Starting phenix.real_space_refine on Fri Feb 14 05:15:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7a_10391/02_2025/6t7a_10391.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7a_10391/02_2025/6t7a_10391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t7a_10391/02_2025/6t7a_10391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7a_10391/02_2025/6t7a_10391.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7a_10391/02_2025/6t7a_10391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7a_10391/02_2025/6t7a_10391.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.021 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 190 5.49 5 S 10 5.16 5 C 5889 2.51 5 N 1960 2.21 5 O 2289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10338 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1936 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "J" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1959 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 178 Time building chain proxies: 5.89, per 1000 atoms: 0.57 Number of scatterers: 10338 At special positions: 0 Unit cell: (85.05, 115.5, 129.15, 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 10 16.00 P 190 15.00 O 2289 8.00 N 1960 7.00 C 5889 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 812.3 milliseconds 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 68.2% alpha, 1.9% beta 93 base pairs and 171 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.965A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.511A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.534A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.769A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 4.227A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.160A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.810A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.184A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.540A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.585A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.331A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.722A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 31 through 41 removed outlier: 4.046A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.809A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.185A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.540A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.584A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.331A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.602A pdb=" N VAL K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 91 through 94 Processing helix chain 'K' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.264A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 7.451A 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: 7.507A 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 'G' and resid 42 through 43 removed outlier: 7.375A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 408 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 171 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 3.36 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: 1653 1.33 - 1.44: 3477 1.44 - 1.56: 5364 1.56 - 1.68: 378 1.68 - 1.80: 20 Bond restraints: 10892 Sorted by residual: bond pdb=" C3' DT I 87 " pdb=" O3' DT I 87 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.32e+00 bond pdb=" C ILE K 96 " pdb=" N PRO K 97 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.75e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.492 1.418 0.074 5.00e-02 4.00e+02 2.19e+00 bond pdb=" CA ILE F 26 " pdb=" C ILE F 26 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.27e-02 6.20e+03 2.11e+00 bond pdb=" CB ASN G 110 " pdb=" CG ASN G 110 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 ... (remaining 10887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 14698 1.85 - 3.69: 692 3.69 - 5.54: 56 5.54 - 7.39: 12 7.39 - 9.23: 6 Bond angle restraints: 15464 Sorted by residual: angle pdb=" N ILE F 34 " pdb=" CA ILE F 34 " pdb=" C ILE F 34 " ideal model delta sigma weight residual 112.96 107.02 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " ideal model delta sigma weight residual 119.63 115.90 3.73 8.10e-01 1.52e+00 2.12e+01 angle pdb=" C ARG F 23 " pdb=" CA ARG F 23 " pdb=" CB ARG F 23 " ideal model delta sigma weight residual 116.63 111.29 5.34 1.16e+00 7.43e-01 2.12e+01 angle pdb=" C LYS K 88 " pdb=" N MET K 89 " pdb=" CA MET K 89 " ideal model delta sigma weight residual 122.54 115.16 7.38 1.65e+00 3.67e-01 2.00e+01 angle pdb=" CA LYS H 27 " pdb=" CB LYS H 27 " pdb=" CG LYS H 27 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 ... (remaining 15459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 4324 19.65 - 39.31: 919 39.31 - 58.96: 783 58.96 - 78.61: 52 78.61 - 98.26: 17 Dihedral angle restraints: 6095 sinusoidal: 3789 harmonic: 2306 Sorted by residual: dihedral pdb=" CA LYS D 27 " pdb=" C LYS D 27 " pdb=" N ARG D 28 " pdb=" CA ARG D 28 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LYS H 27 " pdb=" C