Starting phenix.real_space_refine on Wed Aug 5 20:37:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thu_41272/08_2026/8thu_41272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thu_41272/08_2026/8thu_41272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2026/8thu_41272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2026/8thu_41272.map" model { file = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2026/8thu_41272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2026/8thu_41272.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.029 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 291 5.49 5 S 12 5.16 5 C 6569 2.51 5 N 2223 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11902 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 773 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 2.21, per 1000 atoms: 0.19 Number of scatterers: 11902 At special positions: 0 Unit cell: (123.54, 124.392, 78.384, 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 291 15.00 O 2807 8.00 N 2223 7.00 C 6569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 227.0 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 71.2% alpha, 1.8% beta 144 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'G' and resid 8 through 13 removed outlier: 3.838A pdb=" N ALA G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.799A pdb=" N ALA G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 84 through 90 Processing helix chain 'C' and resid 8 through 13 removed outlier: 3.581A pdb=" N ALA C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 37 through 66 removed outlier: 3.819A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 3.513A pdb=" N LEU C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 90 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 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.771A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.727A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.062A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.619A 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 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.559A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 36 removed outlier: 7.232A pdb=" N ARG G 35 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 93 through 94 removed outlier: 6.243A pdb=" N THR G 93 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.002A pdb=" N ARG C 35 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 94 removed outlier: 6.444A pdb=" N THR C 93 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.755A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 395 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2785 1.34 - 1.46: 4202 1.46 - 1.58: 5121 1.58 - 1.70: 580 1.70 - 1.82: 22 Bond restraints: 12710 Sorted by residual: bond pdb=" C3' DT J 109 " pdb=" C2' DT J 109 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.45e+01 bond pdb=" C3' DC J 16 " pdb=" C2' DC J 16 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 bond pdb=" C3' DT I 134 " pdb=" C2' DT I 134 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 bond pdb=" C3' DG I 44 " pdb=" C2' DG I 44 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 ... (remaining 12705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 18296 2.93 - 5.87: 116 5.87 - 8.80: 11 8.80 - 11.73: 4 11.73 - 14.66: 1 Bond angle restraints: 18428 Sorted by residual: angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.15e+01 angle pdb=" O4' DG I 4 " pdb=" C4' DG I 4 " pdb=" C3' DG I 4 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 127.36 -14.66 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" N GLY C 34 " pdb=" CA GLY C 34 " pdb=" C GLY C 34 " ideal model delta sigma weight residual 111.36 116.78 -5.42 1.17e+00 7.31e-01 2.14e+01 ... (remaining 18423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 5372 34.71 - 69.43: 1478 69.43 - 104.14: 17 104.14 - 138.86: 1 138.86 - 173.57: 2 Dihedral angle restraints: 6870 sinusoidal: 4666 harmonic: 2204 Sorted by residual: dihedral pdb=" CA THR C 31 " pdb=" C THR C 31 " pdb=" N SER C 32 " pdb=" CA SER C 32 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C4' DC J 3 " pdb=" C3' DC J 3 " pdb=" O3' DC J 3 " pdb=" P DG J 4 " ideal model delta sinusoidal sigma weight residual -140.00 33.57 -173.57 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 134 " pdb=" C3' DT I 134 " pdb=" O3' DT I 134 " pdb=" P DA I 135 " ideal model delta sinusoidal sigma weight residual 220.00 51.93 168.07 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1412 0.041 - 0.082: 544 0.082 - 0.122: 143 0.122 - 0.163: 13 0.163 - 0.204: 2 Chirality restraints: 2114 Sorted by residual: chirality pdb=" C3' DG J 25 " pdb=" C4' DG J 25 " pdb=" O3' DG J 25 " pdb=" C2' DG J 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL H 69 " pdb=" N VAL H 69 " pdb=" C VAL H 69 " pdb=" CB VAL H 69 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" P DA I 135 " pdb=" OP1 DA I 135 " pdb=" OP2 DA I 135 " pdb=" O5' DA I 135 " both_signs ideal model delta sigma weight residual True 2.34 -2.50 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2111 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 81 " 0.263 9.50e-02 1.11e+02 1.18e-01 8.56e+00 pdb=" NE ARG C 81 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 81 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 81 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 81 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 87 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CG ASP G 87 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP G 87 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP G 87 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.03e+00 pdb=" N9 DG I 121 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.002 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 4 2.20 - 2.88: 3707 2.88 - 3.55: 16699 3.55 - 4.23: 31285 4.23 - 4.90: 47126 Nonbonded interactions: 98821 Sorted by model distance: nonbonded pdb=" NH1 ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 1.528 3.120 nonbonded pdb=" NH2 ARG B 92 " pdb=" CD2 