Starting phenix.real_space_refine on Fri Jul 3 04:20:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f10_50120/07_2026/9f10_50120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f10_50120/07_2026/9f10_50120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2026/9f10_50120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2026/9f10_50120.map" model { file = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2026/9f10_50120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2026/9f10_50120.cif" } resolution = 2.94 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= 0.001 sd= 0.056 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: 6 Type Number sf(0) Gaussians P 181 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 7123 2.51 5 N 2238 2.21 5 O 2708 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: 12286 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1982 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1739 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 749 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "E" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 906 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 972 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 867 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4306 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.06, per 1000 atoms: 0.25 Number of scatterers: 12286 At special positions: 0 Unit cell: (93.225, 131.175, 182.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 181 15.00 Mg 1 11.99 O 2708 8.00 N 2238 7.00 C 7123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 551.3 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 46.1% alpha, 17.1% beta 71 base pairs and 160 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.577A pdb=" N PHE C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 18 through 39 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'E' and resid 20 through 34 Processing helix chain 'E' and resid 36 through 52 Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'F' and resid 20 through 34 removed outlier: 4.138A pdb=" N SER F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 Processing helix chain 'F' and resid 75 through 90 Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.067A pdb=" N SER G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 removed outlier: 3.801A pdb=" N HIS G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 92 through 108 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.598A pdb=" N THR H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 102 through 118 Processing helix chain 'H' and resid 184 through 192 Processing helix chain 'H' and resid 192 through 210 Processing helix chain 'H' and resid 219 through 222 removed outlier: 3.618A pdb=" N GLY H 222 " --> pdb=" O GLY H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 222' Processing helix chain 'H' and resid 231 through 234 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 250 through 262 Processing helix chain 'H' and resid 269 through 285 removed outlier: 3.669A pdb=" N LYS H 273 " --> pdb=" O ASP H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 302 removed outlier: 3.609A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP H 300 " --> pdb=" O ASP H 296 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU H 301 " --> pdb=" O GLN H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 576 through 594 Processing helix chain 'H' and resid 603 through 622 Processing helix chain 'H' and resid 642 through 650 removed outlier: 3.815A pdb=" N TYR H 645 " --> pdb=" O ARG H 642 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG H 647 " --> pdb=" O ARG H 644 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP H 648 " --> pdb=" O TYR H 645 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET H 649 " --> pdb=" O LEU H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 696 through 698 No H-bonds generated for 'chain 'H' and resid 696 through 698' Processing helix chain 'H' and resid 793 through 797 removed outlier: 4.033A pdb=" N MET H 797 " --> pdb=" O GLN H 794 " (cutoff:3.500A) Processing helix chain 'H' and resid 798 through 808 removed outlier: 3.509A pdb=" N SER H 808 " --> pdb=" O GLY H 804 " (cutoff:3.500A) Processing helix chain 'H' and resid 822 through 827 removed outlier: 3.771A pdb=" N LYS H 826 " --> pdb=" O ARG H 822 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 19 Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 19 Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 19 Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 7 removed outlier: 4.347A pdb=" N GLY H 79 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN H 155 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL H 140 " --> pdb=" O ALA H 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'H' and resid 122 through 123 Processing sheet with id=AB2, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB3, first strand: chain 'H' and resid 568 through 572 removed outlier: 6.678A pdb=" N VAL H 788 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR H 815 " --> pdb=" O VAL H 788 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA H 790 " --> pdb=" O TYR H 815 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 628 through 636 removed outlier: 6.501A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 756 through 759 removed outlier: 6.403A pdb=" N VAL H 748 " --> pdb=" O VAL H 737 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL H 737 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 161 hydrogen bonds 318 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 160 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.39 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: 2661 1.33 - 1.45: 3493 1.45 - 1.57: 6299 1.57 - 1.69: 360 1.69 - 1.81: 67 Bond restraints: 12880 Sorted by residual: bond pdb=" C3' DT B 63 " pdb=" O3' DT B 63 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C3' DA A 32 " pdb=" C2' DA A 32 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA A 80 " pdb=" O3' DA A 80 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.12e+01 bond pdb=" C3' DC B 75 " pdb=" C2' DC B 75 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT A 64 " pdb=" O3' DT A 64 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.63e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 17022 1.55 - 3.11: 1059 3.11 - 4.66: 62 4.66 - 6.22: 16 6.22 - 7.77: 5 Bond angle restraints: 18164 Sorted by residual: angle pdb=" O4' DT A 46 " pdb=" C4' DT A 46 " pdb=" C3' DT A 46 " ideal model delta sigma weight residual 106.00 102.24 3.76 6.00e-01 2.78e+00 3.93e+01 angle pdb=" N3 DT B 87 " pdb=" C4 DT B 87 " pdb=" O4 DT B 87 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT A 88 " pdb=" C4 DT A 88 " pdb=" O4 DT A 88 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT B 21 " pdb=" C4 DT B 21 " pdb=" O4 DT B 21 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT B 76 " pdb=" C4 DT B 76 " pdb=" O4 DT B 76 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 18159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 6604 35.83 - 71.66: 793 71.66 - 107.49: 5 107.49 - 143.32: 2 143.32 - 179.15: 5 Dihedral angle restraints: 7409 sinusoidal: 4261 harmonic: 3148 Sorted by residual: dihedral pdb=" CA VAL H 229 " pdb=" C VAL H 229 " pdb=" N PRO H 230 " pdb=" CA PRO H 230 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA MET H 29 " pdb=" C MET H 29 " pdb=" N GLY H 30 " pdb=" CA GLY H 30 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PHE E 4 " pdb=" C PHE E 4 " pdb=" N GLY E 5 " pdb=" CA GLY E 5 " ideal model delta harmonic sigma weight residual 180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1971 0.115 - 0.231: 38 0.231 - 0.346: 0 0.346 - 0.462: 3 0.462 - 0.577: 4 Chirality restraints: 2016 Sorted by residual: chirality pdb=" P DG A 9 " pdb=" OP1 DG A 9 " pdb=" OP2 DG A 9 " pdb=" O5' DG A 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" P DT B 82 " pdb=" OP1 DT B 82 " pdb=" OP2 DT B 82 " pdb=" O5' DT B 82 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" P DT A 8 " pdb=" OP1 DT A 8 " pdb=" OP2 DT A 8 " pdb=" O5' DT A 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.50 2.00e-01 2.50e+01 6.14e+00 ... (remaining 2013 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 60 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO C 61 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 60 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO H 61 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 60 " -0.024 2.00e-02 2.50e+03 1.14e-02 3.27e+00 pdb=" N1 DT A 60 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT A 60 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT A 60 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT A 60 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT A 60 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT A 60 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DT A 60 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT A 60 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT A 60 " 0.005 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 43 2.47 - 3.07: 7888 3.07 - 3.68: 19407 3.68 - 4.29: 30240 4.29 - 4.90: 45459 Nonbonded interactions: 103037 Sorted by model distance: nonbonded pdb=" OP1 DG A -1 " pdb="MG MG H1801 " model vdw 1.857 2.170 nonbonded pdb=" O3' DT A 1 " pdb="MG MG H1801 " model vdw 1.997 2.170 nonbonded pdb=" NE2 HIS H 157 " pdb="MG MG H1801 " model vdw 2.047 2.250 nonbonded pdb=" OG SER H 122 " pdb=" OG SER H 176 " model vdw 2.101 3.040 nonbonded pdb=" OD1 ASP G 75 " pdb=" OG1 THR G 78 " model vdw 2.220 3.040 ... (remaining 103032 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 'E' and (resid 11 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 60 or (resid 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 or (resid 64 through 66 and ( \ name N or name CA or name C or name O or