Starting phenix.real_space_refine on Fri Sep 11 19:23:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6k_65694/09_2026/9w6k_65694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6k_65694/09_2026/9w6k_65694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w6k_65694/09_2026/9w6k_65694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6k_65694/09_2026/9w6k_65694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w6k_65694/09_2026/9w6k_65694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6k_65694/09_2026/9w6k_65694.map" } resolution = 3.71 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= 0.002 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: 5 Type Number sf(0) Gaussians P 256 5.49 5 S 14 5.16 5 C 6137 2.51 5 N 2064 2.21 5 O 2552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11023 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "H" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2639 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "J" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2609 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Time building chain proxies: 2.47, per 1000 atoms: 0.22 Number of scatterers: 11023 At special positions: 0 Unit cell: (118.8, 119.9, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 256 15.00 O 2552 8.00 N 2064 7.00 C 6137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.90 Conformation dependent library (CDL) restraints added in 237.7 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 71.8% alpha, 2.5% beta 126 base pairs and 173 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.718A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.557A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.720A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.860A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.505A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.521A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.533A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.738A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 122 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.773A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.952A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.717A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.502A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 41 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.741A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 120 removed outlier: 4.067A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.973A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.398A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.925A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.129A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.275A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.729A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 372 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 173 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1479 1.33 - 1.45: 4238 1.45 - 1.57: 5491 1.57 - 1.69: 510 1.69 - 1.81: 24 Bond restraints: 11742 Sorted by residual: bond pdb=" N VAL D 48 " pdb=" CA VAL D 48 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA I 42 " pdb=" C2' DA I 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I -11 " pdb=" C2' DC I -11 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 ... (remaining 11737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 15109 1.01 - 2.03: 1377 2.03 - 3.04: 451 3.04 - 4.05: 15 4.05 - 5.07: 6 Bond angle restraints: 16958 Sorted by residual: angle pdb=" O4' DG J 27 " pdb=" C4' DG J 27 " pdb=" C3' DG J 27 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT I -23 " pdb=" C4 DT I -23 " pdb=" O4 DT I -23 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 ... (remaining 16953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4600 17.73 - 35.46: 756 35.46 - 53.20: 748 53.20 - 70.93: 252 70.93 - 88.66: 22 Dihedral angle restraints: 6378 sinusoidal: 4272 harmonic: 2106 Sorted by residual: dihedral pdb=" CA ARG F 19 " pdb=" CB ARG F 19 " pdb=" CG ARG F 19 " pdb=" CD ARG F 19 " ideal model delta sinusoidal sigma weight residual 180.00 131.58 48.42 3 1.50e+01 4.44e-03 8.64e+00 dihedral pdb=" N PHE C 25 " pdb=" CA PHE C 25 " pdb=" CB PHE C 25 " pdb=" CG PHE C 25 " ideal model delta sinusoidal sigma weight residual -60.00 -103.43 43.43 3 1.50e+01 4.44e-03 7.81e+00 dihedral pdb=" CA LYS H 108 " pdb=" CB LYS H 108 " pdb=" CG LYS H 108 " pdb=" CD LYS H 108 " ideal model delta sinusoidal sigma weight residual 60.00 102.52 -42.52 3 1.50e+01 4.44e-03 7.63e+00 ... (remaining 6375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1264 0.035 - 0.071: 488 0.071 - 0.106: 156 0.106 - 0.141: 24 0.141 - 0.177: 2 Chirality restraints: 1934 Sorted by residual: chirality pdb=" CA PHE A 78 " pdb=" N PHE A 78 " pdb=" C PHE A 78 " pdb=" CB PHE A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA VAL D 48 " pdb=" N VAL D 48 " pdb=" C VAL D 48 " pdb=" CB VAL D 48 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA GLN D 47 " pdb=" N GLN D 47 " pdb=" C GLN D 47 " pdb=" CB GLN D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1931 not shown) Planarity restraints: 1257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 49 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO D 50 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 77 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ASP A 77 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A 77 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 78 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -32 " 0.007 2.00e-02 2.50e+03 9.44e-03 2.23e+00 pdb=" N1 DT I -32 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DT I -32 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DT I -32 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DT I -32 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I -32 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DT I -32 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT I -32 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I -32 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT I -32 " 0.001 2.00e-02 2.50e+03 ... (remaining 1254 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1432 2.76 - 3.29: 9854 3.29 - 3.83: 21319 3.83 - 4.36: 23108 4.36 - 4.90: 34808 Nonbonded interactions: 90521 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.262 3.040 nonbonded pdb=" O ASN H 63 " pdb=" ND2 ASN H 67 " model vdw 2.307 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.308 3.040 nonbonded pdb=" O LEU G 85 " pdb=" ND2 ASN G 89 " model vdw 2.314 3.120 ... (remaining 90516 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 18 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 36 through 121) selection = chain 'H' } 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: 1.310 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.330 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 0.043 11742 Z= 0.494 Angle : 0.659 5.068 16958 Z= 0.626 Chirality : 0.041 0.177 1934 Planarity : 0.003 0.042 1257 Dihedral : 25.116 88.661 5022 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: 3.53 (0.32), residues: 712 helix: 3.29 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -0.23 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.006 0.001 TYR D 83 PHE 0.009 0.001 PHE A 78 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.49 (11742) covalent geometry : angle 0.65888 / 0.63 (16958) hydrogen bonds : bond 0.10414 / 7.73 ( 700) hydrogen bonds : angle 2.98146 / 2.10 ( 1763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.6497 (p) cc_final: 0.6093 (t) REVERT: A 112 ILE cc_start: 0.8133 (mt) cc_final: 0.7784 (mm) REVERT: A 117 VAL cc_start: 0.8986 (t) cc_final: 0.8779 (t) REVERT: A 119 ILE cc_start: 0.8062 (pt) cc_final: 0.7780 (pt) REVERT: B 59 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8313 (tttp) REVERT: B 75 HIS cc_start: 0.7418 (t70) cc_final: 0.6965 (t-90) REVERT: D 42 TYR cc_start: 0.7463 (t80) cc_final: 0.6964 (t80) REVERT: D 76 GLU cc_start: 0.7354 (tp30) cc_final: 0.6891 (tp30) REVERT: D 83 TYR cc_start: 0.5883 (t80) cc_final: 0.5624 (t80) REVERT: D 85 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8022 (mmtt) REVERT: E 76 GLN cc_start: 0.7341 (pt0) cc_final: 0.6151 (pt0) REVERT: F 88 TYR cc_start: 0.7601 (m-80) cc_final: 0.7067 (m-80) REVERT: G 20 ARG cc_start: 0.7344 (ttm170) cc_final: 0.7075 (mtm-85) REVERT: G 64 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7709 (tp30) REVERT: H 83 TYR cc_start: 0.6815 (t80) cc_final: 0.6352 (t80) REVERT: H 113 GLU cc_start: 0.8067 (tp30) cc_final: 0.7817 (tp30) REVERT: H 118 VAL cc_start: 0.8221 (p) cc_final: 0.7960 (p) REVERT: H 120 LYS cc_start: 0.7912 (tttt) cc_final: 0.7306 (ttpt) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1592 time to fit residues: 55.7434 Evaluate side-chains 150 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 93 GLN B 75 HIS D 47 GLN F 75 HIS H 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096346 restraints weight = 29639.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097971 restraints weight = 17264.