Starting phenix.real_space_refine on Sun Dec 29 21:07:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5r_14334/12_2024/7r5r_14334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5r_14334/12_2024/7r5r_14334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r5r_14334/12_2024/7r5r_14334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5r_14334/12_2024/7r5r_14334.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5r_14334/12_2024/7r5r_14334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5r_14334/12_2024/7r5r_14334.cif" } resolution = 2.44 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= -0.001 sd= 0.049 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 266 5.49 5 S 8 5.16 5 C 6528 2.51 5 N 2145 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11625 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2729 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2724 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain breaks: 1 Chain: "K" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 178 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 185 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 7.62, per 1000 atoms: 0.66 Number of scatterers: 11625 At special positions: 0 Unit cell: (81.888, 116.861, 119.42, 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 8 16.00 P 266 15.00 O 2678 8.00 N 2145 7.00 C 6528 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: 2.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 68.5% alpha, 2.8% beta 124 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.293A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.751A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.703A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.666A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.063A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.515A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.640A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.687A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.851A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.656A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.646A 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 49 through 76 removed outlier: 3.944A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.853A pdb=" N ASN A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.437A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.319A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.925A pdb=" N ASN E 85 " --> 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 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.306A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 Processing sheet with id=AB2, first strand: chain 'L' and resid 516 through 517 389 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 286 hydrogen bonds 572 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 3.31 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: 2058 1.33 - 1.45: 4086 1.45 - 1.57: 5694 1.57 - 1.69: 527 1.69 - 1.81: 14 Bond restraints: 12379 Sorted by residual: bond pdb=" O3' DA I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 1.607 1.683 -0.076 1.50e-02 4.44e+03 2.54e+01 bond pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.57e+01 bond pdb=" C1' DG J 34 " pdb=" N9 DG J 34 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1' DG I -20 " pdb=" N9 DG I -20 " ideal model delta sigma weight residual 1.460 1.394 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.87e+00 ... (remaining 12374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 17797 3.19 - 6.37: 46 6.37 - 9.56: 12 9.56 - 12.74: 2 12.74 - 15.93: 3 Bond angle restraints: 17860 Sorted by residual: angle pdb=" C4' DA J -18 " pdb=" C3' DA J -18 " pdb=" O3' DA J -18 " ideal model delta sigma weight residual 110.00 94.07 15.93 1.50e+00 4.44e-01 1.13e+02 angle pdb=" C3' DA I 17 " pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 120.20 134.92 -14.72 1.50e+00 4.44e-01 9.64e+01 angle pdb=" O3' DT I 18 " pdb=" C3' DT I 18 " pdb=" C2' DT I 18 " ideal model delta sigma weight residual 111.50 98.04 13.46 1.50e+00 4.44e-01 8.05e+01 angle pdb=" O3' DA J -18 " pdb=" C3' DA J -18 " pdb=" C2' DA J -18 " ideal model delta sigma weight residual 111.50 100.12 11.38 1.50e+00 4.44e-01 5.76e+01 angle pdb=" C4' DT I 18 " pdb=" C3' DT I 18 " pdb=" O3' DT I 18 " ideal model delta sigma weight residual 110.00 99.69 10.31 1.50e+00 4.44e-01 4.73e+01 ... (remaining 17855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 5618 35.80 - 71.60: 1193 71.60 - 107.40: 19 107.40 - 143.19: 0 143.19 - 178.99: 2 Dihedral angle restraints: 6832 sinusoidal: 4587 harmonic: 2245 Sorted by residual: dihedral pdb=" C4' DA J -49 " pdb=" C3' DA J -49 " pdb=" O3' DA J -49 " pdb=" P DG J -48 " ideal model delta sinusoidal sigma weight residual 220.00 41.01 178.99 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J -16 " pdb=" C3' DG J -16 " pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sinusoidal sigma weight residual -140.00 30.40 -170.