Starting phenix.real_space_refine on Wed Aug 5 13:53:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3m_46538/08_2026/9d3m_46538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3m_46538/08_2026/9d3m_46538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3m_46538/08_2026/9d3m_46538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3m_46538/08_2026/9d3m_46538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3m_46538/08_2026/9d3m_46538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3m_46538/08_2026/9d3m_46538.map" } resolution = 2.9 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= 0.003 sd= 0.051 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 202 5.49 5 S 14 5.16 5 C 5768 2.51 5 N 1939 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 10203 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2079 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Chain: "J" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2062 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Time building chain proxies: 2.02, per 1000 atoms: 0.20 Number of scatterers: 10203 At special positions: 0 Unit cell: (90.695, 104.72, 115.94, 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 14 16.00 P 202 15.00 O 2280 8.00 N 1939 7.00 C 5768 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: 0.92 Conformation dependent library (CDL) restraints added in 243.7 milliseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1426 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 72.0% alpha, 2.9% beta 100 base pairs and 178 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.809A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.818A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.517A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.514A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.683A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.690A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.510A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.446A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.579A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.698A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.367A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.206A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.806A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.159A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 407 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 262 hydrogen bonds 524 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 178 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2138 1.33 - 1.45: 3112 1.45 - 1.57: 5106 1.57 - 1.69: 402 1.69 - 1.81: 26 Bond restraints: 10784 Sorted by residual: bond pdb=" C3' DA I 9 " pdb=" O3' DA I 9 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C3' DG J 22 " pdb=" C2' DG J 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC I -20 " pdb=" C2' DC I -20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT J 3 " pdb=" C2' DT J 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.76e+00 bond pdb=" C3' DA J -16 " pdb=" C2' DA J -16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.61e+00 ... (remaining 10779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 13663 1.04 - 2.08: 1330 2.08 - 3.13: 381 3.13 - 4.17: 25 4.17 - 5.21: 10 Bond angle restraints: 15409 Sorted by residual: angle pdb=" O4' DT I 18 " pdb=" C4' DT I 18 " pdb=" C3' DT I 18 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.79e+01 angle pdb=" N3 DT J -12 " pdb=" C4 DT J -12 " pdb=" O4 DT J -12 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J -34 " pdb=" C4 DT J -34 " pdb=" O4 DT J -34 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I -42 " pdb=" C4 DT I -42 " pdb=" O4 DT I -42 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 40 " pdb=" C4 DT J 40 " pdb=" O4 DT J 40 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 15404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 4890 35.44 - 70.87: 1074 70.87 - 106.31: 13 106.31 - 141.74: 0 141.74 - 177.18: 2 Dihedral angle restraints: 5979 sinusoidal: 3768 harmonic: 2211 Sorted by residual: dihedral pdb=" C4' DA J -16 " pdb=" C3' DA J -16 " pdb=" O3' DA J -16 " pdb=" P DG J -15 " ideal model delta sinusoidal sigma weight residual -140.00 37.18 -177.18 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 21 " pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " pdb=" P DG J 22 " ideal model delta sinusoidal sigma weight residual 220.00 77.44 142.56 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" CG ARG A 116 " pdb=" CD ARG A 116 " pdb=" NE ARG A 116 " pdb=" CZ ARG A 116 " ideal model delta sinusoidal sigma weight residual -90.00 -133.06 43.06 2 1.50e+01 4.44e-03 9.95e+00 ... (remaining 5976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 960 0.031 - 0.063: 539 0.063 - 0.094: 156 0.094 - 0.125: 86 0.125 - 0.157: 11 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CG LEU A 48 " pdb=" CB LEU A 48 " pdb=" CD1 LEU A 48 " pdb=" CD2 LEU A 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" C3' DT I 12 " pdb=" C4' DT I 12 " pdb=" O3' DT I 12 " pdb=" C2' DT I 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1749 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO G 80 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -2 " -0.019 2.00e-02 2.50e+03 8.68e-03 2.07e+00 pdb=" N9 DA I -2 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA I -2 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -2 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -2 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I -2 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -2 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I -2 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -2 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA I -2 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA I -2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 28 " 0.019 2.00e-02 2.50e+03 