Starting phenix.real_space_refine on Tue Jul 29 19:12:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fq8_4299/07_2025/6fq8_4299.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fq8_4299/07_2025/6fq8_4299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fq8_4299/07_2025/6fq8_4299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fq8_4299/07_2025/6fq8_4299.map" model { file = "/net/cci-nas-00/data/ceres_data/6fq8_4299/07_2025/6fq8_4299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fq8_4299/07_2025/6fq8_4299.cif" } resolution = 4.8 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= 0.027 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 294 5.49 5 S 12 5.16 5 C 6575 2.51 5 N 2231 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11913 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 765 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 7.26, per 1000 atoms: 0.61 Number of scatterers: 11913 At special positions: 0 Unit cell: (77, 123.2, 110.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 294 15.00 O 2801 8.00 N 2231 7.00 C 6575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 810.9 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 75.1% alpha, 2.7% beta 145 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.625A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 47 through 77 removed outlier: 4.170A pdb=" N TYR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.563A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.374A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.726A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.678A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.845A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.687A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.011A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.586A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 4.020A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.346A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.968A 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 removed outlier: 3.653A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 7.050A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.439A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.007A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.817A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 404 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 3.51 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: 1837 1.33 - 1.45: 4571 1.45 - 1.57: 5708 1.57 - 1.69: 586 1.69 - 1.81: 22 Bond restraints: 12724 Sorted by residual: bond pdb=" C ARG E 42 " pdb=" N PRO E 43 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.97e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.36e-02 5.41e+03 5.41e+00 bond pdb=" C3' DT J 31 " pdb=" O3' DT J 31 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.06e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.98e+00 ... (remaining 12719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 17956 2.93 - 5.86: 450 5.86 - 8.79: 41 8.79 - 11.72: 6 11.72 - 14.65: 1 Bond angle restraints: 18454 Sorted by residual: angle pdb=" N LEU B 22 " pdb=" CA LEU B 22 " pdb=" C LEU B 22 " ideal model delta sigma weight residual 111.17 120.49 -9.32 1.41e+00 5.03e-01 4.37e+01 angle pdb=" O4' DA I 26 " pdb=" C1' DA I 26 " pdb=" N9 DA I 26 " ideal model delta sigma weight residual 108.40 100.85 7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" C ASP C 90 " pdb=" N GLU C 91 " pdb=" CA GLU C 91 " ideal model delta sigma weight residual 120.82 128.36 -7.54 1.50e+00 4.44e-01 2.53e+01 angle pdb=" OP1 DC J 10 " pdb=" P DC J 10 " pdb=" O5' DC J 10 " ideal model delta sigma weight residual 109.00 94.35 14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" N PRO E 43 " pdb=" CA PRO E 43 " pdb=" C PRO E 43 " ideal model delta sigma weight residual 111.26 118.60 -7.34 1.63e+00 3.76e-01 2.03e+01 ... (remaining 18449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.58: 5446 32.58 - 65.15: 1398 65.15 - 97.73: 37 97.73 - 130.30: 4 130.30 - 162.88: 2 Dihedral angle restraints: 6887 sinusoidal: 4725 harmonic: 2162 Sorted by residual: dihedral pdb=" CA VAL B 21 " pdb=" C VAL B 21 " pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 57.12 162.88 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 59.56 160.44 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1523 0.070 - 0.140: 494 0.140 - 0.210: 84 0.210 - 0.280: 4 0.280 - 0.350: 5 Chirality restraints: 2110 Sorted by residual: chirality pdb=" C1' DG I 20 " pdb=" O4' DG I 20 " pdb=" C2' DG I 20 " pdb=" N9 DG I 20 " both_signs ideal model delta sigma weight residual False 2.42 2.07 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C1' DA J 16 " pdb=" O4' DA J 16 " pdb=" C2' DA J 16 " pdb=" N9 DA J 16 " both_signs ideal model delta sigma weight residual False 2.42 2.10 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1' DT I 33 " pdb=" O4' DT I 33 " pdb=" C2' DT I 33 " pdb=" N1 DT I 33 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2107 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 54 " 0.061 2.00e-02 2.50e+03 2.88e-02 2.07e+01 pdb=" N1 DT I 54 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DT I 54 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DT I 54 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT I 54 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DT I 54 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT I 54 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DT I 54 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 54 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 54 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.065 2.00e-02 2.50e+03 2.71e-02 2.02e+01 pdb=" N9 DA I 26 " 0.048 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.019 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.028 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -15 " 0.062 2.00e-02 2.50e+03 2.67e-02 1.96e+01 pdb=" N9 DA I -15 " -0.054 2.00e-02 2.50e+03 pdb=" C8 DA I -15 " -0.012 2.00e-02 2.50e+03 pdb=" N7 DA I -15 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA I -15 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA I -15 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -15 " 0.025 2.00e-02 2.50e+03 pdb=" N1 DA I -15 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I -15 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DA I -15 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA I -15 " -0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2096 2.78 - 3.31: 11080 3.31 - 3.84: 25147 3.84 - 4.37: 28356 4.37 - 4.90: 39116 Nonbonded interactions: 105795 Sorted by model distance: nonbonded pdb=" OH TYR H 39 " pdb=" OP2 DG J -52 " model vdw 2.252 3.040 nonbonded pdb=" O2 DC I 61 " pdb=" N2 DG J -61 " model vdw 2.256 2.496 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.277 3.040 nonbonded pdb=" O ILE B 50 " pdb=" OG1 THR B 54 " model vdw 2.278 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.320 3.040 ... (remaining 105790 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 40 through 132) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 100) selection = (chain 'F' and resid 20 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 117) } 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: 0.180 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.810 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.008 0.074 12724 Z= 0.383 Angle : 1.161 14.650 18454 Z= 0.684 Chirality : 0.067 0.350 2110 Planarity : 0.008 0.041 1313 Dihedral : 26.946 162.875 5491 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % 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: -0.86 (0.27), residues: 728 helix: -0.24 (0.20), residues: 502 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS G 82 PHE 0.044 0.005 PHE A 104 TYR 0.034 0.003 TYR A 41 ARG 0.006 0.001 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.13949 ( 774) hydrogen bonds : angle 6.31798 ( 1921) covalent geometry : bond 0.00843 (12724) covalent geometry : angle 1.16112 (18454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.940 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9089 (tp30) cc_final: 0.8845 (tm-30) REVERT: A 100 LEU cc_start: 0.9661 (mt) cc_final: 0.9352 (pp) REVERT: B 31 LYS cc_start: 0.8792 (tttp) cc_final: 0.8568 (tmtt) REVERT: B 63 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 84 MET cc_start: 0.9144 (mmt) cc_final: 0.8793 (mpp) REVERT: C 38 ASN cc_start: 0.7504 (m-40) cc_final: 0.7167 (m-40) REVERT: C 64 GLU cc_start: 0.9468 (tt0) cc_final: 0.9213 (tp30) REVERT: D 54 LYS cc_start: 0.9408 (mttt) cc_final: 0.9084 (tmtt) REVERT: D 99 LEU cc_start: 0.9593 (mt) cc_final: 0.9326 (tp) REVERT: E 110 CYS cc_start: 0.8827 (m) cc_final: 0.8223 (m) REVERT: E 124 ILE cc_start: 0.9503 (mt) cc_final: 0.9259 (mp) REVERT: F 62 LEU cc_start: 0.9610 (mt) cc_final: 0.9184 (pp) REVERT: F 64 ASN cc_start: 0.9392 (m-40) cc_final: 0.8992 (t0) REVERT: F 68 ASP cc_start: 0.9423 (m-30) cc_final: 0.9068 (m-30) REVERT: F 72 TYR cc_start: 0.9186 (m-80) cc_final: 0.8865 (m-80) REVERT: F 