LYS H 27 " pdb=" N ARG H 28 " pdb=" CA ARG H 28 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 6092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1240 0.048 - 0.096: 373 0.096 - 0.144: 85 0.144 - 0.191: 15 0.191 - 0.239: 2 Chirality restraints: 1715 Sorted by residual: chirality pdb=" CB THR C 59 " pdb=" CA THR C 59 " pdb=" OG1 THR C 59 " pdb=" CG2 THR C 59 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB THR G 59 " pdb=" CA THR G 59 " pdb=" OG1 THR G 59 " pdb=" CG2 THR G 59 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1712 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C ASP F 24 " -0.069 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 60 " 0.028 2.00e-02 2.50e+03 1.50e-02 5.64e+00 pdb=" N1 DT I 60 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT I 60 " -0.014 2.00e-02 2.50e+03 pdb=" O2 DT I 60 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 60 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 60 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT I 60 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 60 " -0.012 2.00e-02 2.50e+03 pdb=" C6 DT I 60 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO C 80 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 146 2.62 - 3.19: 7862 3.19 - 3.76: 18565 3.76 - 4.33: 24486 4.33 - 4.90: 35606 Nonbonded interactions: 86665 Sorted by model distance: nonbonded pdb=" CB GLU E 73 " pdb=" CG ASN F 25 " model vdw 2.044 2.936 nonbonded pdb=" CD GLU E 73 " pdb=" CG ASN F 25 " model vdw 2.167 2.800 nonbonded pdb=" OE1 GLU E 73 " pdb=" CB ASN F 25 " model vdw 2.167 3.440 nonbonded pdb=" CB HIS F 18 " pdb=" OP1 DT I 87 " model vdw 2.168 3.440 nonbonded pdb=" CG GLU E 73 " pdb=" OD1 ASN F 25 " model vdw 2.219 2.752 ... (remaining 86660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 16 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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: 0.250 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.700 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.006 0.074 10892 Z= 0.370 Angle : 0.870 9.233 15464 Z= 0.526 Chirality : 0.048 0.239 1715 Planarity : 0.006 0.058 1327 Dihedral : 26.125 98.264 4657 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.81 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.23), residues: 829 helix: -1.95 (0.16), residues: 569 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.009 0.002 PHE D 62 TYR 0.027 0.002 TYR F 98 ARG 0.007 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9019 (t80) cc_final: 0.8623 (t80) REVERT: B 59 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8236 (mtpt) REVERT: B 60 VAL cc_start: 0.9049 (m) cc_final: 0.8010 (p) REVERT: B 63 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7510 (mt-10) REVERT: B 92 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7676 (ttp80) REVERT: C 73 ASN cc_start: 0.8815 (t0) cc_final: 0.8556 (t0) REVERT: C 84 GLN cc_start: 0.8744 (tp40) cc_final: 0.8352 (tp-100) REVERT: D 85 THR cc_start: 0.9519 (m) cc_final: 0.9088 (p) REVERT: E 86 SER cc_start: 0.8750 (m) cc_final: 0.8499 (m) REVERT: E 124 ILE cc_start: 0.9285 (mt) cc_final: 0.8917 (mp) REVERT: F 59 LYS cc_start: 0.8804 (tttm) cc_final: 0.8597 (tttm) REVERT: F 60 VAL cc_start: 0.9172 (p) cc_final: 0.8677 (m) REVERT: F 70 VAL cc_start: 0.9486 (t) cc_final: 0.8584 (t) REVERT: F 71 THR cc_start: 0.9268 (p) cc_final: 0.8683 (p) REVERT: G 56 GLU cc_start: 0.8182 (tt0) cc_final: 0.7931 (tt0) REVERT: G 71 ARG cc_start: 0.8832 (ttp-170) cc_final: 0.8617 (ttp80) REVERT: H 51 ILE cc_start: 0.8660 (tt) cc_final: 0.8417 (tt) REVERT: H 73 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7633 (mm-30) REVERT: H 80 TYR cc_start: 0.8678 (m-10) cc_final: 0.7979 (m-10) REVERT: H 85 THR cc_start: 0.9140 (m) cc_final: 0.8620 (p) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3475 time to fit residues: 147.6825 Evaluate side-chains 232 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 89 ASN C 112 GLN D 92 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055390 restraints weight = 37676.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057180 restraints weight = 18795.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058367 restraints weight = 12435.291| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10892 Z= 0.234 Angle : 0.641 7.730 15464 Z= 0.375 Chirality : 0.037 0.167 1715 Planarity : 0.005 0.034 1327 Dihedral : 29.174 87.335 3109 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.04 % Allowed : 16.02 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 829 helix: 0.23 (0.20), residues: 579 sheet: None (None), residues: 0 loop : -1.12 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.008 0.001 PHE F 100 TYR 0.021 0.002 TYR D 80 ARG 0.007 0.001 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9319 (tt0) cc_final: 0.8894 (tm-30) REVERT: A 94 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8541 (tp30) REVERT: B 27 GLN cc_start: 0.8758 (mp10) cc_final: 0.8553 (mp10) REVERT: B 67 ARG cc_start: 0.9182 (ttm110) cc_final: 0.8825 (ttm110) REVERT: B 