name CB )) or resid 67 through 113)) selection = (chain 'F' and (resid 11 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or (resid 62 and (name N or name CA or name C or name \ O or name CB )) or resid 63 or (resid 64 through 66 and (name N or name CA or na \ me C or name O or name CB )) or resid 67 through 113)) selection = (chain 'G' and (resid 11 through 60 or resid 62 through 113)) } 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: 20.070 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 0.045 12880 Z= 0.524 Angle : 0.749 7.771 18164 Z= 0.617 Chirality : 0.054 0.577 2016 Planarity : 0.004 0.048 1716 Dihedral : 22.948 179.153 5371 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.11 % Allowed : 1.66 % Favored : 98.23 % 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: 0.73 (0.25), residues: 1074 helix: 1.57 (0.23), residues: 464 sheet: 1.08 (0.38), residues: 166 loop : -0.93 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 44 TYR 0.012 0.002 TYR H 669 PHE 0.013 0.002 PHE F 108 TRP 0.007 0.001 TRP H 702 HIS 0.004 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.52 (12880) covalent geometry : angle 0.74888 / 0.62 (18164) hydrogen bonds : bond 0.12728 / 14.27 ( 608) hydrogen bonds : angle 6.47464 / 8.19 ( 1605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.339 Fit side-chains REVERT: C 11 TYR cc_start: 0.8973 (t80) cc_final: 0.8465 (t80) REVERT: C 24 LYS cc_start: 0.9110 (ttmm) cc_final: 0.8878 (ttmp) REVERT: C 40 ASN cc_start: 0.8612 (m-40) cc_final: 0.8408 (m-40) REVERT: C 42 GLU cc_start: 0.8368 (tt0) cc_final: 0.7908 (mt-10) REVERT: C 93 ASN cc_start: 0.8012 (m-40) cc_final: 0.7210 (p0) REVERT: E 1 MET cc_start: 0.6187 (mtm) cc_final: 0.5325 (mmp) REVERT: E 3 ARG cc_start: 0.7643 (tpt170) cc_final: 0.6785 (ttp80) REVERT: H 29 MET cc_start: 0.4956 (ptp) cc_final: 0.4246 (tpt) REVERT: H 198 ARG cc_start: 0.7365 (ttp-170) cc_final: 0.7051 (mtp85) REVERT: H 741 SER cc_start: 0.8215 (t) cc_final: 0.7978 (p) outliers start: 1 outliers final: 1 residues processed: 253 average time/residue: 0.6597 time to fit residues: 178.6811 Evaluate side-chains 141 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 60 ASN H 108 GLN H 116 GLN H 780 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.151012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.123265 restraints weight = 14344.834| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.19 r_work: 0.3430 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12880 Z= 0.181 Angle : 0.671 7.604 18164 Z= 0.389 Chirality : 0.046 0.346 2016 Planarity : 0.005 0.052 1716 Dihedral : 27.557 178.991 3278 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.75 % Allowed : 14.24 % Favored : 82.01 % 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: 0.99 (0.26), residues: 1074 helix: 1.98 (0.23), residues: 463 sheet: 0.89 (0.37), residues: 186 loop : -0.97 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 32 TYR 0.015 0.002 TYR F 52 PHE 0.021 0.002 PHE H 16 TRP 0.012 0.002 TRP H 33 HIS 0.011 0.001 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (12880) covalent geometry : angle 0.67137 / 0.39 (18164) hydrogen bonds : bond 0.04750 / 5.35 ( 608) hydrogen bonds : angle 4.92458 / 6.49 ( 1605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.304 Fit side-chains REVERT: C 11 TYR cc_start: 0.8826 (t80) cc_final: 0.8472 (t80) REVERT: C 40 ASN cc_start: 0.8432 (m-40) cc_final: 0.8166 (m-40) REVERT: C 93 ASN cc_start: 0.7910 (m-40) cc_final: 0.7275 (p0) REVERT: D 68 ASP cc_start: 0.7805 (m-30) cc_final: 0.7550 (t70) REVERT: E 1 MET cc_start: 0.6276 (mtm) cc_final: 0.5933 (mmp) REVERT: E 3 ARG cc_start: 0.7379 (tpt170) cc_final: 0.7008 (ttp80) REVERT: E 66 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7633 (tm) REVERT: G 14 VAL cc_start: 0.6819 (t) cc_final: 0.6553 (m) REVERT: H 29 MET cc_start: 0.4701 (ptp) cc_final: 0.4152 (tpt) REVERT: H 198 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.7049 (mtp85) outliers start: 34 outliers final: 9 residues processed: 172 average time/residue: 0.6119 time to fit residues: 113.2984 Evaluate side-chains 143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3674 r_free = 0.3674 target = 0.122173 restraints weight = 14434.139| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.31 r_work: 0.3421 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12880 Z= 0.163 Angle : 0.638 9.626 18164 Z= 0.368 Chirality : 0.043 0.338 2016 Planarity : 0.004 0.052 1716 Dihedral : 27.676 178.457 3276 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.08 % Allowed : 15.23 % Favored : 80.68 % 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: 1.02 (0.26), residues: 1074 helix: 2.09 (0.23), residues: 460 sheet: 0.54 (0.36), residues: 197 loop : -0.89 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 73 TYR 0.016 0.001 TYR F 52 PHE 0.024 0.002 PHE H 16 TRP 0.014 0.001 TRP H 33 HIS 0.010 0.001 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (12880) covalent