9.22e-03 1.91e+00 pdb=" N1 DC I 28 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DC I 28 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DC I 28 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 28 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 28 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 28 " -0.004 2.00e-02 2.50e+03 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 258 2.67 - 3.23: 8681 3.23 - 3.78: 18255 3.78 - 4.34: 24623 4.34 - 4.90: 35721 Nonbonded interactions: 87538 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.238 3.040 nonbonded pdb=" O ILE G 78 " pdb=" OG SER H 55 " model vdw 2.255 3.040 nonbonded pdb=" O SER H 123 " pdb=" OG SER H 123 " model vdw 2.264 3.040 nonbonded pdb=" O ASN G 73 " pdb=" OD1 ASN G 73 " model vdw 2.265 3.040 ... (remaining 87533 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' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'C' and (resid 15 through 113 or (resid 114 through 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 through 117)) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.610 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.050 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 0.044 10784 Z= 0.502 Angle : 0.690 5.210 15409 Z= 0.599 Chirality : 0.045 0.157 1752 Planarity : 0.004 0.036 1256 Dihedral : 27.356 177.180 4553 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.58 % Allowed : 21.96 % Favored : 76.46 % 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: 1.21 (0.29), residues: 745 helix: 1.40 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 20 TYR 0.012 0.002 TYR D 42 PHE 0.008 0.002 PHE E 104 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.50 (10784) covalent geometry : angle 0.69027 / 0.60 (15409) hydrogen bonds : bond 0.14670 / 16.71 ( 669) hydrogen bonds : angle 4.70283 / 6.19 ( 1727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.307 Fit side-chains REVERT: D 57 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8462 (mmmt) REVERT: F 84 MET cc_start: 0.8608 (tpp) cc_final: 0.8365 (tpp) outliers start: 10 outliers final: 6 residues processed: 117 average time/residue: 0.8590 time to fit residues: 105.6672 Evaluate side-chains 112 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.187346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122697 restraints weight = 11508.051| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.57 r_work: 0.3291 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10784 Z= 0.150 Angle : 0.587 5.282 15409 Z= 0.352 Chirality : 0.042 0.218 1752 Planarity : 0.004 0.035 1256 Dihedral : 29.768 174.301 3051 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.00 % Allowed : 20.70 % Favored : 76.30 % 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: 2.46 (0.30), residues: 745 helix: 2.45 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.013 0.001 TYR D 40 PHE 0.008 0.001 PHE A 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (10784) covalent geometry : angle 0.58703 / 0.35 (15409) hydrogen bonds : bond 0.05071 / 5.74 ( 669) hydrogen bonds : angle 3.14479 / 4.20 ( 1727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.201 Fit side-chains REVERT: F 84 MET cc_start: 0.8567 (tpp) cc_final: 0.8245 (tpp) REVERT: F 93 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: G 73 ASN cc_start: 0.7361 (t0) cc_final: 0.6896 (t0) REVERT: H 68 ASP cc_start: 0.8535 (t0) cc_final: 0.8303 (t0) REVERT: H 92 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6440 (mtp85) REVERT: H 93 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7641 (mp0) outliers start: 19 outliers final: 6 residues processed: 118 average time/residue: 0.6812 time to fit residues: 84.7429 Evaluate side-chains 111 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 38 ASN C 73 ASN D 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.186140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121348 restraints weight = 11536.531| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.56 r_work: 0.3268 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10784 Z= 0.189 Angle : 0.587 5.338 15409 Z= 0.348 Chirality : 0.043 0.220 1752 Planarity : 0.004 0.033 1256 Dihedral : 29.833 174.587 3047 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.32 % Allowed : 21.33 % Favored : 75.36 % 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 (0.30), residues: 745 helix: 2.52 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.010 0.001 TYR D 40 PHE 0.009 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (10784) covalent geometry : angle 0.58669 / 0.35 (15409) hydrogen bonds : bond 0.05227 / 5.92 ( 669) hydrogen bonds : angle 3.12014 / 4.18 ( 1727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.297 Fit side-chains REVERT: C 74 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7365 (mmtp) REVERT: F 84 MET cc_start: 0.8592 (tpp) cc_final: 0.8281 (tpp) REVERT: F 93 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: G 77 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8004 (ttm170) REVERT: H 92 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6452 (mtp85) REVERT: H 93 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7624 (mp0) outliers start: 21 outliers final: 9 residues processed: 116 average time/residue: 0.8702 time to fit residues: 106.0544 Evaluate side-chains 116 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122172 restraints weight = 11639.482| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.58 r_work: 0.3281 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 0.035 10784 Z= 0.139 Angle : 0.565 5.106 15409 Z= 0.340 Chirality : 0.042 0.218 1752 Planarity : 0.004 0.030 1256 Dihedral : 29.834 174.789 3047 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.00 % Allowed : 21.64 % Favored : 75.36 % 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 (0.30), residues: 745 helix: 2.63 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.95 (0.37), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 32 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (10784) covalent geometry : angle 0.56531 / 0.34 (15409) hydrogen bonds : bond 0.04807 / 5.46 ( 669) hydrogen bonds : angle 3.06421 / 4.11 ( 1727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.205 Fit side-chains REVERT: A 120 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8431 (mtt) REVERT: C 74 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7358 (mmtp) REVERT: F 84 MET cc_start: 0.8583 (tpp) cc_final: 0.8266 (tpp) REVERT: F 93 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: G 77 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: H 92 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6415 (mtp85) REVERT: H 93 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7624 (mp0) outliers start: 19 outliers final: 10 residues processed: 116 average time/residue: 0.8209 time to fit residues: 100.2856 Evaluate side-chains 119 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 46 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 8 optimal weight: 40.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.187124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122126 restraints weight = 11581.603| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.59 r_work: 0.3281 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10784 Z= 0.145 Angle : 0.564 5.070 15409 Z= 0.338 Chirality : 0.042 0.216 1752 Planarity : 0.004 0.031 1256 Dihedral : 29.835 174.425 3047 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.16 % Allowed : 21.64 % Favored : 75.20 % 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: 2.72 (0.30), residues: 745 helix: 2.68 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.010 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (10784) covalent geometry : angle 0.56381 / 0.34 (15409) hydrogen bonds : bond 0.04712 / 5.36 ( 669) hydrogen bonds : angle 3.02763 / 4.09 ( 1727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.292 Fit side-chains REVERT: C 74 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7352 (mmtp) REVERT: F 84 MET cc_start: 0.8577 (tpp) cc_final: 0.8252 (tpp) REVERT: F 93 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: G 24 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7408 (mm-40) REVERT: H 92 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6392 (mtp85) REVERT: H 93 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7630 (mp0) outliers start: 20 outliers final: 10 residues processed: 117 average time/residue: 0.8411 time to fit residues: 103.4980 Evaluate side-chains 119 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122994 restraints weight = 11727.088| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.57 r_work: 0.3292 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10784 Z= 0.139 Angle : 0.558 6.632 15409 Z= 0.335 Chirality : 0.042 0.218 1752 Planarity : 0.004 0.032 1256 Dihedral : 29.833 174.555 3047 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.48 % Allowed : 21.48 % Favored : 75.04 % 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: 2.80 (0.30), residues: 745 helix: 2.79 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.96 (0.36), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.010 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (10784) covalent geometry : angle 0.55805 / 0.34 (15409) hydrogen bonds : bond 0.04567 / 5.19 ( 669) hydrogen bonds : angle 2.99613 / 4.04 ( 1727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.289 Fit side-chains REVERT: A 120 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8383 (mtt) REVERT: C 74 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7337 (mmtp) REVERT: F 31 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8075 (tttt) REVERT: F 84 MET cc_start: 0.8570 (tpp) cc_final: 0.8242 (tpp) REVERT: F 93 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: G 24 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: H 93 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7611 (mp0) outliers start: 22 outliers final: 13 residues processed: 117 average time/residue: 0.7877 time to fit residues: 97.2059 Evaluate side-chains 122 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.185521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120656 restraints weight = 11572.777| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.56 r_work: 0.3257 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10784 Z= 0.193 Angle : 0.592 5.750 15409 Z= 0.347 Chirality : 0.043 0.225 1752 Planarity : 0.004 0.038 1256 Dihedral : 29.919 174.445 3047 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.32 % Allowed : 21.48 % Favored : 75.20 % 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: 2.53 (0.30), residues: 745 helix: 2.57 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.00 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.011 0.002 TYR G 57 PHE 0.010 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (10784) covalent geometry : angle 0.59249 / 0.35 (15409) hydrogen bonds : bond 0.05057 / 5.72 ( 669) hydrogen bonds : angle 3.04920 / 4.10 ( 1727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.302 Fit side-chains REVERT: C 29 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: C 35 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6265 (mtt90) REVERT: C 74 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7353 (mmtp) REVERT: F 84 MET cc_start: 0.8613 (tpp) cc_final: 0.8353 (tpp) REVERT: F 93 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: G 24 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7363 (mm-40) REVERT: G 77 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7939 (ttm170) outliers start: 21 outliers final: 11 residues processed: 117 average time/residue: 0.8228 time to fit residues: 101.2810 Evaluate side-chains 120 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 53 optimal weight: 0.0060 