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099059 restraints weight = 12508.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099686 restraints weight = 10533.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099983 restraints weight = 9682.647| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11742 Z= 0.195 Angle : 0.621 6.020 16958 Z= 0.378 Chirality : 0.043 0.219 1934 Planarity : 0.005 0.037 1257 Dihedral : 29.391 84.069 3589 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.80 % Allowed : 11.35 % Favored : 85.86 % 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: 2.85 (0.32), residues: 712 helix: 2.73 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -0.47 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.020 0.002 TYR D 83 PHE 0.015 0.002 PHE G 25 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.20 (11742) covalent geometry : angle 0.62103 / 0.38 (16958) hydrogen bonds : bond 0.05679 / 3.91 ( 700) hydrogen bonds : angle 2.85885 / 1.98 ( 1763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.363 Fit side-chains REVERT: A 119 ILE cc_start: 0.8163 (pt) cc_final: 0.7935 (pt) REVERT: D 42 TYR cc_start: 0.7630 (t80) cc_final: 0.7026 (t80) REVERT: D 76 GLU cc_start: 0.7254 (tp30) cc_final: 0.6773 (tp30) REVERT: D 93 GLU cc_start: 0.7888 (mp0) cc_final: 0.7297 (mp0) REVERT: F 50 ILE cc_start: 0.8703 (mm) cc_final: 0.8316 (tp) REVERT: F 88 TYR cc_start: 0.7484 (m-80) cc_final: 0.7013 (m-10) REVERT: G 20 ARG cc_start: 0.7581 (ttm170) cc_final: 0.7285 (mtm-85) REVERT: H 83 TYR cc_start: 0.7077 (t80) cc_final: 0.6528 (t80) REVERT: H 120 LYS cc_start: 0.8148 (tttt) cc_final: 0.7620 (ttpt) outliers start: 17 outliers final: 10 residues processed: 168 average time/residue: 0.1142 time to fit residues: 26.7996 Evaluate side-chains 148 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 93 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.121977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090961 restraints weight = 29203.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092563 restraints weight = 17400.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093621 restraints weight = 12838.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094217 restraints weight = 10920.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094469 restraints weight = 10059.238| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11742 Z= 0.175 Angle : 0.596 6.721 16958 Z= 0.360 Chirality : 0.042 0.204 1934 Planarity : 0.005 0.038 1257 Dihedral : 29.739 84.558 3589 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.30 % Allowed : 14.97 % Favored : 82.73 % 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: 2.51 (0.31), residues: 712 helix: 2.51 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.67 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 45 TYR 0.013 0.002 TYR H 42 PHE 0.011 0.002 PHE G 25 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (11742) covalent geometry : angle 0.59609 / 0.36 (16958) hydrogen bonds : bond 0.05741 / 3.97 ( 700) hydrogen bonds : angle 2.77155 / 1.97 ( 1763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.294 Fit side-chains REVERT: A 76 GLN cc_start: 0.8244 (tp40) cc_final: 0.7785 (tp40) REVERT: B 79 LYS cc_start: 0.7584 (pttt) cc_final: 0.6846 (mttp) REVERT: D 42 TYR cc_start: 0.7694 (t80) cc_final: 0.7207 (t80) REVERT: F 50 ILE cc_start: 0.8775 (mm) cc_final: 0.8407 (tp) REVERT: F 92 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7881 (mtp85) REVERT: G 68 ASN cc_start: 0.8519 (t0) cc_final: 0.8029 (t0) REVERT: H 120 LYS cc_start: 0.8294 (tttt) cc_final: 0.7821 (ttpt) outliers start: 14 outliers final: 6 residues processed: 157 average time/residue: 0.1302 time to fit residues: 27.6736 Evaluate side-chains 133 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 0.0070 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 93 GLN B 93 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.122305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092097 restraints weight = 29714.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094067 restraints weight = 19114.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094148 restraints weight = 12914.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094349 restraints weight = 12420.