geometry : angle 0.63777 / 0.37 (18164) hydrogen bonds : bond 0.04210 / 4.69 ( 608) hydrogen bonds : angle 4.56581 / 6.12 ( 1605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.297 Fit side-chains REVERT: C 11 TYR cc_start: 0.8821 (t80) cc_final: 0.8417 (t80) REVERT: C 42 GLU cc_start: 0.7922 (tt0) cc_final: 0.7642 (mt-10) REVERT: D 68 ASP cc_start: 0.7742 (m-30) cc_final: 0.7535 (t70) REVERT: E 1 MET cc_start: 0.6308 (mtm) cc_final: 0.5969 (mmp) REVERT: E 106 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8318 (mp) REVERT: F 40 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: F 72 MET cc_start: 0.8471 (ttm) cc_final: 0.8250 (ttm) REVERT: G 14 VAL cc_start: 0.6953 (t) cc_final: 0.6704 (m) REVERT: H 29 MET cc_start: 0.4807 (ptp) cc_final: 0.4131 (tpt) REVERT: H 182 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8070 (mppt) REVERT: H 198 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.7112 (mtm110) outliers start: 37 outliers final: 18 residues processed: 167 average time/residue: 0.5670 time to fit residues: 101.9723 Evaluate side-chains 149 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 182 LYS Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN H 660 ASN H 780 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.148462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120862 restraints weight = 14458.614| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.23 r_work: 0.3382 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12880 Z= 0.206 Angle : 0.683 9.925 18164 Z= 0.387 Chirality : 0.046 0.359 2016 Planarity : 0.005 0.054 1716 Dihedral : 27.844 175.447 3276 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.19 % Allowed : 15.23 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1074 helix: 2.00 (0.23), residues: 460 sheet: 0.42 (0.35), residues: 212 loop : -1.07 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 3 TYR 0.015 0.002 TYR G 52 PHE 0.029 0.002 PHE H 16 TRP 0.014 0.002 TRP H 33 HIS 0.010 0.001 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.21 (12880) covalent geometry : angle 0.68350 / 0.39 (18164) hydrogen bonds : bond 0.04843 / 5.31 ( 608) hydrogen bonds : angle 4.55837 / 6.12 ( 1605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.406 Fit side-chains REVERT: E 1 MET cc_start: 0.6411 (mtm) cc_final: 0.6085 (mmp) REVERT: E 106 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8439 (mp) REVERT: F 40 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: G 14 VAL cc_start: 0.7135 (t) cc_final: 0.6849 (m) REVERT: H 709 LYS cc_start: 0.8787 (mppt) cc_final: 0.8519 (mttt) outliers start: 47 outliers final: 20 residues processed: 166 average time/residue: 0.5234 time to fit residues: 94.0638 Evaluate side-chains 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128448 restraints weight = 14603.022| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 0.74 r_work: 0.3436 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12880 Z= 0.186 Angle : 0.664 10.004 18164 Z= 0.376 Chirality : 0.044 0.342 2016 Planarity : 0.005 0.052 1716 Dihedral : 27.895 176.441 3276 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.97 % Allowed : 16.23 % Favored : 78.81 % 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: 0.83 (0.25), residues: 1074 helix: 2.01 (0.23), residues: 461 sheet: 0.42 (0.35), residues: 212 loop : -1.13 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 77 TYR 0.018 0.002 TYR G 52 PHE 0.021 0.002 PHE H 16 TRP 0.022 0.002 TRP H 33 HIS 0.003 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (12880) covalent geometry : angle 0.66385 / 0.38 (18164) hydrogen bonds : bond 0.04274 / 4.71 ( 608) hydrogen bonds : angle 4.46999 / 6.04 ( 1605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.361 Fit side-chains REVERT: C 15 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8529 (mtpm) REVERT: C 36 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7984 (mtt90) REVERT: E 1 MET cc_start: 0.6307 (mtm) cc_final: 0.6007 (mmp) REVERT: G 14 VAL cc_start: 0.7138 (t) cc_final: 0.6848 (m) REVERT: G 73 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6047 (ttm170) REVERT: H 709 LYS cc_start: 0.8751 (mppt) cc_final: 0.8495 (mttt) outliers start: 45 outliers final: 23 residues processed: 165 average time/residue: 0.5515 time to fit residues: 98.6511 Evaluate side-chains 154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0030 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN G 50 HIS H 780 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126817 restraints weight = 14559.946| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 0.82 r_work: 0.3417 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12880 Z= 0.240 Angle : 0.723 10.942 18164 Z= 0.403 Chirality : 0.047 0.365 2016 Planarity : 0.005 0.055 1716 Dihedral : 27.951 174.654 3276 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.96 % Allowed : 16.78 % Favored : 77.26 % 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: 