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.186998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122243 restraints weight = 11564.233| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.57 r_work: 0.3284 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10784 Z= 0.132 Angle : 0.566 5.448 15409 Z= 0.336 Chirality : 0.042 0.216 1752 Planarity : 0.004 0.047 1256 Dihedral : 29.916 174.923 3047 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.32 % Allowed : 21.48 % Favored : 75.20 % 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: 2.76 (0.30), residues: 745 helix: 2.73 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.011 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.13 (10784) covalent geometry : angle 0.56580 / 0.34 (15409) hydrogen bonds : bond 0.04545 / 5.18 ( 669) hydrogen bonds : angle 2.97799 / 4.01 ( 1727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.294 Fit side-chains REVERT: C 35 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6223 (mtt90) REVERT: C 74 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7350 (mmtp) REVERT: D 83 TYR cc_start: 0.7662 (m-10) cc_final: 0.7354 (t80) REVERT: F 84 MET cc_start: 0.8576 (tpp) cc_final: 0.8241 (tpp) REVERT: F 93 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: G 19 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7925 (p) REVERT: G 24 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7360 (mm-40) outliers start: 21 outliers final: 11 residues processed: 118 average time/residue: 0.7122 time to fit residues: 88.5642 Evaluate side-chains 119 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 40.0000 chunk 39 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 60 optimal weight: 0.2980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.186663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122118 restraints weight = 11552.767| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.55 r_work: 0.3279 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10784 Z= 0.158 Angle : 0.569 6.144 15409 Z= 0.336 Chirality : 0.042 0.225 1752 Planarity : 0.004 0.041 1256 Dihedral : 29.913 174.409 3047 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.53 % Allowed : 22.27 % Favored : 75.20 % 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: 2.76 (0.30), residues: 745 helix: 2.74 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.92 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.011 0.001 TYR G 57 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (10784) covalent geometry : angle 0.56947 / 0.34 (15409) hydrogen bonds : bond 0.04585 / 5.21 ( 669) hydrogen bonds : angle 2.97915 / 4.02 ( 1727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.285 Fit side-chains REVERT: C 35 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6228 (mtt90) REVERT: C 74 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7365 (mmtp) REVERT: F 84 MET cc_start: 0.8587 (tpp) cc_final: 0.8258 (tpp) REVERT: F 93 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: G 19 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7924 (p) REVERT: G 24 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7325 (mm-40) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 0.6764 time to fit residues: 78.3486 Evaluate side-chains 115 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.0670 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119668 restraints weight = 11469.555| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.57 r_work: 0.3244 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10784 Z= 0.217 Angle : 0.614 6.293 15409 Z= 0.354 Chirality : 0.044 0.228 1752 Planarity : 0.005 0.045 1256 Dihedral : 29.995 174.307 3047 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.53 % Allowed : 22.12 % Favored : 75.36 % 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: 2.35 (0.30), residues: 745 helix: 2.43 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.08 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 86 TYR 0.014 0.002 TYR G 57 PHE 0.011 0.002 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (10784) covalent geometry : angle 0.61419 / 0.35 (15409) hydrogen bonds : bond 0.05297 / 5.98 ( 669) hydrogen bonds : angle 3.11555 / 4.21 ( 1727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.212 Fit side-chains REVERT: C 35 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6259 (mtt90) REVERT: C 74 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7368 (mmtp) REVERT: F 84 MET cc_start: 0.8629 (tpp) cc_final: 0.8349 (tpp) REVERT: F 93 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: G 24 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7350 (mm-40) REVERT: G 73 ASN cc_start: 0.7476 (t0) cc_final: 0.6907 (t0) REVERT: G 77 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7910 (ttm170) outliers start: 16 outliers final: 9 residues processed: 112 average time/residue: 0.7680 time to fit residues: 90.4484 Evaluate side-chains 116 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.185531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120417 restraints weight = 11554.975| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.58 r_work: 0.3256 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10784 Z= 0.158 Angle : 0.591 6.091 15409 Z= 0.345 Chirality : 0.043 0.224 1752 Planarity : 0.004 0.044 1256 Dihedral : 29.999 174.454 3046 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.69 % Allowed : 22.27 % Favored : 75.04 % 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: 2.40 (0.30), residues: 745 helix: 2.47 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.06 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.014 0.002 TYR G 57 PHE 0.010 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (10784) covalent geometry : angle 0.59110 / 0.34 (15409) hydrogen bonds : bond 0.04999 / 5.65 ( 669) hydrogen bonds : angle 3.07287 / 4.16 ( 1727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3619.65 seconds wall clock time: 62 minutes 9.86 seconds (3729.86 seconds total)