92 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7671 (ttp80) REVERT: C 36 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9021 (mmmm) REVERT: C 64 GLU cc_start: 0.8520 (tt0) cc_final: 0.7932 (tm-30) REVERT: C 73 ASN cc_start: 0.9180 (t0) cc_final: 0.8825 (t0) REVERT: C 84 GLN cc_start: 0.8739 (tp40) cc_final: 0.8278 (tp40) REVERT: C 92 GLU cc_start: 0.8149 (pm20) cc_final: 0.7808 (pm20) REVERT: D 68 GLU cc_start: 0.8997 (tp30) cc_final: 0.8780 (tp30) REVERT: D 77 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8800 (mp) REVERT: D 83 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.8140 (mmm-85) REVERT: D 90 GLU cc_start: 0.9223 (mp0) cc_final: 0.8677 (mp0) REVERT: E 86 SER cc_start: 0.9006 (m) cc_final: 0.8726 (p) REVERT: E 120 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7445 (mtt) REVERT: F 59 LYS cc_start: 0.9183 (tttm) cc_final: 0.8630 (tttm) REVERT: F 63 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8399 (mp0) REVERT: F 70 VAL cc_start: 0.9612 (t) cc_final: 0.8962 (m) REVERT: F 71 THR cc_start: 0.9317 (p) cc_final: 0.9109 (p) REVERT: F 88 TYR cc_start: 0.8812 (m-10) cc_final: 0.8158 (m-10) REVERT: G 41 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8257 (mp0) REVERT: G 56 GLU cc_start: 0.8931 (tt0) cc_final: 0.8338 (tt0) REVERT: G 104 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: H 34 TYR cc_start: 0.9380 (m-80) cc_final: 0.9060 (m-10) REVERT: H 73 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7883 (mm-30) REVERT: H 85 THR cc_start: 0.9144 (m) cc_final: 0.8584 (p) REVERT: H 117 LYS cc_start: 0.9412 (mtmt) cc_final: 0.9145 (mtmt) outliers start: 26 outliers final: 16 residues processed: 285 average time/residue: 0.2473 time to fit residues: 93.8144 Evaluate side-chains 254 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 68 GLN E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.075188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.054175 restraints weight = 38087.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056017 restraints weight = 18737.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057228 restraints weight = 12259.847| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10892 Z= 0.222 Angle : 0.625 7.217 15464 Z= 0.367 Chirality : 0.037 0.152 1715 Planarity : 0.004 0.030 1327 Dihedral : 28.944 87.720 3109 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.89 % Allowed : 21.15 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.28), residues: 829 helix: 1.46 (0.21), residues: 569 sheet: None (None), residues: 0 loop : -0.86 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.006 0.001 PHE F 100 TYR 0.032 0.002 TYR D 80 ARG 0.011 0.001 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9325 (tt0) cc_final: 0.8915 (tm-30) REVERT: A 51 ILE cc_start: 0.9296 (mt) cc_final: 0.9026 (mm) REVERT: A 62 ILE cc_start: 0.9122 (pp) cc_final: 0.8617 (pp) REVERT: A 93 GLN cc_start: 0.9206 (tt0) cc_final: 0.8612 (tp40) REVERT: A 97 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 53 GLU cc_start: 0.9091 (tp30) cc_final: 0.8860 (tp30) REVERT: B 67 ARG cc_start: 0.9215 (ttm110) cc_final: 0.8966 (ttm110) REVERT: B 92 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7883 (ttp80) REVERT: C 64 GLU cc_start: 0.8587 (tt0) cc_final: 0.7974 (tm-30) REVERT: C 73 ASN cc_start: 0.9169 (t0) cc_final: 0.8801 (t0) REVERT: C 84 GLN cc_start: 0.8602 (tp40) cc_final: 0.8105 (tp40) REVERT: C 92 GLU cc_start: 0.8021 (pm20) cc_final: 0.7638 (pm20) REVERT: D 39 TYR cc_start: 0.8888 (t80) cc_final: 0.8676 (t80) REVERT: D 56 MET cc_start: 0.8023 (tpp) cc_final: 0.7811 (tpp) REVERT: D 68 GLU cc_start: 0.9021 (tp30) cc_final: 0.8805 (tp30) REVERT: D 77 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8683 (mp) REVERT: D 90 GLU cc_start: 0.9256 (mp0) cc_final: 0.8639 (mp0) REVERT: D 105 LYS cc_start: 0.9329 (ptpp) cc_final: 0.8335 (ptpp) REVERT: D 110 GLU cc_start: 0.9078 (tp30) cc_final: 0.8846 (tp30) REVERT: E 50 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8588 (mm-30) REVERT: E 56 LYS cc_start: 0.9349 (mtpp) cc_final: 0.9082 (mtmm) REVERT: E 86 SER cc_start: 0.9061 (m) cc_final: 0.8828 (p) REVERT: E 94 GLU cc_start: 0.8701 (tp30) cc_final: 0.8494 (tp30) REVERT: E 123 ASP cc_start: 0.9057 (m-30) cc_final: 0.8790 (m-30) REVERT: F 63 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8259 (mt-10) REVERT: F 88 TYR cc_start: 0.8725 (m-10) cc_final: 0.8350 (m-10) REVERT: G 41 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8335 (mp0) REVERT: G 56 GLU cc_start: 0.8965 (tt0) cc_final: 0.8375 (tt0) REVERT: G 64 GLU cc_start: 0.8494 (tp30) cc_final: 0.8255 (tp30) REVERT: H 34 TYR cc_start: 0.9399 (m-80) cc_final: 0.9102 (m-10) REVERT: H 54 LYS cc_start: 0.8778 (ptpt) cc_final: 0.8518 (ptmt) REVERT: H 73 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8169 (tp30) REVERT: H 83 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8108 (tpp-160) REVERT: H 85 THR cc_start: 0.8970 (m) cc_final: 0.8386 (p) REVERT: H 98 LEU cc_start: 0.8768 (mm) cc_final: 0.8555 (mm) REVERT: H 117 LYS cc_start: 0.9478 (mtmt) cc_final: 0.9149 (mtmt) outliers start: 25 outliers final: 15 residues processed: 277 average time/residue: 0.2762 time to fit residues: 100.2183 Evaluate side-chains 252 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 4 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 25 optimal weight: 0.0980 chunk 1 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 7.