Starting phenix.real_space_refine on Thu Jul 2 20:22:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3m_46538/07_2026/9d3m_46538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3m_46538/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3m_46538/07_2026/9d3m_46538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3m_46538/07_2026/9d3m_46538.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3m_46538/07_2026/9d3m_46538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3m_46538/07_2026/9d3m_46538.cif" } 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): 0.01s 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: 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: 1.63, per 1000 atoms: 0.16 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: 0.72 Conformation dependent library (CDL) restraints added in 249.0 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: 0.86 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: 1.34 Time building geometry restraints manager: 0.95 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: 13717 1.04 - 2.08: 1279 2.08 - 3.13: 378 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: 0.890 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 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:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- 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= 0.501 Angle : 0.684 5.210 15409 Z= 0.594 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 0.68387 / 0.59 (15409) hydrogen bonds : bond 0.14670 / 16.62 ( 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 : 0.207 Fit side-chains REVERT: D 57 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8463 (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: 0.6808 time to fit residues: 83.8900 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 : 0.273 ------------------------------------------------------------------------------- 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 = 0.187300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122643 restraints weight = 11505.308| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.58 r_work: 0.3281 rms_B_bonded: 3.08 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: 0.8035 moved from start: 0.0673 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= 0.153 Angle : 0.574 5.255 15409 Z= 0.349 Chirality : 0.042 0.221 1752 Planarity : 0.004 0.033 1256 Dihedral : 29.826 173.663 3051 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.00 % Allowed : 20.38 % Favored : 76.62 % 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: 2.41 (0.30), residues: 745 helix: 2.40 (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 0.005 0.000 ARG C 71 TYR 0.013 0.001 TYR D 40 PHE 0.008 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (10784) covalent geometry : angle 0.57395 / 0.35 (15409) hydrogen bonds : bond 0.05380 / 6.08 ( 669) hydrogen bonds : angle 3.18137 / 4.24 ( 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 125 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.263 Fit side-chains REVERT: D 47 GLN cc_start: 0.8772 (mt0) cc_final: 0.8548 (mt0) REVERT: F 84 MET cc_start: 0.8567 (tpp) cc_final: 0.8244 (tpp) REVERT: F 93 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: G 73 ASN cc_start: 0.7297 (t0) cc_final: 0.6863 (t0) REVERT: H 68 ASP cc_start: 0.8556 (t0) cc_final: 0.8305 (t0) REVERT: H 92 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6460 (mtp85) REVERT: H 93 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7653 (mp0) outliers start: 19 outliers final: 7 residues processed: 118 average time/residue: 0.7020 time to fit residues: 87.2223 Evaluate side-chains 112 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 38 ASN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.185774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120522 restraints weight = 11534.075| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.61 r_work: 0.3253 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10784 Z= 0.195 Angle : 0.583 5.423 15409 Z= 0.349 Chirality : 0.043 0.221 1752 Planarity : 0.004 0.035 1256 Dihedral : 29.919 174.356 3048 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.79 % Allowed : 20.70 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.49 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 32 TYR 0.012 0.002 TYR D 40 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 0.00410 / 0.20 (10784) covalent geometry : angle 0.58260 / 0.35 (15409) hydrogen bonds : bond 0.05356 / 6.03 ( 669) hydrogen bonds : angle 3.12694 / 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 128 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.211 Fit side-chains REVERT: C 29 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7925 (ttm-80) REVERT: C 32 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8198 (ttp80) REVERT: C 74 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7375 (mmtp) REVERT: D 47 GLN cc_start: 0.8793 (mt0) cc_final: 0.8582 (mt0) REVERT: F 84 MET cc_start: 0.8602 (tpp) cc_final: 0.8294 (tpp) REVERT: F 93 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: G 32 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7454 (mtm110) REVERT: G 77 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7955 (ttm170) REVERT: H 92 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.6532 (mtp85) outliers start: 24 outliers final: 10 residues processed: 117 average time/residue: 0.7040 time to fit residues: 86.6961 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 : 0.277 ------------------------------------------------------------------------------- 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 C residue 29 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 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain H residue 118 VAL 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: 8.9990 chunk 63 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 40.0000 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.187089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122154 restraints weight = 11648.733| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.57 r_work: 0.3279 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10784 Z= 0.138 Angle : 0.554 5.945 15409 Z= 0.336 Chirality : 0.041 0.215 1752 Planarity : 0.004 0.033 1256 Dihedral : 29.931 174.411 3047 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.21 % Allowed : 22.43 % 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: 2.65 (0.30), residues: 745 helix: 2.64 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.99 (0.37), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.010 0.001 TYR H 40 PHE 0.009 0.001 PHE F 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (10784) covalent geometry : angle 0.55423 / 0.34 (15409) hydrogen bonds : bond 0.04733 / 5.35 ( 669) hydrogen bonds : angle 3.03837 / 4.09 ( 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 120 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.205 Fit side-chains REVERT: C 32 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8150 (ttp80) REVERT: C 74 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7374 (mmtp) REVERT: D 47 GLN cc_start: 0.8777 (mt0) cc_final: 0.8562 (mt0) REVERT: F 84 MET cc_start: 0.8582 (tpp) cc_final: 0.8274 (tpp) REVERT: F 93 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: G 32 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7386 (mtm110) REVERT: H 93 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7634 (mp0) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 0.6476 time to fit residues: 77.6979 Evaluate side-chains 114 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 H residue 93 GLU 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: 0.9980 chunk 3 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 40.