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLY E 134 " pdb=" C GLY E 134 " pdb=" N LEU E 135 " pdb=" CA LEU E 135 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1975 0.098 - 0.196: 47 0.196 - 0.295: 8 0.295 - 0.393: 2 0.393 - 0.491: 1 Chirality restraints: 2033 Sorted by residual: chirality pdb=" C3' DA J -18 " pdb=" C4' DA J -18 " pdb=" O3' DA J -18 " pdb=" C2' DA J -18 " both_signs ideal model delta sigma weight residual False -2.66 -3.15 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" C3' DT I 18 " pdb=" C4' DT I 18 " pdb=" O3' DT I 18 " pdb=" C2' DT I 18 " both_signs ideal model delta sigma weight residual False -2.66 -3.04 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C3' DT J -15 " pdb=" C4' DT J -15 " pdb=" O3' DT J -15 " pdb=" C2' DT J -15 " both_signs ideal model delta sigma weight residual False -2.66 -2.96 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2030 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -16 " -0.019 2.00e-02 2.50e+03 2.08e-02 1.29e+01 pdb=" N9 DG J -16 " 0.045 2.00e-02 2.50e+03 pdb=" C8 DG J -16 " -0.025 2.00e-02 2.50e+03 pdb=" N7 DG J -16 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J -16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -16 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG J -16 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG J -16 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J -16 " -0.041 2.00e-02 2.50e+03 pdb=" N2 DG J -16 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DG J -16 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG J -16 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -19 " 0.015 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" N9 DG J -19 " 0.002 2.00e-02 2.50e+03 pdb=" C8 DG J -19 " -0.027 2.00e-02 2.50e+03 pdb=" N7 DG J -19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J -19 " 0.030 2.00e-02 2.50e+03 pdb=" C6 DG J -19 " 0.042 2.00e-02 2.50e+03 pdb=" O6 DG J -19 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J -19 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DG J -19 " -0.009 2.00e-02 2.50e+03 pdb=" N2 DG J -19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG J -19 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG J -19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " 0.013 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 DA I 20 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.024 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.044 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.015 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1514 2.76 - 3.30: 9716 3.30 - 3.83: 21549 3.83 - 4.37: 25862 4.37 - 4.90: 37546 Nonbonded interactions: 96187 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE2 GLU D 71 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.259 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.273 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR E 113 " pdb=" OD2 ASP E 125 " model vdw 2.334 3.040 ... (remaining 96182 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 46 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 111) selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 515 through 535) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.740 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12379 Z= 0.187 Angle : 0.656 15.927 17860 Z= 0.422 Chirality : 0.040 0.491 2033 Planarity : 0.004 0.041 1328 Dihedral : 26.939 178.993 5382 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.31 % Allowed : 12.13 % Favored : 87.56 % 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: -0.10 (0.27), residues: 759 helix: 1.05 (0.20), residues: 533 sheet: None (None), residues: 0 loop : -2.86 (0.29), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 86 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE H 70 TYR 0.006 0.001 TYR B 51 ARG 0.005 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 1.014 Fit side-chains REVERT: B 31 LYS cc_start: 0.5334 (ttmm) cc_final: 0.4862 (tttp) REVERT: B 84 MET cc_start: 0.5751 (mmm) cc_final: 0.5455 (mmm) REVERT: B 91 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6527 (ttpt) REVERT: C 99 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6787 (mtp85) REVERT: D 68 ASP cc_start: 0.5710 (t0) cc_final: 0.5390 (t0) REVERT: D 86 ARG cc_start: 0.6545 (mmt-90) cc_final: 0.6246 (mmt90) REVERT: F 44 LYS cc_start: 0.5833 (tttt) cc_final: 0.5629 (tttm) REVERT: G 41 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6423 (mp0) REVERT: G 77 ARG cc_start: 0.7094 (mtm-85) cc_final: 0.6762 (mmm-85) REVERT: H 86 ARG cc_start: 0.6084 (mmt90) cc_final: 0.5810 (mpt-90) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 2.3653 time to fit residues: 330.7052 Evaluate side-chains 115 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 93 GLN C 94 ASN E 87 GLN F 75 HIS F 93 GLN G 73 ASN G 94 ASN H 84 ASN H 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3853 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12379 Z= 0.289 Angle : 0.636 8.789 17860 Z= 0.375 Chirality : 0.037 0.135 2033 Planarity : 0.005 0.042 1328 Dihedral : 30.458 178.653 3885 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.18 % Allowed : 15.86 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 759 helix: 1.93 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.30 (0.32), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.004 0.001 HIS E 115 PHE 0.012 0.002 PHE A 78 TYR 0.012 0.002 TYR B 51 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.942 Fit side-chains REVERT: B 31 LYS cc_start: 0.5258 (ttmm) cc_final: 0.4888 (tttp) REVERT: B 84 MET cc_start: 