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094377 restraints weight = 12120.299| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11742 Z= 0.141 Angle : 0.549 8.102 16958 Z= 0.333 Chirality : 0.039 0.202 1934 Planarity : 0.004 0.032 1257 Dihedral : 29.741 81.877 3589 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.32 % Allowed : 17.43 % Favored : 81.25 % 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: 2.82 (0.31), residues: 712 helix: 2.75 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.59 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.016 0.001 TYR H 83 PHE 0.007 0.001 PHE G 25 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 (11742) covalent geometry : angle 0.54925 / 0.33 (16958) hydrogen bonds : bond 0.04980 / 3.44 ( 700) hydrogen bonds : angle 2.67578 / 1.90 ( 1763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8198 (tp40) cc_final: 0.7773 (tp40) REVERT: B 79 LYS cc_start: 0.7442 (pttt) cc_final: 0.6942 (mttp) REVERT: C 89 ASN cc_start: 0.7666 (m-40) cc_final: 0.7298 (m110) REVERT: D 42 TYR cc_start: 0.7676 (t80) cc_final: 0.7169 (t80) REVERT: F 50 ILE cc_start: 0.8665 (mm) cc_final: 0.8330 (tp) REVERT: F 88 TYR cc_start: 0.7871 (m-10) cc_final: 0.7631 (m-10) REVERT: F 92 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7978 (mtp85) REVERT: H 120 LYS cc_start: 0.8307 (tttt) cc_final: 0.7832 (ttpt) outliers start: 8 outliers final: 5 residues processed: 142 average time/residue: 0.1207 time to fit residues: 23.8107 Evaluate side-chains 134 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 79 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN B 75 HIS E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.117651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086421 restraints weight = 28879.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088080 restraints weight = 17256.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089138 restraints weight = 12704.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089752 restraints weight = 10802.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089969 restraints weight = 9933.147| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11742 Z= 0.178 Angle : 0.626 6.937 16958 Z= 0.364 Chirality : 0.042 0.216 1934 Planarity : 0.005 0.048 1257 Dihedral : 29.943 83.137 3589 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.47 % Allowed : 17.93 % Favored : 79.61 % 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: 2.36 (0.31), residues: 712 helix: 2.51 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.97 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.018 0.002 TYR H 83 PHE 0.016 0.002 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (11742) covalent geometry : angle 0.62648 / 0.36 (16958) hydrogen bonds : bond 0.06072 / 4.17 ( 700) hydrogen bonds : angle 2.85822 / 2.05 ( 1763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7824 (tp40) REVERT: B 79 LYS cc_start: 0.7580 (pttt) cc_final: 0.7186 (mttp) REVERT: D 42 TYR cc_start: 0.7879 (t80) cc_final: 0.7479 (t80) REVERT: E 120 MET cc_start: 0.6683 (tpp) cc_final: 0.6282 (ttm) REVERT: E 124 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8896 (tt) REVERT: F 50 ILE cc_start: 0.8767 (mm) cc_final: 0.8427 (tp) REVERT: G 68 ASN cc_start: 0.8533 (t0) cc_final: 0.8069 (t0) REVERT: H 120 LYS cc_start: 0.8478 (tttt) cc_final: 0.8008 (ttmt) outliers start: 15 outliers final: 10 residues processed: 140 average time/residue: 0.1103 time to fit residues: 21.9364 Evaluate side-chains 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN ** G 84 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 = 0.3848 r_free = 0.3848 target = 0.118155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.087023 restraints weight = 29103.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088732 restraints weight = 17228.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089833 restraints weight = 12606.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090464 restraints weight = 10662.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090678 restraints weight = 9781.982| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11742 Z= 0.142 Angle : 0.564 8.128 16958 Z= 0.336 Chirality : 0.039 0.214 1934 Planarity : 0.004 0.033 1257 Dihedral : 29.930 83.313 3589 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.64 % Allowed : 18.75 % Favored : 79.61 % 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: 2.61 (0.32), residues: 712 helix: 2.72 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.010 0.001 TYR H 83 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (11742) covalent geometry : angle 0.56448 / 0.34 (16958) hydrogen bonds : bond 0.05219 / 3.59 ( 700) hydrogen bonds : angle 2.72393 / 1.95 ( 1763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7609 (pttt) cc_final: 0.7171 (mttp) REVERT: D 42 TYR cc_start: 0.7875 (t80) cc_final: 0.7428 (t80) REVERT: E 120 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6203 (ttm) REVERT: F 50 ILE cc_start: 0.8744 (mm) cc_final: 0.8456 (tp) REVERT: F 92 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7753 (mtp85) REVERT: G 68 ASN cc_start: 0.8591 (t0) cc_final: 0.8088 (t0) REVERT: H 120 LYS cc_start: 0.8437 (tttt) cc_final: 0.8008 (ttmt) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.1136 time to fit residues: 22.0092 Evaluate side-chains 133 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 50.0000 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.115043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083701 restraints weight = 28329.