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.186688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121849 restraints weight = 11604.405| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.56 r_work: 0.3277 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10784 Z= 0.166 Angle : 0.558 5.661 15409 Z= 0.335 Chirality : 0.042 0.217 1752 Planarity : 0.004 0.033 1256 Dihedral : 29.963 174.134 3047 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.16 % Allowed : 21.96 % Favored : 74.88 % 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: 2.67 (0.30), residues: 745 helix: 2.67 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.94 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.00327 / 0.17 (10784) covalent geometry : angle 0.55761 / 0.34 (15409) hydrogen bonds : bond 0.04715 / 5.33 ( 669) hydrogen bonds : angle 2.99370 / 4.04 ( 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 123 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7864 (ttm-80) REVERT: C 32 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8257 (ttp80) REVERT: C 35 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6212 (mtt90) REVERT: C 74 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7368 (mmtp) REVERT: F 84 MET cc_start: 0.8580 (tpp) cc_final: 0.8252 (tpp) REVERT: F 93 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: G 24 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7397 (mm-40) REVERT: G 32 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7351 (mtm110) REVERT: G 77 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7924 (ttm170) REVERT: H 92 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6390 (mtp85) REVERT: H 93 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7604 (mp0) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 0.6801 time to fit residues: 82.1255 Evaluate side-chains 121 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 59 GLU 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 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: 0.1980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 7 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.187715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123051 restraints weight = 11714.224| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.57 r_work: 0.3294 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1027 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= 0.127 Angle : 0.538 5.128 15409 Z= 0.328 Chirality : 0.041 0.211 1752 Planarity : 0.004 0.040 1256 Dihedral : 29.961 174.486 3047 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.32 % Allowed : 21.96 % Favored : 74.72 % 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: 2.88 (0.30), residues: 745 helix: 2.82 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.00191 / 0.13 (10784) covalent geometry : angle 0.53825 / 0.33 (15409) hydrogen bonds : bond 0.04410 / 5.00 ( 669) hydrogen bonds : angle 2.94261 / 3.97 ( 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 125 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: C 32 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8244 (ttp80) REVERT: C 35 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6193 (mtt90) REVERT: C 74 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7379 (mmtp) REVERT: F 84 MET cc_start: 0.8564 (tpp) cc_final: 0.8306 (tpp) REVERT: F 93 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: G 19 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7925 (p) REVERT: G 24 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7343 (mm-40) REVERT: H 68 ASP cc_start: 0.8564 (t70) cc_final: 0.8341 (t0) REVERT: H 93 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7600 (mp0) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 0.6982 time to fit residues: 86.7929 Evaluate side-chains 118 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 C residue 35 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 59 GLU 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 G residue 100 VAL Chi-restraints excluded: chain H residue 93 GLU 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: 1.9990 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 0.0030 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN G 89 ASN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122157 restraints weight = 11584.687| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.55 r_work: 0.3283 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1051 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= 0.164 Angle : 0.553 6.012 15409 Z= 0.332 Chirality : 0.042 0.222 1752 Planarity : 0.004 0.039 1256 Dihedral : 29.974 174.168 3047 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.32 % Allowed : 21.64 % 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: 2.78 (0.30), residues: 745 helix: 2.74 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 88 TYR 0.011 0.001 TYR G 57 PHE 0.010 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (10784) covalent geometry : angle 0.55343 / 0.33 (15409) hydrogen bonds : bond 0.04634 / 5.24 ( 669) hydrogen bonds : angle 2.95657 / 3.99 ( 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 121 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: C 32 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8254 (ttp80) REVERT: C 35 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6225 (mtt90) REVERT: C 74 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7363 (mmtp) REVERT: D 83 TYR cc_start: 0.7680 (m-10) cc_final: 0.7398 (t80) REVERT: F 31 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8106 (tttt) REVERT: F 84 MET cc_start: 0.8587 (tpp) cc_final: 0.8321 (tpp) REVERT: F 93 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7249 (mp10) REVERT: G 19 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7918 (p) REVERT: G 24 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7322 (mm-40) REVERT: G 32 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7419 (mtm110) REVERT: G 77 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: H 93 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7640 (mp0) outliers start: 21 outliers final: 10 residues processed: 112 average time/residue: 0.7376 time to fit residues: 86.7483 Evaluate side-chains 118 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 77 LYS 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 59 GLU 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 77 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL 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: 3.