0.5718 (mmm) cc_final: 0.5446 (mmm) REVERT: D 86 ARG cc_start: 0.6731 (mmt-90) cc_final: 0.6247 (mmt90) REVERT: G 41 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6413 (mp0) REVERT: G 77 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6631 (mtm-85) REVERT: H 86 ARG cc_start: 0.6051 (mmt90) cc_final: 0.5850 (mpt-90) REVERT: H 108 LYS cc_start: 0.6302 (mtpp) cc_final: 0.6013 (mttt) REVERT: H 122 THR cc_start: 0.7611 (t) cc_final: 0.7271 (p) outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 2.1986 time to fit residues: 303.9379 Evaluate side-chains 119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3818 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12379 Z= 0.175 Angle : 0.575 7.591 17860 Z= 0.345 Chirality : 0.034 0.129 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.371 179.149 3883 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.49 % Allowed : 16.33 % Favored : 81.18 % 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: 1.95 (0.29), residues: 759 helix: 2.54 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE F 61 TYR 0.011 0.001 TYR B 51 ARG 0.003 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.926 Fit side-chains REVERT: B 31 LYS cc_start: 0.5149 (ttmm) cc_final: 0.4778 (tttp) REVERT: B 84 MET cc_start: 0.5707 (mmm) cc_final: 0.5418 (mmm) REVERT: D 68 ASP cc_start: 0.5714 (t0) cc_final: 0.5443 (t0) REVERT: D 86 ARG cc_start: 0.6685 (mmt-90) cc_final: 0.6200 (mmt90) REVERT: G 41 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6414 (mp0) REVERT: G 77 ARG cc_start: 0.6930 (mtm-85) cc_final: 0.6579 (mtm-85) REVERT: H 86 ARG cc_start: 0.6006 (mmt90) cc_final: 0.5723 (mpt-90) REVERT: H 108 LYS cc_start: 0.6245 (mtpp) cc_final: 0.5957 (mttt) outliers start: 16 outliers final: 9 residues processed: 127 average time/residue: 2.1998 time to fit residues: 292.7151 Evaluate side-chains 122 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3824 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12379 Z= 0.190 Angle : 0.565 7.920 17860 Z= 0.339 Chirality : 0.034 0.126 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.284 178.669 3883 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.64 % Allowed : 16.33 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.30), residues: 759 helix: 2.80 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 47 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.898 Fit side-chains REVERT: B 31 LYS cc_start: 0.5228 (ttmm) cc_final: 0.4854 (tttp) REVERT: B 84 MET cc_start: 0.5757 (mmm) cc_final: 0.5468 (mmm) REVERT: D 68 ASP cc_start: 0.5853 (t0) cc_final: 0.5548 (t0) REVERT: D 86 ARG cc_start: 0.6672 (mmt-90) cc_final: 0.6202 (mmt90) REVERT: G 41 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6428 (mp0) REVERT: G 77 ARG cc_start: 0.6910 (mtm-85) cc_final: 0.6511 (mtm-85) REVERT: H 86 ARG cc_start: 0.5945 (mmt90) cc_final: 0.5660 (mpt-90) REVERT: H 122 THR cc_start: 0.7498 (t) cc_final: 0.7139 (p) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 2.1481 time to fit residues: 283.8574 Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3878 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 12379 Z= 0.401 Angle : 0.692 9.280 17860 Z= 0.405 Chirality : 0.041 0.153 2033 Planarity : 0.006 0.050 1328 Dihedral : 30.609 177.974 3883 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 17.73 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.29), residues: 759 helix: 2.26 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.81 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.002 PHE A 78 TYR 0.013 0.002 TYR H 42 ARG 0.005 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.937 Fit side-chains REVERT: B 31 LYS cc_start: 0.5298 (ttmm) cc_final: 0.4915 (tttp) REVERT: B 84 MET cc_start: 0.5682 (mmm) cc_final: 0.5409 (mmm) REVERT: D 86 ARG cc_start: 0.6812 (mmt-90) cc_final: 0.6258 (mmt90) REVERT: G 41 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6381 (mp0) REVERT: G 77 ARG cc_start: 0.6879 (mtm-85) cc_final: 0.6430 (mtm-85) REVERT: H 108 LYS cc_start: 0.6351 (mtpp) cc_final: 0.6059 (mttt) REVERT: H 122 THR cc_start: 0.7665 (t) cc_final: 0.7326 (p) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 2.2337 time to fit residues: 299.7263 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3847 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12379 Z= 0.212 Angle : 0.605 8.207 17860 Z= 0.360 Chirality : 0.035 0.129 2033 Planarity : 0.004 0.041 1328 Dihedral : 30.483 178.207 3883 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 17.88 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.30), residues: 759 helix: 2.59 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 78 TYR 0.011 0.001 TYR B 51 ARG 0.003 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.929 Fit side-chains REVERT: B 31 LYS cc_start: 0.5160 (ttmm) cc_final: 0.4797 (tttp) REVERT: B 84 MET cc_start: 0.5688 (mmm) cc_final: 0.5424 (mmm) REVERT: D 68 ASP cc_start: 0.5682 (t0) cc_final: 0.5447 (t0) REVERT: D 86 ARG cc_start: 0.6746 (mmt-90) cc_final: 0.6192 (mmt90) REVERT: G 41 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6414 (mp0) REVERT: G 77 ARG cc_start: 0.6882 (mtm-85) cc_final: 0.6454 (mtm-85) outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 2.4366 time to fit residues: 321.4612 Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.0040 