LEU D 101 " model vdw 1.954 3.540 nonbonded pdb=" CZ ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 1.976 3.270 nonbonded pdb=" NH2 ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 2.055 3.120 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.208 3.040 ... (remaining 98816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 6 through 66 or (resid 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 108)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12710 Z= 0.526 Angle : 0.841 14.663 18428 Z= 0.719 Chirality : 0.044 0.204 2114 Planarity : 0.006 0.118 1317 Dihedral : 28.562 173.573 5446 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 18.48 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.30), residues: 744 helix: 2.07 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -2.14 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 79 TYR 0.029 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.53 (12710) covalent geometry : angle 0.84136 / 0.72 (18428) hydrogen bonds : bond 0.10874 / 7.29 ( 762) hydrogen bonds : angle 3.34017 / 2.46 ( 1907) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.354 Fit side-chains REVERT: C 69 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7608 (tttt) REVERT: D 68 ASP cc_start: 0.9168 (t0) cc_final: 0.8951 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1293 time to fit residues: 22.5715 Evaluate side-chains 115 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.053740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039852 restraints weight = 51275.201| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.93 r_work: 0.2679 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12710 Z= 0.160 Angle : 0.616 6.645 18428 Z= 0.375 Chirality : 0.043 0.294 2114 Planarity : 0.004 0.045 1317 Dihedral : 31.110 171.432 4024 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.62 % Allowed : 16.86 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.31), residues: 744 helix: 2.62 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.14 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.016 0.001 TYR D 83 PHE 0.006 0.001 PHE E 67 HIS 0.003 0.000 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.16 (12710) covalent geometry : angle 0.61610 / 0.37 (18428) hydrogen bonds : bond 0.05205 / 3.71 ( 762) hydrogen bonds : angle 2.74642 / 2.01 ( 1907) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.203 Fit side-chains REVERT: G 47 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9249 (mp) REVERT: C 69 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8079 (tttm) REVERT: C 85 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: H 76 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8746 (mm-30) outliers start: 10 outliers final: 3 residues processed: 130 average time/residue: 0.1252 time to fit residues: 21.6476 Evaluate side-chains 126 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.037132 restraints weight = 50461.923| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 1.95 r_work: 0.2580 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12710 Z= 0.267 Angle : 0.694 6.982 18428 Z= 0.401 Chirality : 0.047 0.301 2114 Planarity : 0.005 0.040 1317 Dihedral : 31.421 169.705 4024 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.24 % Allowed : 16.37 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.31), residues: 744 helix: 2.73 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.41 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.036 0.002 TYR D 83 PHE 0.011 0.001 PHE B 61 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.27 (12710) covalent geometry : angle 0.69378 / 0.40 (18428) hydrogen bonds : bond 0.06950 / 4.92 ( 762) hydrogen bonds : angle 3.08873 / 2.26 ( 1907) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.283 Fit side-chains REVERT: G 47 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9270 (mp) REVERT: C 11 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8565 (tm-30) REVERT: C 69 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8073 (tttt) REVERT: C 83 ASP cc_start: 0.8057 (t0) cc_final: 0.7584 (t0) REVERT: C 87 ASP cc_start: 0.8693 (t0) cc_final: 0.8377 (t0) REVERT: C 91 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9139 (mmtm) REVERT: E 115 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8971 (mtmm) REVERT: F 79 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8831 (tppt) REVERT: H 34 LYS cc_start: 0.8961 (mmpt) cc_final: 0.8728 (mmpt) REVERT: H 76 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8704 (mm-30) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 0.1111 time to fit residues: 19.3182 Evaluate side-chains 124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 30.0000 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 68 optimal weight: 0.0770 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3269 r_free = 0.3269 target = 0.053336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.039279 restraints weight = 51114.152| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.96 r_work: 0.2659 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12710 Z= 0.143 Angle : 0.586 5.677 18428 Z= 0.357 Chirality : 0.042 0.287 2114 Planarity : 0.004 0.040 1317 Dihedral : 31.225 170.500 4024 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.46 % Allowed : 18.15 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.32), residues: 744 helix: 2.88 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.16 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 29 TYR 0.028 0.001 TYR D 83 PHE 0.007 0.001 PHE F 61 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.14 (12710) covalent geometry : angle 0.58642 / 0.36 (18428) hydrogen bonds : bond 0.04941 / 3.49 ( 762) hydrogen bonds : angle 2.68400 / 1.96 ( 1907) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.210 Fit side-chains REVERT: G 29 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8416 (tpp80) REVERT: G 47 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9284 (mp) REVERT: C 11 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8594 (tm-30) REVERT: C 33 