0.62 (0.25), residues: 1074 helix: 1.88 (0.23), residues: 459 sheet: 0.24 (0.34), residues: 213 loop : -1.25 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 46 TYR 0.014 0.002 TYR H 645 PHE 0.031 0.002 PHE H 16 TRP 0.019 0.002 TRP H 33 HIS 0.009 0.001 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (12880) covalent geometry : angle 0.72257 / 0.40 (18164) hydrogen bonds : bond 0.05164 / 5.64 ( 608) hydrogen bonds : angle 4.57913 / 6.14 ( 1605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 0.440 Fit side-chains REVERT: C 36 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7946 (mtt90) REVERT: E 1 MET cc_start: 0.6273 (mtm) cc_final: 0.5984 (mmp) REVERT: E 106 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8495 (mp) REVERT: F 40 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: G 14 VAL cc_start: 0.7113 (t) cc_final: 0.6839 (m) REVERT: H 75 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7693 (mmm160) REVERT: H 252 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7142 (mmtp) REVERT: H 263 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5684 (mtmt) REVERT: H 709 LYS cc_start: 0.8831 (mppt) cc_final: 0.8537 (mttt) outliers start: 54 outliers final: 26 residues processed: 167 average time/residue: 0.5107 time to fit residues: 92.6417 Evaluate side-chains 158 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.148474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.128235 restraints weight = 14451.032| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 0.71 r_work: 0.3440 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12880 Z= 0.173 Angle : 0.672 13.205 18164 Z= 0.377 Chirality : 0.044 0.335 2016 Planarity : 0.005 0.053 1716 Dihedral : 27.948 176.161 3276 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.42 % Allowed : 18.21 % Favored : 77.37 % 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: 0.67 (0.25), residues: 1074 helix: 1.96 (0.23), residues: 461 sheet: 0.19 (0.34), residues: 215 loop : -1.25 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.012 0.001 TYR C 11 PHE 0.024 0.002 PHE H 16 TRP 0.021 0.002 TRP H 33 HIS 0.003 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (12880) covalent geometry : angle 0.67222 / 0.38 (18164) hydrogen bonds : bond 0.04174 / 4.61 ( 608) hydrogen bonds : angle 4.45070 / 6.02 ( 1605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.383 Fit side-chains REVERT: C 36 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7883 (mtt90) REVERT: E 1 MET cc_start: 0.6164 (mtm) cc_final: 0.5899 (mmp) REVERT: E 106 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8465 (mp) REVERT: G 14 VAL cc_start: 0.7129 (t) cc_final: 0.6847 (m) REVERT: G 31 ASN cc_start: 0.8045 (t0) cc_final: 0.7478 (m110) REVERT: G 73 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6073 (ttm170) REVERT: H 75 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7641 (mmm160) REVERT: H 198 ARG cc_start: 0.7424 (ttp-170) cc_final: 0.6980 (ptm160) REVERT: H 263 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5631 (mtmt) outliers start: 40 outliers final: 26 residues processed: 162 average time/residue: 0.5055 time to fit residues: 88.6918 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN H 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.148845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128674 restraints weight = 14486.338| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 0.70 r_work: 0.3444 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12880 Z= 0.168 Angle : 0.667 15.184 18164 Z= 0.372 Chirality : 0.044 0.332 2016 Planarity : 0.004 0.052 1716 Dihedral : 27.916 175.917 3276 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.42 % Allowed : 18.65 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1074 helix: 2.02 (0.23), residues: 461 sheet: 0.28 (0.34), residues: 209 loop : -1.26 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 101 TYR 0.019 0.001 TYR D 93 PHE 0.026 0.002 PHE H 16 TRP 0.018 0.002 TRP H 33 HIS 0.009 0.001 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (12880) covalent geometry : angle 0.66691 / 0.37 (18164) hydrogen bonds : bond 0.04059 / 4.51 ( 608) hydrogen bonds : angle 4.39808 / 5.96 ( 1605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.273 Fit side-chains REVERT: C 15 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8483 (mtpm) REVERT: C 36 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7872 (mtt90) REVERT: E 1 MET cc_start: 0.6123 (mtm) cc_final: 0.5845 (mmp) REVERT: E 106 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8445 (mp) REVERT: F 40 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: G 14 VAL cc_start: 0.7061 (t) cc_final: 0.6828 (m) REVERT: G 73 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6040 (ttm170) REVERT: H 198 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.6991 (ptm160) REVERT: H 263 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5640 (mtmt) outliers start: 40 outliers final: 23 