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3820 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12379 Z= 0.177 Angle : 0.569 7.447 17860 Z= 0.342 Chirality : 0.033 0.127 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.284 177.788 3883 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.56 % Allowed : 18.97 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.30), residues: 759 helix: 2.88 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.007 0.001 TYR E 110 ARG 0.003 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.990 Fit side-chains REVERT: B 31 LYS cc_start: 0.5181 (ttmm) cc_final: 0.4808 (tttp) REVERT: B 84 MET cc_start: 0.5724 (mmm) cc_final: 0.5442 (mmm) REVERT: B 91 LYS cc_start: 0.7208 (tttp) cc_final: 0.6531 (ttpt) REVERT: D 68 ASP cc_start: 0.5780 (t0) cc_final: 0.5485 (t0) REVERT: D 86 ARG cc_start: 0.6661 (mmt-90) cc_final: 0.6162 (mmt90) REVERT: G 41 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6415 (mp0) REVERT: G 77 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6499 (mtm-85) outliers start: 10 outliers final: 7 residues processed: 124 average time/residue: 2.1967 time to fit residues: 285.9643 Evaluate side-chains 118 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3851 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.244 Angle : 0.607 8.349 17860 Z= 0.360 Chirality : 0.035 0.130 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.344 177.548 3883 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.56 % Allowed : 19.75 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.30), residues: 759 helix: 2.72 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE A 78 TYR 0.008 0.001 TYR H 42 ARG 0.004 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.898 Fit side-chains REVERT: B 31 LYS cc_start: 0.5275 (ttmm) cc_final: 0.4879 (tttp) REVERT: B 84 MET cc_start: 0.5708 (mmm) cc_final: 0.5442 (mmm) REVERT: D 86 ARG cc_start: 0.6679 (mmt-90) cc_final: 0.6172 (mmt90) REVERT: G 41 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6384 (mp0) REVERT: G 77 ARG cc_start: 0.6875 (mtm-85) cc_final: 0.6451 (mtm-85) outliers start: 10 outliers final: 9 residues processed: 120 average time/residue: 2.2432 time to fit residues: 281.6420 Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3867 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12379 Z= 0.300 Angle : 0.646 8.723 17860 Z= 0.381 Chirality : 0.038 0.136 2033 Planarity : 0.005 0.045 1328 Dihedral : 30.453 177.460 3883 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 19.13 % Favored : 78.54 % 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: 2.06 (0.29), residues: 759 helix: 2.52 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 PHE 0.015 0.002 PHE A 78 TYR 0.011 0.002 TYR B 51 ARG 0.003 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.001 Fit side-chains REVERT: B 31 LYS cc_start: 0.5268 (ttmm) cc_final: 0.4886 (tttp) REVERT: B 84 MET cc_start: 0.5726 (mmm) cc_final: 0.5475 (mmm) REVERT: D 68 ASP cc_start: 0.5777 (t0) cc_final: 0.5552 (t0) REVERT: D 86 ARG cc_start: 0.6725 (mmt-90) cc_final: 0.6178 (mmt90) REVERT: G 41 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6380 (mp0) REVERT: G 77 ARG cc_start: 0.6875 (mtm-85) cc_final: 0.6531 (mtm-85) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 2.2069 time to fit residues: 286.6124 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3856 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12379 Z= 0.201 Angle : 0.625 8.446 17860 Z= 0.370 Chirality : 0.035 0.129 2033 Planarity : 0.004 0.041 1328 Dihedral : 30.442 177.517 3883 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.09 % Allowed : 20.22 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.30), residues: 759 helix: 2.62 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 78 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG D 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.905 Fit side-chains REVERT: B 31 LYS cc_start: 0.5239 (ttmm) cc_final: 0.4883 (tttp) REVERT: B 84 MET cc_start: 0.5689 (mmm) cc_final: 0.5446 (mmm) REVERT: D 68 ASP cc_start: 0.5739 (t0) cc_final: 0.5508 (t0) REVERT: D 86 ARG cc_start: 0.6667 (mmt-90) cc_final: 0.6117 (mmt90) REVERT: G 41 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6379 (mp0) REVERT: G 77 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.6535 (mtm-85) outliers start: 7 outliers final: 6 residues processed: 119 average time/residue: 2.3085 time to fit residues: 287.0644 Evaluate side-chains 120 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.147694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098618 restraints weight = 15974.101| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.39 r_work: 0.3122 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12379 Z= 0.277 Angle : 0.634 10.875 17860 Z= 0.374 Chirality : 0.037 0.132 2033 Planarity : 0.005 0.042 1328 Dihedral : 30.417 177.130 3883 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.56 % Allowed : 19.28 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.30), residues: 759 helix: 2.60 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE A 78 TYR 0.010 0.002 TYR B 51 ARG 0.004 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4873.21 seconds wall clock time: 87 minutes 25.37 seconds (5245.37 seconds total)