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8419 (m170) REVERT: C 69 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8041 (tttm) REVERT: C 87 ASP cc_start: 0.8653 (t0) cc_final: 0.8303 (t0) REVERT: C 91 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9094 (mmtm) REVERT: F 79 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8751 (tppt) REVERT: H 34 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8679 (mmpt) REVERT: H 71 GLU cc_start: 0.8896 (tp30) cc_final: 0.8540 (mm-30) outliers start: 9 outliers final: 3 residues processed: 129 average time/residue: 0.1161 time to fit residues: 19.9754 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3238 r_free = 0.3238 target = 0.052170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.038163 restraints weight = 51113.922| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.92 r_work: 0.2617 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12710 Z= 0.206 Angle : 0.628 6.836 18428 Z= 0.370 Chirality : 0.044 0.292 2114 Planarity : 0.004 0.038 1317 Dihedral : 31.307 169.947 4024 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.43 % Allowed : 17.67 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.32), residues: 744 helix: 2.89 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.19 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.041 0.002 TYR D 83 PHE 0.009 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (12710) covalent geometry : angle 0.62839 / 0.37 (18428) hydrogen bonds : bond 0.05776 / 4.08 ( 762) hydrogen bonds : angle 2.83897 / 2.08 ( 1907) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9268 (mp) REVERT: C 11 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 33 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8451 (m170) REVERT: C 69 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8065 (tttm) REVERT: C 83 ASP cc_start: 0.8076 (t0) cc_final: 0.7615 (t0) REVERT: C 87 ASP cc_start: 0.8738 (t0) cc_final: 0.8383 (t0) REVERT: C 91 LYS cc_start: 0.9475 (mmmt) cc_final: 0.9135 (mmtm) REVERT: D 68 ASP cc_start: 0.9100 (t0) cc_final: 0.8880 (t0) REVERT: E 115 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8881 (mtmm) REVERT: F 79 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8854 (tppt) REVERT: H 34 LYS cc_start: 0.9005 (mmpt) cc_final: 0.8739 (mmpt) outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 0.1264 time to fit residues: 21.7992 Evaluate side-chains 127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3257 r_free = 0.3257 target = 0.052866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.038878 restraints weight = 50988.863| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.93 r_work: 0.2641 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12710 Z= 0.154 Angle : 0.588 6.282 18428 Z= 0.355 Chirality : 0.042 0.290 2114 Planarity : 0.004 0.037 1317 Dihedral : 31.261 170.051 4024 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.78 % Allowed : 18.64 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.32), residues: 744 helix: 2.94 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.12 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.028 0.001 TYR D 83 PHE 0.007 0.001 PHE B 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12710) covalent geometry : angle 0.58832 / 0.36 (18428) hydrogen bonds : bond 0.05064 / 3.57 ( 762) hydrogen bonds : angle 2.70098 / 1.97 ( 1907) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.314 Fit side-chains REVERT: G 47 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9288 (mp) REVERT: C 11 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8430 (tm-30) REVERT: C 69 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8050 (tttm) REVERT: C 83 ASP cc_start: 0.8054 (t0) cc_final: 0.7585 (t0) REVERT: C 87 ASP cc_start: 0.8721 (t0) cc_final: 0.8324 (t0) REVERT: C 91 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9103 (mmtm) REVERT: E 115 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8831 (mtmm) REVERT: F 79 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8846 (tppt) REVERT: H 34 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8799 (mmtt) REVERT: H 76 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8681 (mm-30) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 0.1368 time to fit residues: 23.5945 Evaluate side-chains 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3250 r_free = 0.3250 target = 0.052656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.038572 restraints weight = 51010.896| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.93 r_work: 0.2632 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12710 Z= 0.178 Angle : 0.606 7.958 18428 Z= 0.361 Chirality : 0.043 0.291 2114 Planarity : 0.004 0.037 1317 Dihedral : 31.284 169.688 4024 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.27 % Allowed : 18.48 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.32), residues: 744 helix: 2.92 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.15 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.018 0.001 TYR D 83 PHE 0.008 0.001 PHE B 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (12710) covalent geometry : angle 0.60583 / 0.36 (18428) hydrogen bonds : bond 0.05307 / 3.74 ( 762) hydrogen bonds : angle 2.74778 / 2.01 ( 1907) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9275 (mp) REVERT: C 11 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8426 (tm-30) REVERT: C 33 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8444 (m170) REVERT: C 69 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8021 (tttm) REVERT: C 87 ASP cc_start: 0.8740 (t0) cc_final: 0.8390 (t0) REVERT: C 91 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9151 (mmtm) REVERT: E 115 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8850 (mtmm) REVERT: F 79 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8924 (tppt) REVERT: H 76 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8681 (mm-30) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.1346 time to fit residues: 23.8577 Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3281 r_free = 0.3281 target = 