residues processed: 159 average time/residue: 0.5641 time to fit residues: 96.8163 Evaluate side-chains 151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.148474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128372 restraints weight = 14442.095| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 0.72 r_work: 0.3439 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12880 Z= 0.178 Angle : 0.671 14.846 18164 Z= 0.374 Chirality : 0.044 0.337 2016 Planarity : 0.005 0.053 1716 Dihedral : 27.905 175.550 3276 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.53 % Allowed : 19.98 % Favored : 76.49 % 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: 0.74 (0.25), residues: 1074 helix: 2.02 (0.23), residues: 461 sheet: 0.31 (0.34), residues: 209 loop : -1.24 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.013 0.001 TYR G 52 PHE 0.025 0.002 PHE H 16 TRP 0.017 0.002 TRP H 33 HIS 0.003 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (12880) covalent geometry : angle 0.67130 / 0.37 (18164) hydrogen bonds : bond 0.04167 / 4.62 ( 608) hydrogen bonds : angle 4.41370 / 5.98 ( 1605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8472 (mtpm) REVERT: C 36 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7871 (mtt90) REVERT: E 1 MET cc_start: 0.6155 (mtm) cc_final: 0.5863 (mmp) REVERT: E 106 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8487 (mp) REVERT: F 40 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: G 14 VAL cc_start: 0.7081 (t) cc_final: 0.6848 (m) REVERT: G 73 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6041 (ttm170) REVERT: H 152 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7180 (mm-40) REVERT: H 198 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.7013 (ptm160) REVERT: H 263 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5636 (mtmt) outliers start: 32 outliers final: 22 residues processed: 155 average time/residue: 0.5572 time to fit residues: 93.4261 Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.0270 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.149115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128517 restraints weight = 14507.728| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 0.69 r_work: 0.3458 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12880 Z= 0.151 Angle : 0.663 16.298 18164 Z= 0.369 Chirality : 0.043 0.322 2016 Planarity : 0.004 0.053 1716 Dihedral : 27.912 176.299 3276 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.42 % Allowed : 20.20 % Favored : 76.38 % 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: 0.79 (0.25), residues: 1074 helix: 2.05 (0.23), residues: 461 sheet: 0.34 (0.34), residues: 209 loop : -1.22 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 642 TYR 0.024 0.001 TYR D 93 PHE 0.027 0.002 PHE H 16 TRP 0.016 0.002 TRP H 33 HIS 0.003 0.001 HIS H 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12880) covalent geometry : angle 0.66283 / 0.37 (18164) hydrogen bonds : bond 0.03915 / 4.37 ( 608) hydrogen bonds : angle 4.38349 / 5.96 ( 1605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8445 (mtpm) REVERT: C 36 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7837 (mtt90) REVERT: E 1 MET cc_start: 0.6107 (mtm) cc_final: 0.5819 (mmp) REVERT: F 40 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: G 14 VAL cc_start: 0.7091 (t) cc_final: 0.6775 (m) REVERT: G 73 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6013 (ttm170) REVERT: H 152 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7222 (mm-40) REVERT: H 198 ARG cc_start: 0.7505 (ttp-170) cc_final: 0.7026 (ptm160) REVERT: H 263 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5641 (mtmt) outliers start: 31 outliers final: 20 residues processed: 152 average time/residue: 0.5234 time to fit residues: 86.0518 Evaluate side-chains 148 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.149249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121718 restraints weight = 14374.348| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.19 r_work: 0.3405 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12880 Z= 0.158 Angle : 0.661 15.003 18164 Z= 0.368 Chirality : 0.043 0.326 2016 Planarity : 0.004 0.053 1716 Dihedral : 27.922 175.954 3276 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.87 % Allowed : 20.64 % Favored : 76.49 % 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: 0.75 (0.25), residues: 1074 helix: 2.06 (0.23), residues: 461 sheet: 0.32 (0.34), residues: 213 loop : -1.31 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.019 0.001 TYR D 93 PHE 0.027 0.002 PHE H 16 TRP 0.017 0.001 TRP H 33 HIS 0.002 0.001 HIS H 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12880) covalent geometry : angle 0.66063 / 0.37 (18164) hydrogen bonds : bond 0.03911 / 4.38 ( 608) hydrogen bonds : angle 4.36021 / 5.93 ( 1605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4511.31 seconds wall clock time: 77 minutes 21.09 seconds (4641.09 seconds total)