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.071600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050536 restraints weight = 38655.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052260 restraints weight = 19383.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053398 restraints weight = 12867.162| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10892 Z= 0.358 Angle : 0.681 8.865 15464 Z= 0.394 Chirality : 0.039 0.152 1715 Planarity : 0.004 0.033 1327 Dihedral : 29.046 89.585 3109 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.44 % Allowed : 23.02 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.28), residues: 829 helix: 2.01 (0.21), residues: 559 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.011 0.002 PHE F 100 TYR 0.028 0.002 TYR F 98 ARG 0.006 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9347 (tt0) cc_final: 0.8909 (tm-30) REVERT: A 51 ILE cc_start: 0.9340 (mt) cc_final: 0.9064 (mm) REVERT: A 93 GLN cc_start: 0.9279 (tt0) cc_final: 0.9076 (tt0) REVERT: A 97 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7895 (mt-10) REVERT: B 53 GLU cc_start: 0.9212 (tp30) cc_final: 0.8976 (tp30) REVERT: B 67 ARG cc_start: 0.9229 (ttm110) cc_final: 0.8994 (ttm110) REVERT: B 84 MET cc_start: 0.6825 (tpp) cc_final: 0.6222 (tpp) REVERT: B 92 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8069 (ttp80) REVERT: C 64 GLU cc_start: 0.8662 (tt0) cc_final: 0.8068 (tm-30) REVERT: C 73 ASN cc_start: 0.9229 (t0) cc_final: 0.8866 (t0) REVERT: C 75 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8883 (tptp) REVERT: C 84 GLN cc_start: 0.8694 (tp40) cc_final: 0.8191 (tp40) REVERT: C 92 GLU cc_start: 0.7820 (pm20) cc_final: 0.7125 (pm20) REVERT: C 104 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7703 (mm-40) REVERT: D 68 GLU cc_start: 0.8910 (tp30) cc_final: 0.8704 (tp30) REVERT: D 83 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8302 (mmm-85) REVERT: D 90 GLU cc_start: 0.9261 (mp0) cc_final: 0.8624 (mp0) REVERT: D 102 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8182 (mm-30) REVERT: D 105 LYS cc_start: 0.9041 (ptpp) cc_final: 0.8728 (ptpp) REVERT: D 110 GLU cc_start: 0.9069 (tp30) cc_final: 0.8822 (tp30) REVERT: D 117 LYS cc_start: 0.9463 (mmmt) cc_final: 0.9059 (ttmt) REVERT: E 50 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8696 (mm-30) REVERT: E 56 LYS cc_start: 0.9432 (mtpp) cc_final: 0.9166 (mtmm) REVERT: E 82 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8732 (mm) REVERT: F 63 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8331 (mt-10) REVERT: F 88 TYR cc_start: 0.8809 (m-10) cc_final: 0.8000 (m-10) REVERT: G 56 GLU cc_start: 0.9014 (tt0) cc_final: 0.8436 (tt0) REVERT: G 61 GLU cc_start: 0.8990 (tp30) cc_final: 0.8781 (tp30) REVERT: G 64 GLU cc_start: 0.8621 (tp30) cc_final: 0.8287 (tp30) REVERT: G 75 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8983 (mmtp) REVERT: G 104 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8846 (pm20) REVERT: H 34 TYR cc_start: 0.9439 (m-80) cc_final: 0.9170 (m-10) REVERT: H 44 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8550 (tm-30) REVERT: H 73 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8097 (tp30) REVERT: H 85 THR cc_start: 0.8970 (m) cc_final: 0.8716 (p) REVERT: H 98 LEU cc_start: 0.8849 (mm) cc_final: 0.8460 (mm) REVERT: H 110 GLU cc_start: 0.9249 (tp30) cc_final: 0.8863 (tp30) REVERT: H 117 LYS cc_start: 0.9478 (mtmt) cc_final: 0.9115 (mtmt) outliers start: 35 outliers final: 24 residues processed: 260 average time/residue: 0.2698 time to fit residues: 93.3258 Evaluate side-chains 254 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 29 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN E 68 GLN E 93 GLN E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.073058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052056 restraints weight = 37489.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053804 restraints weight = 18968.