Starting phenix.real_space_refine on Fri Jul 3 02:39:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thu_41272/07_2026/8thu_41272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thu_41272/07_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_41272/07_2026/8thu_41272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thu_41272/07_2026/8thu_41272.map" model { file = "/net/cci-nas-00/data/ceres_data/8thu_41272/07_2026/8thu_41272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thu_41272/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.06, per 1000 atoms: 0.26 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: 1.02 Conformation dependent library (CDL) restraints added in 251.2 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: 1.54 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: 2.23 Time building geometry restraints manager: 1.41 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: 18297 2.93 - 5.87: 115 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: 2.790 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.200 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- 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 : 0.834 14.663 18428 Z= 0.712 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 0.83396 / 0.71 (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 : 0.280 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: 0.1612 time to fit residues: 27.9469 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 : 0.292 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.053663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.039733 restraints weight = 51167.133| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.94 r_work: 0.2676 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12710 Z= 0.152 Angle : 0.613 6.803 18428 Z= 0.374 Chirality : 0.043 0.262 2114 Planarity : 0.004 0.045 1317 Dihedral : 31.154 170.902 4024 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.62 % Allowed : 17.18 % Favored : 81.20 % 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: 2.13 (0.31), residues: 744 helix: 2.62 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -2.15 (0.35), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 29 TYR 0.018 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 0.00237 / 0.15 (12710) covalent geometry : angle 0.61327 / 0.37 (18428) hydrogen bonds : bond 0.05321 / 3.78 ( 762) hydrogen bonds : angle 2.75910 / 2.02 ( 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 136 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.322 Fit side-chains REVERT: G 47 ILE cc_start: 0.9619 (OUTLIER) cc_final: 0.9270 (mp) REVERT: C 69 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8082 (tttm) REVERT: C 85 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: H 76 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8691 (mm-30) outliers start: 10 outliers final: 3 residues processed: 129 average time/residue: 0.1520 time to fit residues: 25.9120 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.0030 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.053594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.039454 restraints weight = 51058.253| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.03 r_work: 0.2661 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12710 Z= 0.150 Angle : 0.571 5.697 18428 Z= 0.354 Chirality : 0.042 0.265 2114 Planarity : 0.004 0.041 1317 Dihedral : 31.195 170.108 4024 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.43 % Allowed : 16.53 % Favored : 81.04 % 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: 2.48 (0.31), residues: 744 helix: 2.87 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.08 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.022 0.001 TYR D 83 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.15 (12710) covalent geometry : angle 0.57101 / 0.35 (18428) hydrogen bonds : bond 0.04983 / 3.51 ( 762) hydrogen bonds : angle 2.67592 / 1.95 ( 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 138 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.251 Fit side-chains REVERT: G 47 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9297 (mp) REVERT: C 11 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8428 (tm-30) REVERT: C 69 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8085 (tttm) REVERT: C 87 ASP cc_start: 0.8583 (t0) cc_final: 0.8246 (t0) REVERT: C 91 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9082 (mmtm) REVERT: F 79 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8544 (ttpt) REVERT: H 34 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8656 (mmpt) REVERT: H 76 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8662 (mm-30) outliers start: 15 outliers final: 6 residues processed: 132 average time/residue: 0.1402 time to fit residues: 24.7724 Evaluate side-chains 127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain A residue 59 GLU 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 79 LYS 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: 40.0000 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.038433 restraints weight = 50610.260| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.02 r_work: 0.2620 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1140 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= 0.186 Angle : 0.595 5.678 18428 Z= 0.359 Chirality : 0.043 0.270 2114 Planarity : 0.004 0.038 1317 Dihedral : 31.332 169.170 4024 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.59 % Allowed : 16.37 % Favored : 81.04 % 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: 2.95 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.13 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 29 TYR 0.025 0.002 TYR D 83 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 0.00342 / 0.19 (12710) covalent geometry : angle 0.59521 / 0.36 (18428) hydrogen bonds : bond 0.05576 / 3.95 ( 762) hydrogen bonds : angle 2.78118 / 2.03 ( 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 135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.318 Fit side-chains REVERT: G 47 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9262 (mp) REVERT: C 11 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 33 HIS cc_start: 0.8782 (OUTLIER) cc_final: 0.8464 (m170) REVERT: C 69 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8035 (tttm) REVERT: C 83 ASP cc_start: 0.8008 (t0) cc_final: 0.7502 (t0) REVERT: C 87 ASP cc_start: 0.8651 (t0) cc_final: 0.8292 (t0) REVERT: C 91 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9088 (mmtm) REVERT: D 68 ASP cc_start: 0.9081 (t0) cc_final: 0.8871 (t0) REVERT: D 79 ARG cc_start: 0.8967 (ttp-110) cc_final: 0.8720 (ttp80) REVERT: E 115 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8890 (mtmm) REVERT: F 79 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8688 (ttpt) REVERT: H 34 LYS cc_start: 0.8858 (mmpt) cc_final: 0.8620 (mmpt) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 0.1484 time to fit residues: 26.1215 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 46 optimal weight: 0.0020 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.053825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.039995 restraints weight = 51158.566| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.93 r_work: 0.2682 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12710 Z= 0.138 Angle : 0.557 5.679 18428 Z= 0.346 Chirality : 0.041 0.264 2114 Planarity : 0.004 0.037 1317 Dihedral : 31.214 169.908 4024 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.30 % Allowed : 17.99 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.32), residues: 744 helix: 2.97 (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 0.007 0.000 ARG B 35 TYR 0.023 0.001 TYR D 83 PHE 0.006 0.001 PHE F 61 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.14 (12710) covalent geometry : angle 0.55708 / 0.35 (18428) hydrogen bonds : bond 0.04665 / 3.28 ( 762) hydrogen bonds : angle 2.58147 / 1.88 ( 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 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.218 Fit side-chains REVERT: G 47 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9302 (mp) REVERT: C 11 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8425 (tm-30) REVERT: C 33 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8412 (m170) REVERT: C 69 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8029 (tttm) REVERT: C 87 ASP cc_start: 0.8680 (t0) cc_final: 0.8291 (t0) REVERT: C 91 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9094 (mmtm) REVERT: F 79 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8528 (ttpt) REVERT: H 34 LYS cc_start: 0.8970 (mmpt) cc_final: 0.8660 (mmpt) outliers start: 8 outliers final: 3 residues processed: 127 average time/residue: 0.1349 time to fit residues: 22.9125 Evaluate side-chains 124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 21 VAL Chi-restraints excluded: chain B residue 79 LYS 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: 0.0870 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.0370 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.054556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.040469 restraints weight = 50538.965| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.92 r_work: 0.2699 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12710 Z= 0.135 Angle : 0.552 7.265 18428 Z= 0.342 Chirality : 0.040 0.264 2114 Planarity : 0.004 0.036 1317 Dihedral : 31.129 169.753 4024 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.78 % Allowed : 17.34 % Favored : 80.88 % 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: 2.71 (0.31), residues: 744 helix: 2.97 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.032 0.001 TYR D 83 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.14 (12710) covalent geometry : angle 0.55184 / 0.34 (18428) hydrogen bonds : bond 0.04435 / 3.13 ( 762) hydrogen bonds : angle 2.52323 / 1.84 ( 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 137 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9286 (mp) REVERT: C 11 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 29 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7590 (mmt90) REVERT: C 33 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8414 (m170) REVERT: C 69 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8027 (tttm) REVERT: C 87 ASP cc_start: 0.8638 (t0) cc_final: 0.8238 (t0) REVERT: C 91 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9083 (mmtm) REVERT: D 71 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8692 (mm-30) REVERT: F 79 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8669 (ttpt) outliers start: 11 outliers final: 6 residues processed: 135 average time/residue: 0.1150 time to fit residues: 21.2329 Evaluate side-chains 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 79 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.054274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.040489 restraints weight = 51190.085| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.92 r_work: 0.2698 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1486 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= 0.143 Angle : 0.558 6.973 18428 Z= 0.344 Chirality : 0.040 0.266 2114 Planarity : 0.004 0.035 1317 Dihedral : 31.129 169.446 4024 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.46 % Allowed : 17.67 % Favored : 80.88 % 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: 2.79 (0.31), residues: 744 helix: 3.03 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.033 0.001 TYR D 83 PHE 0.006 0.001 PHE B 61 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 (12710) covalent geometry : angle 0.55799 / 0.34 (18428) hydrogen bonds : bond 0.04540 / 3.19 ( 762) hydrogen bonds : angle 2.52723 / 1.84 ( 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 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9289 (mp) REVERT: C 11 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8409 (tm-30) REVERT: C 33 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8392 (m170) REVERT: C 69 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8029 (tttm) REVERT: C 87 ASP cc_start: 0.8687 (t0) cc_final: 0.8300 (t0) REVERT: C 91 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9102 (mmtm) REVERT: D 71 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8630 (mm-30) REVERT: F 79 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8705 (ttpt) outliers start: 9 outliers final: 5 residues processed: 131 average time/residue: 0.1231 time to fit residues: 21.8515 Evaluate side-chains 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain F residue 43 VAL 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: 0.0770 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 0.0040 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 