Starting phenix.real_space_refine on Sat Aug 23 12:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f10_50120/08_2025/9f10_50120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f10_50120/08_2025/9f10_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_50120/08_2025/9f10_50120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f10_50120/08_2025/9f10_50120.map" model { file = "/net/cci-nas-00/data/ceres_data/9f10_50120/08_2025/9f10_50120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f10_50120/08_2025/9f10_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-2.0-5787/lib/python3.9/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: 3.09, 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: 1.07 Conformation dependent library (CDL) restraints added in 492.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.82 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: 2.72 Time building geometry restraints manager: 1.42 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=" CA ILE C 71 " pdb=" C ILE C 71 " ideal model delta sigma weight residual 1.524 1.505 0.019 8.30e-03 1.45e+04 5.24e+00 bond pdb=" CA ILE H 724 " pdb=" C ILE H 724 " ideal model delta sigma weight residual 1.526 1.510 0.016 7.90e-03 1.60e+04 4.31e+00 bond pdb=" P DG A 9 " pdb=" OP2 DG A 9 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" P DG A 9 " pdb=" OP1 DG A 9 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" P DT B 82 " pdb=" OP1 DT B 82 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 17479 1.55 - 3.11: 611 3.11 - 4.66: 53 4.66 - 6.22: 16 6.22 - 7.77: 5 Bond angle restraints: 18164 Sorted by residual: angle pdb=" O3' DT A 64 " pdb=" P DA A 63 " pdb=" O5' DA A 63 " ideal model delta sigma weight residual 104.00 97.91 6.09 1.50e+00 4.44e-01 1.65e+01 angle pdb=" N LEU H 802 " pdb=" CA LEU H 802 " pdb=" C LEU H 802 " ideal model delta sigma weight residual 111.36 107.08 4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" N GLY H 30 " pdb=" CA GLY H 30 " pdb=" C GLY H 30 " ideal model delta sigma weight residual 113.18 120.95 -7.77 2.37e+00 1.78e-01 1.08e+01 angle pdb=" O3' DA B 83 " pdb=" P DT B 84 " pdb=" O5' DT B 84 " ideal model delta sigma weight residual 104.00 99.59 4.41 1.50e+00 4.44e-01 8.64e+00 angle pdb=" C3' DT A 64 " pdb=" O3' DT A 64 " pdb=" P DA A 63 " ideal model delta sigma weight residual 120.20 124.54 -4.34 1.50e+00 4.44e-01 8.36e+00 ... (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 - 0.113: 1989 0.113 - 0.227: 20 0.227 - 0.340: 0 0.340 - 0.454: 3 0.454 - 0.567: 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 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.03e+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 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.17e+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 2.35 -2.83 -0.49 2.00e-01 2.50e+01 5.89e+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: 15.770 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.440 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.005 0.045 12880 Z= 0.244 Angle : 0.645 7.771 18164 Z= 0.375 Chirality : 0.048 0.567 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 aren 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 covalent geometry : bond 0.00530 (12880) covalent geometry : angle 0.64520 (18164) hydrogen bonds : bond 0.12728 ( 608) hydrogen bonds : angle 6.47464 ( 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 : 0.398 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: 0.7511 time to fit residues: 202.4250 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 : 0.371 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 0.0670 chunk 123 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 ASN H 108 GLN H 780 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.151168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.130010 restraints weight = 14442.384| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 0.72 r_work: 0.3484 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12880 Z= 0.179 Angle : 0.592 9.467 18164 Z= 0.343 Chirality : 0.037 0.159 2016 Planarity : 0.004 0.050 1716 Dihedral : 27.332 174.736 3278 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.42 % Allowed : 13.58 % 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 aren not related in a simple way. whole: 1.10 (0.26), residues: 1074 helix: 2.14 (0.23), residues: 460 sheet: 0.68 (0.36), residues: 197 loop : -0.88 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 566 TYR 0.014 0.001 TYR F 52 PHE 0.021 0.002 PHE H 16 TRP 0.012 0.001 TRP H 33 HIS 0.010 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00386 (12880) covalent geometry : angle 0.59166 (18164) hydrogen bonds : bond 0.04088 ( 608) hydrogen bonds : angle 4.61280 ( 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 200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.414 Fit side-chains REVERT: C 11 TYR cc_start: 0.8791 (t80) cc_final: 0.8411 (t80) REVERT: C 42 GLU cc_start: 0.7926 (tt0) cc_final: 0.7646 (mt-10) REVERT: D 69 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7022 (mptt) REVERT: E 1 MET cc_start: 0.6247 (mtm) cc_final: 0.5976 (mmp) REVERT: E 3 ARG cc_start: 0.7428 (tpt170) cc_final: 0.7051 (ttp80) REVERT: F 40 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: F 72 MET cc_start: 0.8363 (ttm) cc_final: 0.7903 (mtp) REVERT: G 14 VAL cc_start: 0.6937 (t) cc_final: 0.6617 (m) REVERT: G 73 ARG cc_start: 0.7389 (mtt90) cc_final: 0.7047 (mtm180) REVERT: H 29 MET cc_start: 0.4745 (ptp) cc_final: 0.4180 (tpt) REVERT: H 182 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8031 (mppt) REVERT: H 198 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6876 (ptm160) REVERT: H 292 ARG cc_start: 0.3674 (ptm-80) cc_final: 0.2524 (mtm180) outliers start: 40 outliers final: 13 residues processed: 181 average time/residue: 0.7203 time to fit residues: 139.4668 Evaluate side-chains 151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER 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 182 LYS Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 21 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.131683 restraints weight = 14597.530| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 0.69 r_work: 0.3453 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12880 Z= 0.159 Angle : 0.567 10.203 18164 Z= 0.327 Chirality : 0.036 0.158 2016 Planarity : 0.004 0.050 1716 Dihedral : 27.304 175.986 3276 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.75 % Allowed : 17.11 % Favored : 79.14 % 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 aren not related in a simple way. whole: 1.22 (0.26), residues: 1074 helix: 2.27 (0.23), residues: 462 sheet: 0.84 (0.38), residues: 191 loop : -0.90 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 822 TYR 0.014 0.001 TYR F 52 PHE 0.024 0.001 PHE H 16 TRP 0.010 0.001 TRP H 33 HIS 0.009 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00345 (12880) covalent geometry : angle 0.56675 (18164) hydrogen bonds : bond 0.03729 ( 608) hydrogen bonds : angle 4.30241 ( 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 178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.409 Fit side-chains REVERT: C 42 GLU cc_start: 0.7957 (tt0) cc_final: 0.7713 (mt-10) REVERT: C 82 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.8117 (tpp80) REVERT: E 1 MET cc_start: 0.6378 (mtm) cc_final: 0.6015 (mmp) REVERT: F 72 MET cc_start: 0.8332 (ttm) cc_final: 0.8095 (mtp) REVERT: G 14 VAL cc_start: 0.6978 (t) cc_final: 0.6694 (m) REVERT: G 35 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7729 (ptt180) REVERT: G 73 ARG cc_start: 0.7378 (mtt90) cc_final: 0.7071 (mtm180) REVERT: H 29 MET cc_start: 0.4799 (ptp) cc_final: 0.4000 (tmt) REVERT: H 198 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6828 (ptm160) REVERT: H 709 LYS cc_start: 0.8761 (mppt) cc_final: 0.8493 (mttt) outliers start: 34 outliers final: 13 residues processed: 163 average time/residue: 0.6831 time to fit residues: 119.6379 Evaluate side-chains 141 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 71 THR 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 110 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS 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 = 0.3946 r_free = 0.3946 target = 0.147002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120099 restraints weight = 14551.541| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.20 r_work: 0.3383 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12880 Z= 0.286 Angle : 0.665 11.409 18164 Z= 0.377 Chirality : 0.042 0.183 2016 Planarity : 0.005 0.053 1716 Dihedral : 27.614 177.835 3276 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.86 % Allowed : 17.00 % Favored : 78.15 % 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 aren not related in a simple way. whole: 0.92 (0.26), residues: 1074 helix: 2.10 (0.23), residues: 459 sheet: 0.45 (0.35), residues: 215 loop : -1.10 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 77 TYR 0.014 0.002 TYR H 645 PHE 0.022 0.002 PHE H 16 TRP 0.014 0.002 TRP H 224 HIS 0.009 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00640 (12880) covalent geometry : angle 0.66492 (18164) hydrogen bonds : bond 0.04977 ( 608) hydrogen bonds : angle 4.54270 ( 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 182 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.489 Fit side-chains REVERT: C 36 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7981 (mtt90) REVERT: E 1 MET cc_start: 0.6341 (mtm) cc_final: 0.6030 (mmp) REVERT: E 106 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8469 (mp) REVERT: G 14 VAL cc_start: 0.7142 (t) cc_final: 0.6861 (m) REVERT: H 263 LYS cc_start: 0.6278 (OUTLIER) cc_final: 0.5942 (mtmt) REVERT: H 709 LYS cc_start: 0.8830 (mppt) cc_final: 0.8565 (mttt) outliers start: 44 outliers final: 22 residues processed: 163 average time/residue: 0.7265 time to fit residues: 127.1122 Evaluate side-chains 150 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 21 ASP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS 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 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 110 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 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3972 r_free = 0.3972 target = 0.149176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.121104 restraints weight = 14611.810| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.26 r_work: 0.3406 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12880 Z= 0.189 Angle : 0.600 11.289 18164 Z= 0.343 Chirality : 0.037 0.150 2016 Planarity : 0.004 0.050 1716 Dihedral : 27.468 175.676 3276 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.30 % Allowed : 18.32 % 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 aren not related in a simple way. whole: 1.09 (0.26), residues: 1074 helix: 2.19 (0.24), residues: 461 sheet: 0.76 (0.38), residues: 184 loop : -0.97 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 73 TYR 0.014 0.001 TYR F 112 PHE 0.027 0.002 PHE H 16 TRP 0.010 0.001 TRP H 224 HIS 0.010 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00415 (12880) covalent geometry : angle 0.60026 (18164) hydrogen bonds : bond 0.03919 ( 608) hydrogen bonds : angle 4.32070 ( 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 175 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.524 Fit side-chains REVERT: C 15 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8579 (ttpt) REVERT: C 36 