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054938 restraints weight = 12641.807| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10892 Z= 0.234 Angle : 0.633 9.330 15464 Z= 0.369 Chirality : 0.037 0.159 1715 Planarity : 0.003 0.030 1327 Dihedral : 28.942 89.717 3109 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.20 % Allowed : 24.42 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.28), residues: 829 helix: 2.23 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.008 0.001 PHE E 78 TYR 0.038 0.002 TYR D 80 ARG 0.005 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9282 (tt0) cc_final: 0.8892 (tm-30) REVERT: A 51 ILE cc_start: 0.9375 (mt) cc_final: 0.9067 (mm) REVERT: A 93 GLN cc_start: 0.9149 (tt0) cc_final: 0.8769 (tp40) REVERT: A 97 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7823 (mt-10) REVERT: B 20 LYS cc_start: 0.8511 (tppp) cc_final: 0.8229 (mmmm) REVERT: B 22 LEU cc_start: 0.8288 (tp) cc_final: 0.8078 (tp) REVERT: B 53 GLU cc_start: 0.9108 (tp30) cc_final: 0.8876 (tp30) REVERT: B 84 MET cc_start: 0.7034 (tpp) cc_final: 0.6348 (tpp) REVERT: B 92 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7999 (ttp80) REVERT: C 64 GLU cc_start: 0.8614 (tt0) cc_final: 0.7977 (tm-30) REVERT: C 73 ASN cc_start: 0.9187 (t0) cc_final: 0.8812 (t0) REVERT: C 84 GLN cc_start: 0.8628 (tp40) cc_final: 0.8185 (tp40) REVERT: C 92 GLU cc_start: 0.7687 (pm20) cc_final: 0.7408 (pm20) REVERT: C 104 GLN cc_start: 0.8572 (mm-40) cc_final: 0.7758 (mm-40) REVERT: C 112 GLN cc_start: 0.8780 (mp10) cc_final: 0.8557 (mp10) REVERT: D 90 GLU cc_start: 0.9203 (mp0) cc_final: 0.8594 (mp0) REVERT: D 102 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8227 (mm-30) REVERT: D 110 GLU cc_start: 0.8875 (tp30) cc_final: 0.8626 (tp30) REVERT: D 117 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9122 (mtmt) REVERT: E 50 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8446 (mm-30) REVERT: E 56 LYS cc_start: 0.9386 (mtpp) cc_final: 0.9127 (mtmm) REVERT: E 82 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8429 (mm) REVERT: E 94 GLU cc_start: 0.8808 (tp30) cc_final: 0.8562 (tp30) REVERT: E 123 ASP cc_start: 0.9066 (m-30) cc_final: 0.8704 (m-30) REVERT: F 60 VAL cc_start: 0.9521 (p) cc_final: 0.8968 (m) REVERT: F 63 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8255 (mt-10) REVERT: F 88 TYR cc_start: 0.8830 (m-10) cc_final: 0.8035 (m-10) REVERT: G 56 GLU cc_start: 0.8978 (tt0) cc_final: 0.8417 (tt0) REVERT: G 61 GLU cc_start: 0.8899 (tp30) cc_final: 0.8685 (tp30) REVERT: G 64 GLU cc_start: 0.8606 (tp30) cc_final: 0.8067 (tp30) REVERT: G 75 LYS cc_start: 0.9238 (mmmm) cc_final: 0.9003 (mmtp) REVERT: G 92 GLU cc_start: 0.8228 (pm20) cc_final: 0.8008 (pm20) REVERT: G 104 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: H 44 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8572 (tm-30) REVERT: H 73 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7622 (mm-30) REVERT: H 83 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8254 (tpp80) REVERT: H 85 THR cc_start: 0.8920 (m) cc_final: 0.8691 (p) REVERT: H 98 LEU cc_start: 0.8856 (mm) cc_final: 0.8632 (mm) REVERT: H 117 LYS cc_start: 0.9468 (mtmt) cc_final: 0.9204 (mtmt) outliers start: 27 outliers final: 20 residues processed: 255 average time/residue: 0.2659 time to fit residues: 89.8644 Evaluate side-chains 251 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN E 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** 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 = 0.3581 r_free = 0.3581 target = 0.074065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053212 restraints weight = 37533.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.054981 restraints weight = 18693.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056135 restraints weight = 12375.509| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10892 Z= 0.204 Angle : 0.630 9.966 15464 Z= 0.365 Chirality : 0.036 0.161 1715 Planarity : 0.003 0.028 1327 Dihedral : 28.831 89.807 3109 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.58 % Allowed : 25.82 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.29), residues: 829 helix: 2.32 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.35 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.009 0.001 PHE E 78 TYR 0.019 0.002 TYR D 80 ARG 0.006 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9281 (tt0) cc_final: 0.8922 (tm-30) REVERT: A 97 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 20 LYS cc_start: 0.8499 (tppp) cc_final: 0.8295 (mmmt) REVERT: B 22 LEU cc_start: 0.8260 (tp) cc_final: 0.8057 (tp) REVERT: B 53 GLU cc_start: 0.9076 (tp30) cc_final: 0.8833 (tp30) REVERT: B 67 ARG cc_start: 0.9141 (ttm110) cc_final: 0.8919 (ttm110) REVERT: B 92 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8001 (ttp80) REVERT: C 64 GLU cc_start: 0.8602 (tt0) cc_final: 0.7956 (tm-30) REVERT: C 73 ASN cc_start: 0.9063 (t0) cc_final: 0.8730 (t0) REVERT: C 84 GLN cc_start: 0.8601 (tp40) cc_final: 0.8107 (tp-100) REVERT: C 104 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7744 (mm-40) REVERT: D 83 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8305 (mmm-85) REVERT: D 90 GLU cc_start: 0.9203 (mp0) cc_final: 0.8581 (mp0) REVERT: D 102 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8450 (mm-30) REVERT: D 110 GLU cc_start: 0.8866 (tp30) cc_final: 0.8585 (tp30) REVERT: D 117 LYS cc_start: 0.9414 (mmmt) cc_final: 0.9085 (mtmt) REVERT: E 50 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8503 (mm-30) REVERT: E 56 LYS cc_start: 0.9404 (mtpp) cc_final: 0.9111 (mtmm) REVERT: E 82 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8947 (mm) REVERT: E 86 SER cc_start: 0.9205 (m) cc_final: 0.8945 (p) REVERT: E 93 GLN cc_start: 0.8784 (tt0) cc_final: 0.8576 (tp40) REVERT: E 123 ASP cc_start: 0.9092 (m-30) cc_final: 0.8832 (m-30) REVERT: F 60 VAL cc_start: 0.9492 (p) cc_final: 0.8936 (m) REVERT: F 63 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8246 (mt-10) REVERT: G 56 GLU cc_start: 0.8954 (tt0) cc_final: 0.8406 (tt0) REVERT: G 61 GLU cc_start: 0.8922 (tp30) cc_final: 0.8698 (tp30) REVERT: G 64 GLU cc_start: 0.8722 (tp30) cc_final: 0.8157 (tp30) REVERT: G 92 GLU cc_start: 0.8086 (pm20) cc_final: 0.7821 (pm20) REVERT: G 104 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: H 44 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8602 (tm-30) REVERT: H 73 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7901 (tp30) REVERT: H 85 THR cc_start: 0.8929 (m) cc_final: 0.8705 (p) REVERT: H 98 LEU cc_start: 0.8860 (mm) cc_final: 0.8423 (mm) REVERT: H 117 LYS cc_start: 0.9465 (mtmt) cc_final: 0.9246 (mtmt) outliers start: 23 outliers final: 18 residues processed: 257 average time/residue: 0.2709 time to fit residues: 91.6403 Evaluate side-chains 259 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 89 ASN D 106 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.072918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.052029 restraints weight = 38233.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053770 restraints weight = 19233.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054907 restraints weight = 12788.800| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10892 Z= 0.253 Angle : 0.658 10.208 15464 Z= 0.378 Chirality : 0.037 0.160 1715 Planarity : 0.004 0.029 1327 Dihedral : 28.756 89.544 3109 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.20 % Allowed : 26.13 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.29), residues: 829 helix: 2.31 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.27 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.008 0.001 PHE F 61 TYR 0.031 0.002 TYR D 80 ARG 0.007 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9292 (tt0) cc_final: 0.8933 (tm-30) REVERT: B 20 LYS cc_start: 0.8720 (tppp) cc_final: 0.8385 (mmmm) REVERT: B 22 LEU cc_start: 0.8280 (tp) cc_final: 0.8016 (tp) REVERT: B 53 GLU cc_start: 0.9110 (tp30) cc_final: 0.8866 (tp30) REVERT: B 67 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8910 (ttm110) REVERT: B 92 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7989 (ttp80) REVERT: C 32 ARG cc_start: 0.8931 (ttp-110) cc_final: 0.8511 (ttp80) REVERT: C 64 GLU cc_start: 0.8625 (tt0) cc_final: 0.7867 (tm-30) REVERT: C 73 ASN cc_start: 0.9053 (t0) cc_final: 0.8725 (t0) REVERT: C 84 GLN cc_start: 0.8595 (tp40) cc_final: 0.8109 (tp40) REVERT: C 92 GLU cc_start: 0.7856 (pm20) cc_final: 0.7649 (pm20) REVERT: C 104 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7822 (mm-40) REVERT: D 44 GLN cc_start: 0.9173 (tt0) cc_final: 0.8964 (tm-30) REVERT: D 90 GLU cc_start: 0.9224 (mp0) cc_final: 0.8571 (mp0) REVERT: D 110 GLU cc_start: 0.8892 (tp30) cc_final: 0.8635 (tp30) REVERT: D 117 LYS cc_start: 0.9425 (mmmt) cc_final: 0.9102 (mtmt) REVERT: E 50 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8545 (mm-30) REVERT: E 56 LYS cc_start: 0.9415 (mtpp) cc_final: 0.9094 (mtmm) REVERT: E 94 GLU cc_start: 0.8789 (tp30) cc_final: 0.8477 (tp30) REVERT: E 123 ASP cc_start: 0.9115 (m-30) cc_final: 0.8856 (m-30) REVERT: F 60 VAL cc_start: 0.9481 (p) cc_final: 0.8885 (p) REVERT: F 63 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8348 (mt-10) REVERT: G 56 GLU cc_start: 0.9042 (tt0) cc_final: 0.8515 (tt0) REVERT: G 57 TYR cc_start: 0.9405 (t80) cc_final: 0.9095 (t80) REVERT: G 61 GLU cc_start: 0.8930 (tp30) cc_final: 0.8697 (tp30) REVERT: G 64 GLU cc_start: 0.8742 (tp30) cc_final: 0.8179 (tp30) REVERT: G 92 GLU cc_start: 0.7975 (pm20) cc_final: 0.7672 (pm20) REVERT: H 44 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8614 (tm-30) REVERT: H 73 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8014 (tp30) REVERT: H 98 LEU cc_start: 0.8841 (mm) cc_final: 0.8362 (mm) REVERT: H 117 LYS cc_start: 0.9468 (mtmt) cc_final: 0.9227 (mtmt) outliers start: 27 outliers final: 20 residues processed: 250 average time/residue: 0.2796 time to fit residues: 91.7162 Evaluate side-chains 241 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 chunk 81 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 overall best weight: 2.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 89 ASN D 79 HIS ** E 113 HIS ** 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 = 0.3586 r_free = 0.3586 target = 0.074445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053317 restraints weight = 37696.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055042 restraints weight = 19109.