overall best weight: 0.4252 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.055309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.041213 restraints weight = 50417.402| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.95 r_work: 0.2725 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12710 Z= 0.134 Angle : 0.550 8.328 18428 Z= 0.341 Chirality : 0.039 0.264 2114 Planarity : 0.004 0.035 1317 Dihedral : 31.042 169.439 4024 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.62 % Allowed : 17.83 % Favored : 80.55 % 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: 2.81 (0.31), residues: 744 helix: 3.02 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.027 0.001 TYR B 88 PHE 0.006 0.001 PHE F 61 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.13 (12710) covalent geometry : angle 0.54956 / 0.34 (18428) hydrogen bonds : bond 0.04176 / 2.93 ( 762) hydrogen bonds : angle 2.44912 / 1.78 ( 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 140 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.260 Fit side-chains REVERT: G 47 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9277 (mp) REVERT: C 11 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8400 (tm-30) REVERT: C 33 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (m170) REVERT: C 69 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8029 (tttm) REVERT: C 87 ASP cc_start: 0.8684 (t0) cc_final: 0.8276 (t0) REVERT: C 91 LYS cc_start: 0.9427 (mmmt) cc_final: 0.9081 (mmtm) REVERT: A 50 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8316 (mt-10) REVERT: F 79 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8721 (tppt) REVERT: H 76 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8660 (mm-30) outliers start: 10 outliers final: 5 residues processed: 137 average time/residue: 0.1098 time to fit residues: 20.5433 Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 79 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 46 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.054445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.040661 restraints weight = 50921.837| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.92 r_work: 0.2704 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12710 Z= 0.152 Angle : 0.568 7.711 18428 Z= 0.347 Chirality : 0.040 0.268 2114 Planarity : 0.004 0.034 1317 Dihedral : 31.102 168.778 4024 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.62 % Allowed : 18.96 % Favored : 79.42 % 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: 2.83 (0.31), residues: 744 helix: 3.04 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.72 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.033 0.002 TYR D 83 PHE 0.006 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (12710) covalent geometry : angle 0.56784 / 0.35 (18428) hydrogen bonds : bond 0.04637 / 3.25 ( 762) hydrogen bonds : angle 2.55384 / 1.85 ( 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 132 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9292 (mp) REVERT: C 11 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8322 (tm-30) REVERT: C 33 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8343 (m170) REVERT: C 69 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8044 (tttm) REVERT: C 87 ASP cc_start: 0.8698 (t0) cc_final: 0.8303 (t0) REVERT: C 91 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9106 (mmtm) REVERT: A 50 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 59 GLU cc_start: 0.7808 (pm20) cc_final: 0.7553 (pm20) REVERT: F 79 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8730 (ttpt) REVERT: H 76 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8687 (mm-30) outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 0.1254 time to fit residues: 21.6795 Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 79 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.053890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039882 restraints weight = 51048.768| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.93 r_work: 0.2674 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12710 Z= 0.163 Angle : 0.586 8.293 18428 Z= 0.354 Chirality : 0.041 0.272 2114 Planarity : 0.004 0.037 1317 Dihedral : 31.193 167.830 4024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.30 % Allowed : 19.61 % Favored : 79.09 % 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: 2.79 (0.32), residues: 744 helix: 3.02 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.78 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.044 0.002 TYR B 88 PHE 0.007 0.001 PHE B 61 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (12710) covalent geometry : angle 0.58649 / 0.35 (18428) hydrogen bonds : bond 0.04972 / 3.50 ( 762) hydrogen bonds : angle 2.64641 / 1.92 ( 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 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: G 47 ILE cc_start: 0.9608 (OUTLIER) cc_final: 0.9301 (mp) REVERT: C 11 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 69 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8033 (tttm) REVERT: F 79 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8844 (tppt) REVERT: H 76 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8668 (mm-30) outliers start: 8 outliers final: 5 residues processed: 126 average time/residue: 0.1150 time to fit residues: 19.6500 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 79 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.038188 restraints weight = 50970.035| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.91 r_work: 0.2612 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12710 Z= 0.235 Angle : 0.650 8.165 18428 Z= 0.381 Chirality : 0.044 0.275 2114 Planarity : 0.004 0.034 1317 Dihedral : 31.370 166.285 4024 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.30 % Allowed : 19.12 % 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: 2.51 (0.32), residues: 744 helix: 2.86 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.03 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.056 0.003 TYR B 88 PHE 0.009 0.001 PHE D 65 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.24 (12710) covalent geometry : angle 0.65047 / 0.38 (18428) hydrogen bonds : bond 0.06234 / 4.40 ( 762) hydrogen bonds : angle 2.91629 / 2.12 ( 1907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.77 seconds wall clock time: 37 minutes 56.98 seconds (2276.98 seconds total)