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.186975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122362 restraints weight = 11596.683| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.55 r_work: 0.3285 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1060 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= 0.144 Angle : 0.545 5.855 15409 Z= 0.329 Chirality : 0.041 0.215 1752 Planarity : 0.004 0.035 1256 Dihedral : 29.975 174.128 3046 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.16 % Allowed : 22.12 % Favored : 74.72 % 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: 2.76 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.010 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (10784) covalent geometry : angle 0.54549 / 0.33 (15409) hydrogen bonds : bond 0.04542 / 5.14 ( 669) hydrogen bonds : angle 2.95097 / 3.99 ( 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 121 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: C 32 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8255 (ttp80) REVERT: C 35 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6218 (mtt90) REVERT: C 74 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7364 (mmtp) REVERT: D 83 TYR cc_start: 0.7669 (m-10) cc_final: 0.7392 (t80) REVERT: F 31 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8099 (tttt) REVERT: F 84 MET cc_start: 0.8585 (tpp) cc_final: 0.8324 (tpp) REVERT: F 93 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: G 19 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7939 (p) REVERT: G 24 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: G 32 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7397 (mtm110) REVERT: G 77 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: H 93 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7632 (mp0) outliers start: 20 outliers final: 10 residues processed: 113 average time/residue: 0.7545 time to fit residues: 89.6952 Evaluate side-chains 119 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 59 GLU Chi-restraints excluded: chain E residue 80 THR 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 77 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 60 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.187229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122583 restraints weight = 11543.398| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.55 r_work: 0.3292 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10784 Z= 0.134 Angle : 0.541 5.319 15409 Z= 0.328 Chirality : 0.041 0.220 1752 Planarity : 0.004 0.036 1256 Dihedral : 29.977 174.223 3046 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 2.86 (0.30), residues: 745 helix: 2.81 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.011 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 0.00223 / 0.13 (10784) covalent geometry : angle 0.54095 / 0.33 (15409) hydrogen bonds : bond 0.04474 / 5.07 ( 669) hydrogen bonds : angle 2.93266 / 3.96 ( 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 121 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: C 32 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8252 (ttp80) REVERT: C 35 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6214 (mtt90) REVERT: C 74 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7363 (mmtp) REVERT: D 83 TYR cc_start: 0.7655 (m-10) cc_final: 0.7384 (t80) REVERT: F 31 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8087 (tttt) REVERT: F 84 MET cc_start: 0.8587 (tpp) cc_final: 0.8325 (tpp) REVERT: F 93 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: G 19 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7932 (p) REVERT: G 24 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7309 (mm-40) REVERT: G 32 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7403 (mtm110) REVERT: H 93 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7623 (mp0) outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 0.6928 time to fit residues: 83.7833 Evaluate side-chains 117 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 C residue 35 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain E residue 59 GLU 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 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 93 GLU 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 29 optimal weight: 0.0470 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.186199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121212 restraints weight = 11466.519| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.59 r_work: 0.3271 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1101 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= 0.174 Angle : 0.563 5.298 15409 Z= 0.335 Chirality : 0.042 0.218 1752 Planarity : 0.004 0.044 1256 Dihedral : 30.019 174.200 3046 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.00 % Allowed : 21.96 % 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: 2.68 (0.30), residues: 745 helix: 2.67 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.93 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.012 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 0.00358 / 0.17 (10784) covalent geometry : angle 0.56285 / 0.33 (15409) hydrogen bonds : bond 0.04717 / 5.32 ( 669) hydrogen bonds : angle 2.98517 / 4.03 ( 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 118 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: C 32 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8241 (ttp80) REVERT: C 35 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6198 (mtt90) REVERT: C 74 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7348 (mmtp) REVERT: D 83 TYR cc_start: 0.7720 (m-10) cc_final: 0.7395 (t80) REVERT: F 84 MET cc_start: 0.8588 (tpp) cc_final: 0.8243 (tpp) REVERT: F 93 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: G 19 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7933 (p) REVERT: G 24 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7300 (mm-40) REVERT: G 73 ASN cc_start: 0.7407 (t0) cc_final: 0.6819 (t0) REVERT: H 93 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7624 (mp0) outliers start: 19 outliers final: 8 residues processed: 111 average time/residue: 0.7381 time to fit residues: 86.0691 Evaluate side-chains 112 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 C residue 35 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain E residue 59 GLU 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 93 GLU 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: 0.0970 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 50.0000 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 31 optimal weight: 7.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.186561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121953 restraints weight = 11578.174| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.56 r_work: 0.3275 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10784 Z= 0.154 Angle : 0.557 5.250 15409 Z= 0.332 Chirality : 0.041 0.216 1752 Planarity : 0.004 0.041 1256 Dihedral : 30.020 174.183 3046 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.69 % Allowed : 21.80 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.30), residues: 745 helix: 2.69 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.93 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 32 TYR 0.010 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 0.00291 / 0.15 (10784) covalent geometry : angle 0.55655 / 0.33 (15409) hydrogen bonds : bond 0.04611 / 5.21 ( 669) hydrogen bonds : angle 2.96635 / 4.00 ( 1727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.16 seconds wall clock time: 56 minutes 12.20 seconds (3372.20 seconds total)