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056187 restraints weight = 12787.457| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10892 Z= 0.214 Angle : 0.670 14.520 15464 Z= 0.377 Chirality : 0.036 0.163 1715 Planarity : 0.004 0.031 1327 Dihedral : 28.675 89.640 3109 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.20 % Allowed : 26.91 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.29), residues: 829 helix: 2.28 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -0.16 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS D 79 PHE 0.005 0.001 PHE E 67 TYR 0.054 0.002 TYR B 88 ARG 0.007 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9249 (tt0) cc_final: 0.8918 (tm-30) REVERT: A 125 GLN cc_start: 0.8884 (mt0) cc_final: 0.8585 (mp10) REVERT: B 20 LYS cc_start: 0.8712 (tppp) cc_final: 0.8378 (mmmm) REVERT: B 22 LEU cc_start: 0.8205 (tp) cc_final: 0.7974 (tp) REVERT: B 53 GLU cc_start: 0.9063 (tp30) cc_final: 0.8814 (tp30) REVERT: B 67 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8902 (ttm110) REVERT: C 36 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8984 (tptt) REVERT: C 64 GLU cc_start: 0.8589 (tt0) cc_final: 0.7865 (tm-30) REVERT: C 73 ASN cc_start: 0.8989 (t0) cc_final: 0.8665 (t0) REVERT: C 84 GLN cc_start: 0.8532 (tp40) cc_final: 0.8047 (tp40) REVERT: C 104 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7789 (mm-40) REVERT: D 44 GLN cc_start: 0.9158 (tt0) cc_final: 0.8953 (tm-30) REVERT: D 90 GLU cc_start: 0.9259 (mp0) cc_final: 0.8565 (mp0) REVERT: D 110 GLU cc_start: 0.8854 (tp30) cc_final: 0.8576 (tp30) REVERT: D 117 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9095 (mtmt) REVERT: E 50 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8516 (mm-30) REVERT: E 56 LYS cc_start: 0.9420 (mtpp) cc_final: 0.9069 (mtmm) REVERT: E 94 GLU cc_start: 0.8655 (tp30) cc_final: 0.8352 (tp30) REVERT: E 123 ASP cc_start: 0.9052 (m-30) cc_final: 0.8801 (m-30) REVERT: F 88 TYR cc_start: 0.8446 (m-10) cc_final: 0.8000 (m-10) REVERT: G 56 GLU cc_start: 0.9002 (tt0) cc_final: 0.8464 (tt0) REVERT: G 61 GLU cc_start: 0.8920 (tp30) cc_final: 0.8700 (tp30) REVERT: G 64 GLU cc_start: 0.8713 (tp30) cc_final: 0.8145 (tp30) REVERT: H 44 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8597 (tm-30) REVERT: H 73 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7968 (tp30) REVERT: H 80 TYR cc_start: 0.8642 (m-10) cc_final: 0.7505 (m-80) REVERT: H 98 LEU cc_start: 0.8814 (mm) cc_final: 0.8338 (mm) REVERT: H 117 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9238 (mtmt) outliers start: 27 outliers final: 21 residues processed: 258 average time/residue: 0.2699 time to fit residues: 93.9689 Evaluate side-chains 247 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 79 HIS ** E 113 HIS ** 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 = 0.3592 r_free = 0.3592 target = 0.074796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053783 restraints weight = 38033.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055527 restraints weight = 19381.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056675 restraints weight = 12957.276| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10892 Z= 0.216 Angle : 0.700 14.425 15464 Z= 0.390 Chirality : 0.037 0.196 1715 Planarity : 0.004 0.037 1327 Dihedral : 28.622 89.992 3109 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.42 % Allowed : 28.93 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.29), residues: 829 helix: 2.20 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -0.07 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 79 PHE 0.006 0.001 PHE E 78 TYR 0.079 0.003 TYR B 88 ARG 0.011 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9199 (tt0) cc_final: 0.8873 (tm-30) REVERT: A 79 LYS cc_start: 0.8511 (tptp) cc_final: 0.8278 (tptp) REVERT: A 125 GLN cc_start: 0.8874 (mt0) cc_final: 0.8557 (mp10) REVERT: B 20 LYS cc_start: 0.8659 (tppp) cc_final: 0.8279 (mmmm) REVERT: B 22 LEU cc_start: 0.8277 (tp) cc_final: 0.7983 (tp) REVERT: B 53 GLU cc_start: 0.9031 (tp30) cc_final: 0.8766 (tp30) REVERT: B 67 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8901 (ttm110) REVERT: C 36 LYS cc_start: 0.9241 (mmmm) cc_final: 0.9008 (tptt) REVERT: C 64 GLU cc_start: 0.8597 (tt0) cc_final: 0.7813 (tm-30) REVERT: C 75 LYS cc_start: 0.9117 (tppt) cc_final: 0.8655 (tptt) REVERT: C 84 GLN cc_start: 0.8489 (tp40) cc_final: 0.7973 (tp40) REVERT: C 104 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7826 (mm-40) REVERT: D 44 GLN cc_start: 0.9157 (tt0) cc_final: 0.8948 (tm-30) REVERT: D 90 GLU cc_start: 0.9255 (mp0) cc_final: 0.8540 (mp0) REVERT: D 110 GLU cc_start: 0.8805 (tp30) cc_final: 0.8540 (tp30) REVERT: D 117 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9044 (ttmt) REVERT: E 50 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8543 (mm-30) REVERT: E 56 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9025 (mtmm) REVERT: E 94 GLU cc_start: 0.8683 (tp30) cc_final: 0.8412 (tp30) REVERT: E 123 ASP cc_start: 0.9006 (m-30) cc_final: 0.8750 (m-30) REVERT: F 88 TYR cc_start: 0.8371 (m-10) cc_final: 0.7899 (m-10) REVERT: F 91 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8875 (pttm) REVERT: G 56 GLU cc_start: 0.8992 (tt0) cc_final: 0.8453 (tt0) REVERT: G 57 TYR cc_start: 0.9368 (t80) cc_final: 0.9083 (t80) REVERT: G 64 GLU cc_start: 0.8700 (tp30) cc_final: 0.8124 (tp30) REVERT: G 75 LYS cc_start: 0.9233 (mmtp) cc_final: 0.8932 (mmtp) REVERT: G 92 GLU cc_start: 0.8053 (pm20) cc_final: 0.7838 (pm20) REVERT: H 44 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8605 (tm-30) REVERT: H 80 TYR cc_start: 0.8559 (m-10) cc_final: 0.7434 (m-80) REVERT: H 83 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8061 (tpp80) REVERT: H 98 LEU cc_start: 0.8775 (mm) cc_final: 0.8326 (mm) REVERT: H 117 LYS cc_start: 0.9455 (mtmt) cc_final: 0.9245 (mtmt) outliers start: 22 outliers final: 19 residues processed: 249 average time/residue: 0.2541 time to fit residues: 85.1433 Evaluate side-chains 248 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 96 optimal weight: 40.0000 chunk 52 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 89 ASN D 79 HIS ** E 113 HIS ** 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 = 0.3583 r_free = 0.3583 target = 0.074171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053225 restraints weight = 37955.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054923 restraints weight = 19346.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056040 restraints weight = 12970.201| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10892 Z= 0.253 Angle : 0.726 12.733 15464 Z= 0.405 Chirality : 0.038 0.161 1715 Planarity : 0.004 0.040 1327 Dihedral : 28.645 89.809 3109 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.42 % Allowed : 29.55 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.29), residues: 829 helix: 2.22 (0.21), residues: 574 sheet: None (None), residues: 0 loop : 0.28 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 79 PHE 0.005 0.001 PHE A 104 TYR 0.094 0.003 TYR B 88 ARG 0.024 0.001 ARG B 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9201 (tt0) cc_final: 0.8862 (tm-30) REVERT: B 20 LYS cc_start: 0.8677 (tppp) cc_final: 0.8264 (mmmm) REVERT: B 22 LEU cc_start: 0.8385 (tp) cc_final: 0.8133 (tp) REVERT: B 53 GLU cc_start: 0.9054 (tp30) cc_final: 0.8782 (tp30) REVERT: B 67 ARG cc_start: 0.9081 (ttm110) cc_final: 0.8865 (ttm110) REVERT: C 36 LYS cc_start: 0.9245 (mmmm) cc_final: 0.9009 (tptt) REVERT: C 64 GLU cc_start: 0.8593 (tt0) cc_final: 0.7862 (tm-30) REVERT: C 75 LYS cc_start: 0.9062 (tppt) cc_final: 0.8520 (tptt) REVERT: C 84 GLN cc_start: 0.8498 (tp40) cc_final: 0.8020 (tp40) REVERT: C 104 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7790 (mm-40) REVERT: D 44 GLN cc_start: 0.9160 (tt0) cc_final: 0.8958 (tm-30) REVERT: D 90 GLU cc_start: 0.9266 (mp0) cc_final: 0.8551 (mp0) REVERT: D 110 GLU cc_start: 0.8834 (tp30) cc_final: 0.8595 (tp30) REVERT: D 117 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9136 (mtmt) REVERT: E 50 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8602 (mm-30) REVERT: E 56 LYS cc_start: 0.9402 (mtpp) cc_final: 0.9030 (mtmm) REVERT: E 94 GLU cc_start: 0.8749 (tp30) cc_final: 0.8478 (tp30) REVERT: E 123 ASP cc_start: 0.9033 (m-30) cc_final: 0.8755 (m-30) REVERT: F 88 TYR cc_start: 0.8480 (m-10) cc_final: 0.7865 (m-10) REVERT: G 56 GLU cc_start: 0.9004 (tt0) cc_final: 0.8471 (tt0) REVERT: G 64 GLU cc_start: 0.8760 (tp30) cc_final: 0.8165 (tp30) REVERT: G 75 LYS cc_start: 0.9241 (mmtp) cc_final: 0.8892 (mmtp) REVERT: G 92 GLU cc_start: 0.8080 (pm20) cc_final: 0.7858 (pm20) REVERT: H 44 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8615 (tm-30) REVERT: H 80 TYR cc_start: 0.8591 (m-10) cc_final: 0.7687 (m-80) REVERT: H 83 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8048 (tpp80) REVERT: H 98 LEU cc_start: 0.8788 (mm) cc_final: 0.8521 (mm) REVERT: H 117 LYS cc_start: 0.9455 (mtmt) cc_final: 0.9245 (mtmt) outliers start: 22 outliers final: 18 residues processed: 245 average time/residue: 0.2560 time to fit residues: 84.2157 Evaluate side-chains 249 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 92 optimal weight: 40.0000 chunk 70 optimal weight: 0.0970 chunk 58 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 81 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 overall best weight: 4.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 89 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 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 = 0.3565 r_free = 0.3565 target = 0.073465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.052880 restraints weight = 38083.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054553 restraints weight = 19348.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055686 restraints weight = 12928.700| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10892 Z= 0.275 Angle : 0.734 13.301 15464 Z= 0.409 Chirality : 0.038 0.160 1715 Planarity : 0.004 0.035 1327 Dihedral : 28.689 89.781 3109 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.27 % Allowed : 29.39 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 829 helix: 2.19 (0.21), residues: 569 sheet: None (None), residues: 0 loop : 0.30 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.007 0.001 PHE A 104 TYR 0.081 0.003 TYR B 88 ARG 0.015 0.001 ARG B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3213.54 seconds wall clock time: 58 minutes 27.33 seconds (3507.33 seconds total)