond 0.03476 / 2.35 ( 235) hydrogen bonds : angle 6.81956 / 4.73 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.244 Fit side-chains REVERT: A 63 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7893 (mt) REVERT: A 66 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: A 68 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7765 (p) REVERT: B 26 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8362 (mtmm) REVERT: C 56 ASN cc_start: 0.8172 (m-40) cc_final: 0.7776 (m110) REVERT: E 3 GLN cc_start: 0.8064 (mt0) cc_final: 0.7755 (mt0) REVERT: E 13 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7361 (mmtm) REVERT: G 939 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6752 (mt) REVERT: G 968 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7734 (mtpm) REVERT: G 1040 GLU cc_start: 0.7904 (tt0) cc_final: 0.7331 (mp0) REVERT: G 1044 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8490 (tttm) outliers start: 34 outliers final: 20 residues processed: 139 average time/residue: 0.4441 time to fit residues: 65.3020 Evaluate side-chains 142 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 939 ILE Chi-restraints excluded: chain G residue 974 LYS Chi-restraints excluded: chain G residue 1020 ILE Chi-restraints excluded: chain G residue 1044 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN F 16 GLN G 992 GLN G1042 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136175 restraints weight = 7490.164| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.66 r_work: 0.3427 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6678 Z= 0.184 Angle : 0.589 6.173 9086 Z= 0.318 Chirality : 0.045 0.158 975 Planarity : 0.004 0.041 1158 Dihedral : 4.989 18.810 918 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.31 % Allowed : 16.41 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.29), residues: 824 helix: -2.64 (1.87), residues: 6 sheet: -0.33 (0.28), residues: 336 loop : -0.07 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 952 TYR 0.017 0.002 TYR E 34 PHE 0.019 0.002 PHE D 48 TRP 0.013 0.002 TRP C 47 HIS 0.006 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 6667) covalent geometry : angle 0.58679 / 0.32 ( 9064) SS BOND : bond 0.00471 / 0.27 ( 11) SS BOND : angle 1.18262 / 0.81 ( 22) hydrogen bonds : bond 0.03296 / 2.23 ( 235) hydrogen bonds : angle 6.66003 / 4.61 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.231 Fit side-chains REVERT: A 63 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7793 (mt) REVERT: A 68 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7794 (p) REVERT: B 26 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8334 (mtmm) REVERT: C 56 ASN cc_start: 0.8147 (m-40) cc_final: 0.7761 (m110) REVERT: E 3 GLN cc_start: 0.8010 (mt0) cc_final: 0.7714 (mt0) REVERT: E 13 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7285 (mmtm) REVERT: G 939 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6661 (mt) REVERT: G 968 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7650 (mtpm) REVERT: G 1040 GLU cc_start: 0.7935 (tt0) cc_final: 0.7333 (mp0) REVERT: G 1044 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8536 (tttm) outliers start: 31 outliers final: 21 residues processed: 140 average time/residue: 0.4531 time to fit residues: 67.0149 Evaluate side-chains 143 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 927 THR Chi-restraints excluded: chain G residue 939 ILE Chi-restraints excluded: chain G residue 1020 ILE Chi-restraints excluded: chain G residue 1044 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 41 GLN F 16 GLN G1042 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133622 restraints weight = 7469.721| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.65 r_work: 0.3393 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6678 Z= 0.228 Angle : 0.618 6.278 9086 Z= 0.333 Chirality : 0.046 0.156 975 Planarity : 0.005 0.042 1158 Dihedral : 5.054 19.000 918 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.01 % Allowed : 15.99 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.29), residues: 824 helix: -2.54 (1.94), residues: 6 sheet: -0.38 (0.28), residues: 336 loop : -0.09 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 19 TYR 0.017 0.002 TYR E 34 PHE 0.023 0.002 PHE D 48 TRP 0.014 0.002 TRP C 47 HIS 0.006 0.002 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 ( 6667) covalent geometry : angle 0.61502 / 0.33 ( 9064) SS BOND : bond 0.00620 / 0.35 ( 11) SS BOND : angle 1.35021 / 0.89 ( 22) hydrogen bonds : bond 0.03496 / 2.36 ( 235) hydrogen bonds : angle 6.70379 / 4.64 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.167 Fit side-chains REVERT: A 63 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7904 (mt) REVERT: A 68 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 26 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8346 (mtmm) REVERT: C 56 ASN cc_start: 0.8315 (m-40) cc_final: 0.7898 (m110) REVERT: E 3 GLN cc_start: 0.8078 (mt0) cc_final: 0.7755 (mt0) REVERT: E 13 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7328 (mmtm) REVERT: G 939 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6708 (mt) REVERT: G 968 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7672 (mtpm) REVERT: G 1040 GLU cc_start: 0.7926 (tt0) cc_final: 0.7327 (mp0) REVERT: G 1044 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8548 (tttm) outliers start: 36 outliers final: 24 residues processed: 139 average time/residue: 0.4179 time to fit residues: 61.7032 Evaluate side-chains 144 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 16 GLN Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain G residue 927 THR Chi-restraints excluded: chain G residue 939 ILE Chi-restraints excluded: chain G residue 1020 ILE Chi-restraints excluded: chain G residue 1044 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN B 41 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1042 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134420 restraints weight = 7532.470| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.66 r_work: 0.3403 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6678 Z= 0.202 Angle : 0.608 6.259 9086 Z= 0.327 Chirality : 0.046 0.155 975 Planarity : 0.005 0.042 1158 Dihedral : 5.052 19.011 918 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.17 % Allowed : 17.11 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.29), residues: 824 helix: -2.60 (1.89), residues: 6 sheet: -0.43 (0.27), residues: 336 loop : -0.08 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 952 TYR 0.017 0.002 TYR E 34 PHE 0.022 0.002 PHE D 48 TRP 0.014 0.002 TRP C 47 HIS 0.006 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 6667) covalent geometry : angle 0.60511 / 0.33 ( 9064) SS BOND : bond 0.00545 / 0.31 ( 11) SS BOND : angle 1.27868 / 0.86 ( 22) hydrogen bonds : bond 0.03327 / 2.24 ( 235) hydrogen bonds : angle 6.65563 / 4.61 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.255 Fit side-chains REVERT: A 63 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7917 (mt) REVERT: A 68 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 26 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8349 (mtmm) REVERT: E 3 GLN cc_start: 0.8058 (mt0) cc_final: 0.7741 (mt0) REVERT: E 13 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7311 (mmtm) REVERT: G 939 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.6672 (mt) REVERT: G 968 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7657 (mtpm) REVERT: G 1040 GLU cc_start: 0.7931 (tt0) cc_final: 0.7343 (mp0) outliers start: 30 outliers final: 21 residues processed: 140 average time/residue: 0.4369 time to fit residues: 65.0368 Evaluate side-chains 142 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 927 THR Chi-restraints excluded: chain G residue 939 ILE Chi-restraints excluded: chain G residue 1020 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN B 41 GLN C 56 ASN G1042 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135788 restraints weight = 7524.146| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.66 r_work: 0.3418 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6678 Z= 0.184 Angle : 0.596 6.070 9086 Z= 0.321 Chirality : 0.045 0.155 975 Planarity : 0.004 0.041 1158 Dihedral : 5.016 18.949 918 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.03 % Allowed : 17.66 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.29), residues: 824 helix: -2.66 (1.79), residues: 6 sheet: -0.39 (0.27), residues: 336 loop : -0.09 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 952 TYR 0.015 0.002 TYR E 34 PHE 0.020 0.002 PHE D 48 TRP 0.013 0.002 TRP C 47 HIS 0.005 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 6667) covalent geometry : angle 0.59381 / 0.32 ( 9064) SS BOND : bond 0.00466 / 0.27 ( 11) SS BOND : angle 1.17797 / 0.80 ( 22) hydrogen bonds : bond 0.03181 / 2.14 ( 235) hydrogen bonds : angle 6.55323 / 4.54 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.238 Fit side-chains REVERT: A 63 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7840 (mt) REVERT: A 66 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.6419 (ptm-80) REVERT: A 68 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7833 (p) REVERT: B 26 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8333 (mtmm) REVERT: E 3 GLN cc_start: 0.8037 (mt0) cc_final: 0.7746 (mt0) REVERT: E 13 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7285 (mmtm) REVERT: G 968 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7650 (mtpm) REVERT: G 1040 GLU cc_start: 0.7937 (tt0) cc_final: 0.7322 (mp0) outliers start: 29 outliers final: 21 residues processed: 144 average time/residue: 0.3921 time to fit residues: 60.0447 Evaluate side-chains 143 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 927 THR Chi-restraints excluded: chain G residue 1020 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN B 41 GLN C 56 ASN D 88 ASN G1042 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135595 restraints weight = 7419.078| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.64 r_work: 0.3421 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6678 Z= 0.188 Angle : 0.607 6.074 9086 Z= 0.327 Chirality : 0.046 0.175 975 Planarity : 0.005 0.042 1158 Dihedral : 5.044 21.431 918 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.62 % Allowed : 18.50 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.29), residues: 824 helix: -2.59 (1.78), residues: 6 sheet: -0.37 (0.27), residues: 335 loop : -0.07 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 952 TYR 0.016 0.002 TYR B 35 PHE 0.020 0.002 PHE D 48 TRP 0.013 0.002 TRP C 47 HIS 0.005 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 6667) covalent geometry : angle 0.60523 / 0.33 ( 9064) SS BOND : bond 0.00470 / 0.27 ( 11) SS BOND : angle 1.15937 / 0.78 ( 22) hydrogen bonds : bond 0.03154 / 2.13 ( 235) hydrogen bonds : angle 6.55185 / 4.54 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.247 Fit side-chains REVERT: A 63 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7831 (mt) REVERT: A 66 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.6447 (ptm-80) REVERT: A 68 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7853 (p) REVERT: B 26 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8395 (mtmm) REVERT: E 3 GLN cc_start: 0.8042 (mt0) cc_final: 0.7751 (mt0) REVERT: E 13 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7273 (mmtm) REVERT: G 968 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7653 (mtpm) REVERT: G 1040 GLU cc_start: 0.7949 (tt0) cc_final: 0.7340 (mp0) outliers start: 26 outliers final: 21 residues processed: 135 average time/residue: 0.4188 time to fit residues: 59.9997 Evaluate side-chains 140 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 927 THR Chi-restraints excluded: chain G residue 1020 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 11 optimal weight: 0.0030 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN B 41 GLN G1042 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138273 restraints weight = 7442.527| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.62 r_work: 0.3457 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6678 Z= 0.155 Angle : 0.591 5.870 9086 Z= 0.319 Chirality : 0.045 0.153 975 Planarity : 0.005 0.042 1158 Dihedral : 4.978 20.609 918 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.06 % Allowed : 19.61 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.29), residues: 824 helix: -2.61 (1.70), residues: 6 sheet: -0.30 (0.28), residues: 335 loop : -0.07 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 952 TYR 0.014 0.002 TYR B 35 PHE 0.018 0.002 PHE D 48 TRP 0.013 0.002 TRP F 34 HIS 0.005 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 6667) covalent geometry : angle 0.58931 / 0.32 ( 9064) SS BOND : bond 0.00354 / 0.20 ( 11) SS BOND : angle 1.05947 / 0.72 ( 22) hydrogen bonds : bond 0.02958 / 2.01 ( 235) hydrogen bonds : angle 6.37531 / 4.42 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.11 seconds wall clock time: 43 minutes 0.19 seconds (2580.19 seconds total)