0.053730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.039849 restraints weight = 50562.381| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.93 r_work: 0.2676 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12710 Z= 0.138 Angle : 0.579 7.160 18428 Z= 0.351 Chirality : 0.041 0.288 2114 Planarity : 0.004 0.036 1317 Dihedral : 31.152 169.940 4024 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.94 % Allowed : 18.48 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.31), residues: 744 helix: 2.96 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.02 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.029 0.001 TYR D 83 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.14 (12710) covalent geometry : angle 0.57883 / 0.35 (18428) hydrogen bonds : bond 0.04596 / 3.22 ( 762) hydrogen bonds : angle 2.58348 / 1.88 ( 1907) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9605 (OUTLIER) cc_final: 0.9303 (mp) REVERT: C 11 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8425 (tm-30) REVERT: C 33 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8437 (m170) REVERT: C 69 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8010 (tttm) REVERT: C 87 ASP cc_start: 0.8707 (t0) cc_final: 0.8333 (t0) REVERT: C 91 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9114 (mmtm) REVERT: A 50 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8310 (mt-10) REVERT: F 79 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8916 (tppt) REVERT: H 76 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8659 (mm-30) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.1251 time to fit residues: 22.4385 Evaluate side-chains 132 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.3980 chunk 29 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 46 optimal weight: 0.0010 chunk 33 optimal weight: 0.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3286 r_free = 0.3286 target = 0.053929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.040048 restraints weight = 50959.482| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.94 r_work: 0.2686 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12710 Z= 0.140 Angle : 0.578 9.661 18428 Z= 0.350 Chirality : 0.041 0.289 2114 Planarity : 0.004 0.035 1317 Dihedral : 31.106 169.630 4024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 18.31 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.32), residues: 744 helix: 2.95 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 79 TYR 0.018 0.002 TYR B 88 PHE 0.007 0.001 PHE E 67 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.14 (12710) covalent geometry : angle 0.57789 / 0.35 (18428) hydrogen bonds : bond 0.04563 / 3.20 ( 762) hydrogen bonds : angle 2.57266 / 1.87 ( 1907) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9298 (mp) REVERT: C 11 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8389 (tm-30) REVERT: C 29 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7544 (mmt90) REVERT: C 33 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.8397 (m170) REVERT: C 69 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7987 (tttm) REVERT: C 87 ASP cc_start: 0.8694 (t0) cc_final: 0.8492 (t0) REVERT: A 50 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8340 (mt-10) REVERT: D 71 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8736 (mm-30) REVERT: H 76 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8645 (mm-30) outliers start: 12 outliers final: 7 residues processed: 133 average time/residue: 0.1182 time to fit residues: 21.2374 Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3254 r_free = 0.3254 target = 0.052799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.038785 restraints weight = 51199.044| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.93 r_work: 0.2633 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12710 Z= 0.191 Angle : 0.627 7.788 18428 Z= 0.368 Chirality : 0.043 0.295 2114 Planarity : 0.004 0.034 1317 Dihedral : 31.242 168.606 4024 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.46 % Allowed : 19.29 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.32), residues: 744 helix: 2.92 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.09 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.039 0.002 TYR B 88 PHE 0.008 0.001 PHE B 61 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (12710) covalent geometry : angle 0.62715 / 0.37 (18428) hydrogen bonds : bond 0.05482 / 3.86 ( 762) hydrogen bonds : angle 2.75803 / 2.01 ( 1907) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9286 (mp) REVERT: C 11 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8404 (tm-30) REVERT: C 69 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8043 (tttm) REVERT: C 83 ASP cc_start: 0.8041 (t0) cc_final: 0.7687 (t0) REVERT: C 87 ASP cc_start: 0.8662 (t0) cc_final: 0.8432 (t0) REVERT: C 91 LYS cc_start: 0.9330 (mmmt) cc_final: 0.9048 (mmtm) REVERT: H 76 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8676 (mm-30) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.1058 time to fit residues: 18.0617 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3252 r_free = 0.3252 target = 0.052734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.038659 restraints weight = 51048.059| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.92 r_work: 0.2635 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12710 Z= 0.184 Angle : 0.617 8.188 18428 Z= 0.365 Chirality : 0.042 0.294 2114 Planarity : 0.004 0.037 1317 Dihedral : 31.258 168.300 4024 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.94 % Allowed : 19.12 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.32), residues: 744 helix: 2.89 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.12 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.047 0.002 TYR B 88 PHE 0.008 0.001 PHE B 61 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (12710) covalent geometry : angle 0.61676 / 0.36 (18428) hydrogen bonds : bond 0.05369 / 3.78 ( 762) hydrogen bonds : angle 2.76998 / 2.02 ( 1907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.51 seconds wall clock time: 36 minutes 24.47 seconds (2184.47 seconds total)