81 VAL cc_start: 0.8490 (t) cc_final: 0.8265 (t) REVERT: F 84 MET cc_start: 0.8590 (mmm) cc_final: 0.7663 (ttp) REVERT: G 34 LEU cc_start: 0.9500 (mt) cc_final: 0.9267 (mt) REVERT: G 38 ASN cc_start: 0.7500 (m110) cc_final: 0.6328 (t0) REVERT: G 84 GLN cc_start: 0.8676 (tp40) cc_final: 0.8208 (tm-30) REVERT: G 94 ASN cc_start: 0.8077 (t0) cc_final: 0.7855 (t0) REVERT: G 95 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9263 (mmtm) REVERT: H 54 LYS cc_start: 0.9309 (tptm) cc_final: 0.8976 (tptt) REVERT: H 59 MET cc_start: 0.9382 (mmm) cc_final: 0.8843 (mmm) REVERT: H 65 ASP cc_start: 0.8494 (t0) cc_final: 0.8258 (t70) REVERT: H 66 VAL cc_start: 0.8933 (t) cc_final: 0.8710 (m) REVERT: H 81 ASN cc_start: 0.9315 (m-40) cc_final: 0.8926 (p0) REVERT: H 106 HIS cc_start: 0.9397 (m-70) cc_final: 0.9031 (m-70) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3265 time to fit residues: 95.0949 Evaluate side-chains 132 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.051157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.044751 restraints weight = 144390.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.046175 restraints weight = 89447.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.047172 restraints weight = 60383.459| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12724 Z= 0.244 Angle : 0.712 7.922 18454 Z= 0.424 Chirality : 0.040 0.169 2110 Planarity : 0.006 0.048 1313 Dihedral : 32.053 178.868 4038 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.16 % Allowed : 0.65 % Favored : 99.19 % 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: 0.57 (0.29), residues: 728 helix: 1.00 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 82 PHE 0.019 0.002 PHE A 104 TYR 0.035 0.002 TYR B 98 ARG 0.008 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.08093 ( 774) hydrogen bonds : angle 4.05997 ( 1921) covalent geometry : bond 0.00511 (12724) covalent geometry : angle 0.71222 (18454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.806 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9049 (mt) cc_final: 0.8817 (mt) REVERT: A 93 GLN cc_start: 0.9147 (tt0) cc_final: 0.8692 (tp-100) REVERT: A 94 GLU cc_start: 0.9187 (tp30) cc_final: 0.8975 (tm-30) REVERT: A 100 LEU cc_start: 0.9819 (mt) cc_final: 0.9534 (mt) REVERT: B 63 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 68 ASP cc_start: 0.9634 (m-30) cc_final: 0.9385 (m-30) REVERT: B 84 MET cc_start: 0.9201 (mmt) cc_final: 0.8883 (mpp) REVERT: B 97 LEU cc_start: 0.8763 (tp) cc_final: 0.8206 (tp) REVERT: C 38 ASN cc_start: 0.7538 (m-40) cc_final: 0.7276 (m-40) REVERT: C 64 GLU cc_start: 0.9466 (tt0) cc_final: 0.9213 (tp30) REVERT: C 68 ASN cc_start: 0.9310 (m-40) cc_final: 0.9022 (m110) REVERT: D 54 LYS cc_start: 0.9523 (mttt) cc_final: 0.9177 (tmtt) REVERT: D 99 LEU cc_start: 0.9492 (mt) cc_final: 0.9141 (tp) REVERT: E 81 ASP cc_start: 0.7150 (t0) cc_final: 0.5919 (m-30) REVERT: E 104 PHE cc_start: 0.8943 (m-80) cc_final: 0.8720 (m-80) REVERT: E 110 CYS cc_start: 0.9027 (m) cc_final: 0.8376 (m) REVERT: F 60 VAL cc_start: 0.9396 (t) cc_final: 0.9073 (p) REVERT: F 68 ASP cc_start: 0.9630 (m-30) cc_final: 0.9260 (m-30) REVERT: F 72 TYR cc_start: 0.9389 (m-80) cc_final: 0.8940 (m-80) REVERT: G 38 ASN cc_start: 0.7907 (m110) cc_final: 0.6703 (t0) REVERT: G 84 GLN cc_start: 0.8230 (tp40) cc_final: 0.7669 (tm-30) REVERT: G 94 ASN cc_start: 0.7918 (t0) cc_final: 0.7654 (t0) REVERT: H 54 LYS cc_start: 0.9184 (tptm) cc_final: 0.8854 (tptt) REVERT: H 59 MET cc_start: 0.9453 (mmm) cc_final: 0.9068 (mmm) REVERT: H 81 ASN cc_start: 0.9061 (m-40) cc_final: 0.8738 (p0) REVERT: H 103 LEU cc_start: 0.8847 (mt) cc_final: 0.8397 (pp) REVERT: H 106 HIS cc_start: 0.9707 (m-70) cc_final: 0.9080 (m-70) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2795 time to fit residues: 63.1267 Evaluate side-chains 124 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 54 optimal weight: 0.0030 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.049214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.042664 restraints weight = 151825.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044068 restraints weight = 94575.