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085230 restraints weight = 17302.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086242 restraints weight = 12938.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086812 restraints weight = 11057.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087111 restraints weight = 10203.437| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11742 Z= 0.174 Angle : 0.609 7.132 16958 Z= 0.355 Chirality : 0.041 0.214 1934 Planarity : 0.005 0.037 1257 Dihedral : 30.063 84.060 3589 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.30 % Allowed : 18.09 % Favored : 79.61 % 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: 2.44 (0.32), residues: 712 helix: 2.61 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.07 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.013 0.001 TYR H 42 PHE 0.015 0.001 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (11742) covalent geometry : angle 0.60945 / 0.36 (16958) hydrogen bonds : bond 0.05990 / 4.11 ( 700) hydrogen bonds : angle 2.82372 / 2.01 ( 1763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7693 (pttt) cc_final: 0.7340 (mttp) REVERT: D 42 TYR cc_start: 0.7842 (t80) cc_final: 0.7353 (t80) REVERT: E 120 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6227 (ttm) REVERT: E 124 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8939 (tt) REVERT: F 92 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7715 (mtp85) REVERT: G 68 ASN cc_start: 0.8713 (t0) cc_final: 0.8245 (t0) REVERT: H 120 LYS cc_start: 0.8605 (tttt) cc_final: 0.8156 (ttmt) outliers start: 14 outliers final: 10 residues processed: 140 average time/residue: 0.1092 time to fit residues: 21.6727 Evaluate side-chains 139 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 31 HIS G 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.115531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084251 restraints weight = 28355.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085869 restraints weight = 17061.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.086920 restraints weight = 12610.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087518 restraints weight = 10744.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087636 restraints weight = 9887.082| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11742 Z= 0.142 Angle : 0.575 8.362 16958 Z= 0.340 Chirality : 0.039 0.218 1934 Planarity : 0.004 0.034 1257 Dihedral : 30.049 84.733 3589 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.48 % Allowed : 19.74 % Favored : 78.78 % 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: 2.56 (0.32), residues: 712 helix: 2.70 (0.22), residues: 509 sheet: None (None), residues: 0 loop : -1.06 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.019 0.001 TYR F 88 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (11742) covalent geometry : angle 0.57544 / 0.34 (16958) hydrogen bonds : bond 0.05300 / 3.64 ( 700) hydrogen bonds : angle 2.72880 / 1.96 ( 1763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7703 (pttt) cc_final: 0.7330 (mttp) REVERT: D 42 TYR cc_start: 0.7781 (t80) cc_final: 0.7308 (t80) REVERT: E 120 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6162 (ttm) REVERT: F 92 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7734 (mtp85) REVERT: G 68 ASN cc_start: 0.8672 (t0) cc_final: 0.8264 (t0) REVERT: H 120 LYS cc_start: 0.8574 (tttt) cc_final: 0.8152 (ttmt) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.1111 time to fit residues: 21.1047 Evaluate side-chains 132 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 0.0000 chunk 72 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.116788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085703 restraints weight = 28454.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087328 restraints weight = 16981.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088378 restraints weight = 12467.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088948 restraints weight = 10588.