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045057 restraints weight = 64341.162| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12724 Z= 0.226 Angle : 0.676 9.799 18454 Z= 0.401 Chirality : 0.038 0.177 2110 Planarity : 0.005 0.052 1313 Dihedral : 32.262 179.054 4038 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % 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: 0.86 (0.29), residues: 728 helix: 1.27 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 75 PHE 0.019 0.002 PHE A 104 TYR 0.018 0.002 TYR B 98 ARG 0.005 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.07518 ( 774) hydrogen bonds : angle 3.85918 ( 1921) covalent geometry : bond 0.00478 (12724) covalent geometry : angle 0.67636 (18454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.831 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9056 (tt0) cc_final: 0.8658 (tp-100) REVERT: A 94 GLU cc_start: 0.9185 (tp30) cc_final: 0.8975 (tm-30) REVERT: A 100 LEU cc_start: 0.9834 (mt) cc_final: 0.9618 (mt) REVERT: A 104 PHE cc_start: 0.9623 (m-80) cc_final: 0.9272 (m-80) REVERT: A 108 ASN cc_start: 0.9141 (t0) cc_final: 0.8822 (m-40) REVERT: A 120 MET cc_start: 0.8401 (mtt) cc_final: 0.7858 (mpp) REVERT: B 63 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 68 ASP cc_start: 0.9638 (m-30) cc_final: 0.9200 (m-30) REVERT: B 84 MET cc_start: 0.9202 (mmt) cc_final: 0.8898 (mpp) REVERT: B 97 LEU cc_start: 0.8891 (tp) cc_final: 0.8200 (tp) REVERT: B 98 TYR cc_start: 0.8949 (m-80) cc_final: 0.8698 (m-10) REVERT: C 38 ASN cc_start: 0.7783 (m-40) cc_final: 0.7343 (t0) REVERT: C 64 GLU cc_start: 0.9548 (tt0) cc_final: 0.9265 (tp30) REVERT: C 68 ASN cc_start: 0.9356 (m-40) cc_final: 0.9111 (m110) REVERT: D 54 LYS cc_start: 0.9476 (mttt) cc_final: 0.9043 (tptp) REVERT: E 81 ASP cc_start: 0.7362 (t0) cc_final: 0.6096 (m-30) REVERT: E 92 LEU cc_start: 0.8679 (mt) cc_final: 0.8417 (mt) REVERT: E 94 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8892 (mm-30) REVERT: E 104 PHE cc_start: 0.9054 (m-80) cc_final: 0.8803 (m-80) REVERT: E 108 ASN cc_start: 0.9419 (t0) cc_final: 0.9214 (m-40) REVERT: E 110 CYS cc_start: 0.9153 (m) cc_final: 0.8290 (m) REVERT: E 123 ASP cc_start: 0.9419 (m-30) cc_final: 0.9188 (t0) REVERT: F 58 LEU cc_start: 0.9553 (tp) cc_final: 0.9190 (pp) REVERT: F 68 ASP cc_start: 0.9561 (m-30) cc_final: 0.9045 (m-30) REVERT: F 72 TYR cc_start: 0.9351 (m-80) cc_final: 0.8778 (m-80) REVERT: F 84 MET cc_start: 0.7595 (mmp) cc_final: 0.6945 (ttp) REVERT: G 36 LYS cc_start: 0.9603 (mttm) cc_final: 0.9362 (mmtm) REVERT: G 38 ASN cc_start: 0.7953 (m110) cc_final: 0.6672 (t0) REVERT: G 84 GLN cc_start: 0.7998 (tp40) cc_final: 0.7396 (tm-30) REVERT: G 94 ASN cc_start: 0.7754 (t0) cc_final: 0.7515 (m-40) REVERT: H 54 LYS cc_start: 0.9076 (tptm) cc_final: 0.8769 (tptt) REVERT: H 59 MET cc_start: 0.9498 (mmm) cc_final: 0.9173 (mmm) REVERT: H 99 LEU cc_start: 0.9438 (mm) cc_final: 0.9219 (mp) REVERT: H 103 LEU cc_start: 0.8962 (mt) cc_final: 0.8497 (pp) REVERT: H 106 HIS cc_start: 0.9726 (m-70) cc_final: 0.9187 (m-70) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.2762 time to fit residues: 58.6855 Evaluate side-chains 121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.042219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.035877 restraints weight = 154707.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.037086 restraints weight = 98604.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.037970 restraints weight = 68486.121| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 12724 Z= 0.306 Angle : 0.768 12.498 18454 Z= 0.451 Chirality : 0.043 0.184 2110 Planarity : 0.006 0.070 1313 Dihedral : 33.118 179.546 4038 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.32 % Allowed : 2.27 % Favored : 97.41 % 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: 0.34 (0.29), residues: 728 helix: 0.99 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -1.67 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 75 PHE 0.022 0.003 PHE C 25 TYR 0.029 0.003 TYR B 72 ARG 0.008 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.10613 ( 774) hydrogen bonds : angle 4.33157 ( 1921) covalent geometry : bond 0.00649 (12724) covalent geometry : angle 0.76799 (18454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.845 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8793 (tt0) cc_final: 0.8583 (tp-100) REVERT: A 94 GLU cc_start: 0.9365 (tp30) cc_final: 0.9078 (tm-30) REVERT: A 120 MET cc_start: 0.8449 (mtt) cc_final: 0.7750 (mpp) REVERT: B 62 LEU cc_start: 0.9550 (mm) cc_final: 0.9246 (mm) REVERT: B 63 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7653 (mp0) REVERT: B 64 ASN cc_start: 0.9383 (m110) cc_final: 0.9094 (m110) REVERT: B 84 MET cc_start: 0.9211 (mmt) cc_final: 0.8832 (mpp) REVERT: B 92 ARG cc_start: 0.7874 (tmt-80) cc_final: 0.7465 (tmm160) REVERT: B 97 LEU cc_start: 0.8729 (tp) cc_final: 0.8028 (tp) REVERT: C 64 GLU cc_start: 0.9445 (tt0) cc_final: 0.9219 (tp30) REVERT: C 68 ASN cc_start: 0.9313 (m110) cc_final: 0.9055 (m110) REVERT: D 54 LYS cc_start: 0.9548 (mttt) cc_final: 0.9205 (tptm) REVERT: D 56 MET cc_start: 0.5928 (tpt) cc_final: 0.4601 (tpt) REVERT: E 105 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8646 (mm-30) REVERT: E 110 CYS cc_start: 0.8960 (m) cc_final: 0.8263 (m) REVERT: F 64 ASN cc_start: 0.9355 (t0) cc_final: 0.8841 (t0) REVERT: F 72 TYR cc_start: 0.9349 (m-80) cc_final: 0.8978 (m-80) REVERT: F 81 VAL cc_start: 0.8952 (t) cc_final: 0.8572 (t) REVERT: F 84 MET cc_start: 0.7640 (mmp) cc_final: 0.6923 (ttp) REVERT: G 84 GLN cc_start: 0.8394 (tp40) cc_final: 0.7456 (tm-30) REVERT: G 94 ASN cc_start: 0.7978 (t0) cc_final: 0.7680 (t0) REVERT: H 54 LYS cc_start: 0.9227 (tptm) cc_final: 0.8937 (tptt) REVERT: H 59 MET cc_start: 0.9371 (mmm) cc_final: 0.9016 (mmm) REVERT: H 103 LEU cc_start: 0.8972 (mt) cc_final: 0.8429 (pp) REVERT: H 106 HIS cc_start: 0.9744 (m-70) cc_final: 0.9262 (m-70) outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 0.2677 time to fit residues: 50.0200 Evaluate side-chains 103 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.041957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035465 restraints weight = 158084.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.036673 restraints weight = 101886.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.037535 restraints weight = 71688.333| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12724 Z= 0.262 Angle : 0.721 11.577 18454 Z= 0.428 Chirality : 0.041 0.171 2110 Planarity : 0.005 0.058 1313 Dihedral : 33.188 179.705 4038 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 0.32 (0.29), residues: 728 helix: 0.97 (0.21), residues: 513 sheet: None (None), residues: 0 loop : -1.60 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 75 PHE 0.019 0.003 PHE A 104 TYR 0.030 0.003 TYR B 72 ARG 0.004 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.09031 ( 774) hydrogen bonds : angle 4.13246 ( 1921) covalent geometry : bond 0.00557 (12724) covalent geometry : angle 0.72086 (18454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.232 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: 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: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8866 (tt0) cc_final: 0.8578 (tp-100) REVERT: A 94 GLU cc_start: 0.9432 (tp30) cc_final: 0.9118 (tm-30) REVERT: A 120 MET cc_start: 0.8392 (mtt) cc_final: 0.7774 (mpp) REVERT: B 84 MET cc_start: 0.9216 (mmt) cc_final: 0.8828 (mpp) REVERT: B 97 LEU cc_start: 0.8909 (tp) cc_final: 0.8333 (tp) REVERT: C 64 GLU cc_start: 0.9504 (tt0) cc_final: 0.9243 (tp30) REVERT: D 54 LYS cc_start: 0.9533 (mttt) cc_final: 0.9153 (tptm) REVERT: D 99 LEU cc_start: 0.9259 (mm) cc_final: 0.9041 (mm) REVERT: E 104 PHE cc_start: 0.8959 (m-10) cc_final: 0.8697 (m-80) REVERT: E 105 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8747 (mm-30) REVERT: E 110 CYS cc_start: 0.9084 (m) cc_final: 0.8435 (m) REVERT: F 72 TYR cc_start: 0.9355 (m-80) cc_final: 0.8817 (m-80) REVERT: F 81 VAL cc_start: 0.8921 (t) cc_final: 0.8579 (t) REVERT: F 84 MET cc_start: 0.7448 (mmp) cc_final: 0.6874 (ttp) REVERT: G 84 GLN cc_start: 0.8106 (tp40) cc_final: 0.7228 (tm-30) REVERT: G 94 ASN cc_start: 0.7864 (t0) cc_final: 0.7620 (t0) REVERT: H 59 MET cc_start: 0.9463 (mmm) cc_final: 0.9091 (mmm) REVERT: H 102 GLU cc_start: 0.9229 (pt0) cc_final: 0.8857 (pp20) REVERT: H 103 LEU cc_start: 0.8772 (mt) cc_final: 0.7740 (pp) REVERT: H 106 HIS cc_start: 0.9789 (m-70) cc_final: 0.9294 (m-70) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2800 time to fit residues: 49.2921 Evaluate side-chains 96 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 64 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 0.0170 chunk 66 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 overall best weight: 4.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.042117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.035681 restraints weight = 154572.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.036888 restraints weight = 99872.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.037785 restraints weight = 70520.698| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12724 Z= 0.233 Angle : 0.699 12.353 18454 Z= 0.414 Chirality : 0.040 0.181 2110 Planarity : 0.005 0.058 1313 Dihedral : 33.146 178.506 4038 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % 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: 0.49 (0.29), residues: 728 helix: 1.13 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.015 0.002 PHE C 25 TYR 0.029 0.002 TYR B 98 ARG 0.004 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.08114 ( 774) hydrogen bonds : angle 4.05084 ( 1921) covalent geometry : bond 0.00495 (12724) covalent geometry : angle 0.69890 (18454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.965 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8900 (tt0) cc_final: 0.8516 (tp-100) REVERT: A 94 GLU cc_start: 0.9360 (tp30) cc_final: 0.9049 (tm-30) REVERT: A 100 LEU cc_start: 0.9800 (mt) cc_final: 0.9493 (mt) REVERT: A 120 MET cc_start: 0.8871 (mtm) cc_final: 0.8135 (mpp) REVERT: B 84 MET cc_start: 0.9137 (mmt) cc_final: 0.8750 (mpp) REVERT: C 64 GLU cc_start: 0.9503 (tt0) cc_final: 0.9223 (tp30) REVERT: C 68 ASN cc_start: 0.9413 (m-40) cc_final: 0.9134 (m110) REVERT: D 54 LYS cc_start: 0.9567 (mttt) cc_final: 0.9154 (tptp) REVERT: D 56 MET cc_start: 0.5344 (tpt) cc_final: 0.4145 (tpt) REVERT: D 99 LEU cc_start: 0.9236 (mm) cc_final: 0.9005 (mm) REVERT: E 104 PHE cc_start: 0.8943 (m-10) cc_final: 0.8697 (m-80) REVERT: E 105 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8697 (mm-30) REVERT: E 110 CYS cc_start: 0.9039 (m) cc_final: 0.8250 (m) REVERT: F 72 TYR cc_start: 0.9281 (m-80) cc_final: 0.8628 (m-80) REVERT: F 81 VAL cc_start: 0.8826 (t) cc_final: 0.8420 (t) REVERT: F 84 MET cc_start: 0.7537 (mmp) cc_final: 0.6995 (ttp) REVERT: G 84 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: G 94 ASN cc_start: 0.7843 (t0) cc_final: 0.7586 (t0) REVERT: G 100 VAL cc_start: 0.8510 (t) cc_final: 0.8157 (p) REVERT: H 54 LYS cc_start: 0.9211 (tptm) cc_final: 0.8907 (tptt) REVERT: H 59 MET cc_start: 0.9387 (mmm) cc_final: 0.8909 (mmm) REVERT: H 102 GLU cc_start: 0.9220 (pt0) cc_final: 0.8784 (pp20) REVERT: H 103 LEU cc_start: 0.8670 (mt) cc_final: 0.7331 (mt) REVERT: H 106 HIS cc_start: 0.9751 (m-70) cc_final: 0.9242 (m-70) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2509 time to fit residues: 44.6741 Evaluate side-chains 99 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 20 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.043362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036779 restraints weight = 152020.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038019 restraints weight = 98337.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.038922 restraints weight = 69338.895| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12724 Z= 0.203 Angle : 0.681 12.176 18454 Z= 0.402 Chirality : 0.039 0.180 2110 Planarity : 0.005 0.058 1313 Dihedral : 33.077 179.684 4038 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.79 (0.29), residues: 728 helix: 1.35 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.012 0.002 PHE C 25 TYR 0.033 0.002 TYR B 72 ARG 0.003 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.06793 ( 774) hydrogen bonds : angle 3.85217 ( 1921) covalent geometry : bond 0.00432 (12724) covalent geometry : angle 0.68058 (18454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.914 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: 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: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9088 (tt0) cc_final: 0.8744 (tp-100) REVERT: A 94 GLU cc_start: 0.9356 (tp30) cc_final: 0.8997 (tm-30) REVERT: A 120 MET cc_start: 0.8691 (mtm) cc_final: 0.8107 (mpp) REVERT: B 84 MET cc_start: 0.9121 (mmt) cc_final: 0.8759 (mpp) REVERT: C 64 GLU cc_start: 0.9526 (tt0) cc_final: 0.9236 (tp30) REVERT: C 68 ASN cc_start: 0.9405 (m-40) cc_final: 0.9138 (m110) REVERT: D 99 LEU cc_start: 0.9247 (mm) cc_final: 0.9025 (mm) REVERT: E 94 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8987 (mm-30) REVERT: E 104 PHE cc_start: 0.9058 (m-10) cc_final: 0.8824 (m-80) REVERT: E 105 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8710 (mm-30) REVERT: E 110 CYS cc_start: 0.9109 (m) cc_final: 0.8222 (m) REVERT: E 123 ASP cc_start: 0.9272 (m-30) cc_final: 0.9023 (m-30) REVERT: F 72 TYR cc_start: 0.9239 (m-10) cc_final: 0.8670 (m-80) REVERT: F 81 VAL cc_start: 0.8693 (t) cc_final: 0.8443 (t) REVERT: F 84 MET cc_start: 0.7752 (mmp) cc_final: 0.7342 (ttp) REVERT: G 94 ASN cc_start: 0.8037 (t0) cc_final: 0.7789 (m-40) REVERT: G 100 VAL cc_start: 0.8472 (t) cc_final: 0.8163 (p) REVERT: H 54 LYS cc_start: 0.9186 (tptm) cc_final: 0.8869 (tptt) REVERT: H 59 MET cc_start: 0.9355 (mmm) cc_final: 0.8930 (mmm) REVERT: H 102 GLU cc_start: 0.9287 (pt0) cc_final: 0.8930 (pm20) REVERT: H 103 LEU cc_start: 0.8718 (mt) cc_final: 0.8260 (mt) REVERT: H 106 HIS cc_start: 0.9706 (m-70) cc_final: 0.9200 (m-70) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2577 time to fit residues: 44.9395 Evaluate side-chains 94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.048244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.041880 restraints weight = 149095.