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089304 restraints weight = 9752.401| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11742 Z= 0.129 Angle : 0.554 11.044 16958 Z= 0.330 Chirality : 0.038 0.208 1934 Planarity : 0.004 0.033 1257 Dihedral : 29.966 85.118 3589 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.32 % Allowed : 20.07 % Favored : 78.62 % 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: 2.78 (0.32), residues: 712 helix: 2.85 (0.22), residues: 509 sheet: None (None), residues: 0 loop : -0.94 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.013 0.001 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.13 (11742) covalent geometry : angle 0.55420 / 0.33 (16958) hydrogen bonds : bond 0.04695 / 3.24 ( 700) hydrogen bonds : angle 2.58729 / 1.86 ( 1763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7665 (pttt) cc_final: 0.7214 (ptpp) REVERT: D 42 TYR cc_start: 0.7773 (t80) cc_final: 0.7296 (t80) REVERT: F 92 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7675 (mtp85) REVERT: G 68 ASN cc_start: 0.8713 (t0) cc_final: 0.8257 (t0) REVERT: H 108 LYS cc_start: 0.7859 (tmtt) cc_final: 0.7578 (ttpt) REVERT: H 120 LYS cc_start: 0.8523 (tttt) cc_final: 0.8078 (ttmt) outliers start: 8 outliers final: 5 residues processed: 141 average time/residue: 0.1182 time to fit residues: 23.2277 Evaluate side-chains 136 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.117283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.086383 restraints weight = 28670.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088026 restraints weight = 16993.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089089 restraints weight = 12456.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089699 restraints weight = 10519.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089917 restraints weight = 9668.277| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11742 Z= 0.128 Angle : 0.554 9.869 16958 Z= 0.329 Chirality : 0.037 0.204 1934 Planarity : 0.004 0.041 1257 Dihedral : 29.904 85.586 3589 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.99 % Allowed : 21.22 % Favored : 77.80 % 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: 2.89 (0.32), residues: 712 helix: 2.91 (0.22), residues: 509 sheet: None (None), residues: 0 loop : -0.81 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 79 TYR 0.013 0.001 TYR F 88 PHE 0.009 0.001 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.13 (11742) covalent geometry : angle 0.55414 / 0.33 (16958) hydrogen bonds : bond 0.04468 / 3.09 ( 700) hydrogen bonds : angle 2.52198 / 1.81 ( 1763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7572 (pttt) cc_final: 0.7258 (ptpp) REVERT: D 42 TYR cc_start: 0.7722 (t80) cc_final: 0.7203 (t80) REVERT: F 92 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7665 (mtp85) REVERT: G 68 ASN cc_start: 0.8674 (t0) cc_final: 0.8194 (t0) REVERT: H 120 LYS cc_start: 0.8490 (tttt) cc_final: 0.8005 (ttmt) outliers start: 6 outliers final: 4 residues processed: 136 average time/residue: 0.1209 time to fit residues: 22.7861 Evaluate side-chains 134 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 53 optimal weight: 0.0770 chunk 71 optimal weight: 20.0000 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.114291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083071 restraints weight = 28407.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084579 restraints weight = 17192.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085615 restraints weight = 12759.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086206 restraints weight = 10843.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086484 restraints weight = 9989.148| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11742 Z= 0.164 Angle : 0.615 13.912 16958 Z= 0.353 Chirality : 0.040 0.203 1934 Planarity : 0.005 0.039 1257 Dihedral : 30.030 87.328 3589 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.99 % Allowed : 20.56 % Favored : 78.45 % 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: 2.60 (0.32), residues: 712 helix: 2.69 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -0.93 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 79 TYR 0.013 0.001 TYR H 42 PHE 0.013 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (11742) covalent geometry : angle 0.61460 / 0.35 (16958) hydrogen bonds : bond 0.05562 / 3.82 ( 700) hydrogen bonds : angle 2.72366 / 1.95 ( 1763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.69 seconds wall clock time: 33 minutes 20.76 seconds (2000.76 seconds total)