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.043229 restraints weight = 93981.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.044168 restraints weight = 64751.144| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12724 Z= 0.179 Angle : 0.661 11.942 18454 Z= 0.388 Chirality : 0.038 0.162 2110 Planarity : 0.004 0.054 1313 Dihedral : 32.870 177.329 4038 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 1.09 (0.29), residues: 728 helix: 1.59 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.55 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.014 0.002 PHE G 25 TYR 0.030 0.002 TYR D 39 ARG 0.003 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.05857 ( 774) hydrogen bonds : angle 3.64880 ( 1921) covalent geometry : bond 0.00380 (12724) covalent geometry : angle 0.66129 (18454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.855 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: 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 94 GLU cc_start: 0.9335 (tp30) cc_final: 0.9022 (tm-30) REVERT: A 120 MET cc_start: 0.8726 (mtm) cc_final: 0.8153 (mpp) REVERT: B 62 LEU cc_start: 0.9565 (mm) cc_final: 0.9232 (mm) REVERT: B 71 THR cc_start: 0.9185 (p) cc_final: 0.8942 (p) REVERT: B 84 MET cc_start: 0.9117 (mmt) cc_final: 0.8717 (mpp) REVERT: C 64 GLU cc_start: 0.9505 (tt0) cc_final: 0.9238 (tp30) REVERT: C 68 ASN cc_start: 0.9439 (m-40) cc_final: 0.9132 (m110) REVERT: E 94 GLU cc_start: 0.9263 (mm-30) cc_final: 0.9031 (mm-30) REVERT: E 104 PHE cc_start: 0.9001 (m-10) cc_final: 0.8742 (m-80) REVERT: E 105 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8811 (mm-30) REVERT: E 110 CYS cc_start: 0.9021 (m) cc_final: 0.8109 (m) REVERT: E 123 ASP cc_start: 0.9313 (m-30) cc_final: 0.9040 (m-30) REVERT: F 58 LEU cc_start: 0.9489 (tp) cc_final: 0.9104 (pp) REVERT: F 68 ASP cc_start: 0.9490 (m-30) cc_final: 0.8973 (m-30) REVERT: F 72 TYR cc_start: 0.9184 (m-10) cc_final: 0.8659 (m-80) REVERT: F 81 VAL cc_start: 0.8830 (t) cc_final: 0.8609 (t) REVERT: F 84 MET cc_start: 0.7533 (mmp) cc_final: 0.7201 (ttp) REVERT: G 57 TYR cc_start: 0.8547 (t80) cc_final: 0.7925 (t80) REVERT: G 84 GLN cc_start: 0.7261 (tp-100) cc_final: 0.6878 (tm-30) REVERT: G 94 ASN cc_start: 0.7924 (t0) cc_final: 0.7680 (m-40) REVERT: G 100 VAL cc_start: 0.8291 (t) cc_final: 0.8003 (p) REVERT: H 54 LYS cc_start: 0.9188 (tptm) cc_final: 0.8841 (tttm) REVERT: H 59 MET cc_start: 0.9348 (mmm) cc_final: 0.8956 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2756 time to fit residues: 46.9561 Evaluate side-chains 91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.047385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.041168 restraints weight = 152348.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.042476 restraints weight = 96831.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.043377 restraints weight = 66944.385| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12724 Z= 0.198 Angle : 0.663 12.152 18454 Z= 0.392 Chirality : 0.038 0.162 2110 Planarity : 0.005 0.054 1313 Dihedral : 32.926 178.521 4038 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.12 (0.30), residues: 728 helix: 1.61 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.56 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.011 0.002 PHE F 61 TYR 0.033 0.002 TYR B 72 ARG 0.005 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.06638 ( 774) hydrogen bonds : angle 3.73249 ( 1921) covalent geometry : bond 0.00421 (12724) covalent geometry : angle 0.66281 (18454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.883 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: 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: symmetry clash REVERT: A 97 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8591 (pt0) REVERT: A 120 MET cc_start: 0.8707 (mtm) cc_final: 0.8101 (mpp) REVERT: B 84 MET cc_start: 0.9152 (mmt) cc_final: 0.8771 (mpp) REVERT: C 64 GLU cc_start: 0.9510 (tt0) cc_final: 0.9247 (tp30) REVERT: C 68 ASN cc_start: 0.9438 (m-40) cc_final: 0.9134 (m110) REVERT: D 54 LYS cc_start: 0.9525 (mttt) cc_final: 0.9136 (tptm) REVERT: D 99 LEU cc_start: 0.9263 (mm) cc_final: 0.9041 (mm) REVERT: E 104 PHE cc_start: 0.9009 (m-10) cc_final: 0.8805 (m-80) REVERT: E 105 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8821 (mm-30) REVERT: E 110 CYS cc_start: 0.8971 (m) cc_final: 0.8042 (m) REVERT: E 123 ASP cc_start: 0.9299 (m-30) cc_final: 0.9019 (m-30) REVERT: F 58 LEU cc_start: 0.9495 (tp) cc_final: 0.9100 (pp) REVERT: F 68 ASP cc_start: 0.9522 (m-30) cc_final: 0.9050 (m-30) REVERT: F 72 TYR cc_start: 0.9209 (m-10) cc_final: 0.8736 (m-80) REVERT: F 84 MET cc_start: 0.7615 (mmp) cc_final: 0.7252 (ttp) REVERT: G 84 GLN cc_start: 0.7195 (tp-100) cc_final: 0.6673 (tm-30) REVERT: G 94 ASN cc_start: 0.7967 (t0) cc_final: 0.7701 (m-40) REVERT: G 100 VAL cc_start: 0.8374 (t) cc_final: 0.8047 (p) REVERT: H 54 LYS cc_start: 0.9176 (tptm) cc_final: 0.8851 (tptt) REVERT: H 59 MET cc_start: 0.9344 (mmm) cc_final: 0.8958 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2620 time to fit residues: 44.3202 Evaluate side-chains 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 15 optimal weight: 0.0870 chunk 67 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 85 GLN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.041552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.035141 restraints weight = 159101.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.036294 restraints weight = 104103.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037140 restraints weight = 74364.811| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 12724 Z= 0.264 Angle : 0.740 11.849 18454 Z= 0.432 Chirality : 0.042 0.265 2110 Planarity : 0.005 0.058 1313 Dihedral : 33.333 179.664 4038 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.52 (0.30), residues: 728 helix: 1.21 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -2.00 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS H 106 PHE 0.072 0.004 PHE A 67 TYR 0.030 0.003 TYR B 98 ARG 0.006 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.09254 ( 774) hydrogen bonds : angle 4.06745 ( 1921) covalent geometry : bond 0.00568 (12724) covalent geometry : angle 0.73990 (18454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.821 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: 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 97 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8631 (pt0) REVERT: A 120 MET cc_start: 0.8791 (mtm) cc_final: 0.8123 (mpp) REVERT: B 53 GLU cc_start: 0.9403 (tp30) cc_final: 0.9181 (tp30) REVERT: B 62 LEU cc_start: 0.9563 (mm) cc_final: 0.9301 (mm) REVERT: B 84 MET cc_start: 0.9156 (mmt) cc_final: 0.8749 (mpp) REVERT: C 64 GLU cc_start: 0.9488 (tt0) cc_final: 0.9238 (tp30) REVERT: C 68 ASN cc_start: 0.9404 (m-40) cc_final: 0.9144 (m110) REVERT: D 54 LYS cc_start: 0.9573 (mttt) cc_final: 0.9203 (tptm) REVERT: D 77 LEU cc_start: 0.9593 (tp) cc_final: 0.9292 (pp) REVERT: D 99 LEU cc_start: 0.9253 (mm) cc_final: 0.9023 (mm) REVERT: E 105 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8757 (mm-30) REVERT: E 110 CYS cc_start: 0.8928 (m) cc_final: 0.7907 (m) REVERT: E 123 ASP cc_start: 0.9191 (m-30) cc_final: 0.8891 (m-30) REVERT: F 72 TYR cc_start: 0.9262 (m-10) cc_final: 0.8773 (m-80) REVERT: F 84 MET cc_start: 0.7673 (mmp) cc_final: 0.7265 (ttp) REVERT: G 94 ASN cc_start: 0.8091 (t0) cc_final: 0.7847 (m-40) REVERT: G 100 VAL cc_start: 0.8506 (t) cc_final: 0.8242 (p) REVERT: H 54 LYS cc_start: 0.9225 (tptm) cc_final: 0.8883 (tptt) REVERT: H 59 MET cc_start: 0.9360 (mmm) cc_final: 0.9033 (mmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2618 time to fit residues: 41.8662 Evaluate side-chains 86 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 4 optimal weight: 0.0050 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.044143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.037499 restraints weight = 160047.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.038700 restraints weight = 105482.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039558 restraints weight = 75720.700| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12724 Z= 0.191 Angle : 0.684 12.647 18454 Z= 0.399 Chirality : 0.040 0.235 2110 Planarity : 0.005 0.056 1313 Dihedral : 33.159 178.903 4038 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.83 (0.30), residues: 728 helix: 1.42 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.82 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.076 0.003 PHE A 67 TYR 0.039 0.002 TYR B 72 ARG 0.003 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.06187 ( 774) hydrogen bonds : angle 3.72692 ( 1921) covalent geometry : bond 0.00412 (12724) covalent geometry : angle 0.68376 (18454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.52 seconds wall clock time: 53 minutes 49.33 seconds (3229.33 seconds total)