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7946 (mtt90) REVERT: C 42 GLU cc_start: 0.7996 (tt0) cc_final: 0.7754 (mt-10) REVERT: E 1 MET cc_start: 0.6333 (mtm) cc_final: 0.5969 (mmp) REVERT: E 106 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8499 (mp) REVERT: G 14 VAL cc_start: 0.7105 (t) cc_final: 0.6758 (m) REVERT: H 75 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7793 (mmm160) REVERT: H 709 LYS cc_start: 0.8778 (mppt) cc_final: 0.8519 (mttt) outliers start: 39 outliers final: 17 residues processed: 159 average time/residue: 0.7165 time to fit residues: 122.4977 Evaluate side-chains 146 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 106 ILE Chi-restraints excluded: chain F residue 17 LYS 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 71 THR Chi-restraints excluded: chain H residue 48 ASP 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 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0170 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119630 restraints weight = 14616.134| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.33 r_work: 0.3377 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12880 Z= 0.229 Angle : 0.637 11.415 18164 Z= 0.360 Chirality : 0.039 0.184 2016 Planarity : 0.005 0.054 1716 Dihedral : 27.523 176.476 3276 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.75 % Allowed : 18.87 % 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 aren not related in a simple way. whole: 0.93 (0.26), residues: 1074 helix: 2.11 (0.23), residues: 461 sheet: 0.50 (0.35), residues: 208 loop : -1.10 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 73 TYR 0.019 0.002 TYR G 52 PHE 0.024 0.002 PHE H 16 TRP 0.011 0.001 TRP H 224 HIS 0.003 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00508 (12880) covalent geometry : angle 0.63673 (18164) hydrogen bonds : bond 0.04318 ( 608) hydrogen bonds : angle 4.40952 ( 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 176 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.448 Fit side-chains REVERT: E 1 MET cc_start: 0.6446 (mtm) cc_final: 0.6016 (mmp) REVERT: E 106 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8493 (mp) REVERT: F 118 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.5560 (ptm-80) REVERT: G 14 VAL cc_start: 0.6997 (t) cc_final: 0.6753 (m) REVERT: H 152 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7193 (mm-40) outliers start: 43 outliers final: 22 residues processed: 163 average time/residue: 0.6871 time to fit residues: 120.6030 Evaluate side-chains 151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 17 LYS 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 F residue 118 ARG 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 72 MET 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 110 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 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3973 r_free = 0.3973 target = 0.148991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128763 restraints weight = 14556.564| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 0.77 r_work: 0.3430 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12880 Z= 0.185 Angle : 0.608 11.150 18164 Z= 0.344 Chirality : 0.037 0.173 2016 Planarity : 0.004 0.052 1716 Dihedral : 27.436 175.288 3276 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.64 % Allowed : 19.32 % Favored : 76.05 % 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 aren not related in a simple way. whole: 0.97 (0.26), residues: 1074 helix: 2.15 (0.24), residues: 462 sheet: 0.53 (0.36), residues: 203 loop : -1.11 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 73 TYR 0.014 0.001 TYR F 112 PHE 0.031 0.002 PHE H 16 TRP 0.010 0.001 TRP H 224 HIS 0.011 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00408 (12880) covalent geometry : angle 0.60829 (18164) hydrogen bonds : bond 0.03811 ( 608) hydrogen bonds : angle 4.30195 ( 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 173 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.430 Fit side-chains REVERT: C 42 GLU cc_start: 0.8012 (tt0) cc_final: 0.7764 (mt-10) REVERT: E 1 MET cc_start: 0.6218 (mtm) cc_final: 0.5850 (mmp) REVERT: E 106 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8448 (mp) REVERT: G 14 VAL cc_start: 0.6939 (t) cc_final: 0.6656 (m) REVERT: H 263 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.5810 (mtmt) outliers start: 42 outliers final: 26 residues processed: 160 average time/residue: 0.6432 time to fit residues: 111.3794 Evaluate side-chains 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 66 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 E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS 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 72 MET 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 110 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 780 HIS Chi-restraints excluded: chain H residue 787 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: 0.5980 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 60 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3975 r_free = 0.3975 target = 0.149180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129177 restraints weight = 14579.613| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 0.76 r_work: 0.3440 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12880 Z= 0.181 Angle : 0.621 12.469 18164 Z= 0.346 Chirality : 0.037 0.173 2016 Planarity : 0.004 0.052 1716 Dihedral : 27.409 174.941 3276 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.97 % Allowed : 19.76 % Favored : 75.28 % 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 aren not related in a simple way. whole: 0.94 (0.25), residues: 1074 helix: 2.15 (0.24), residues: 461 sheet: 0.47 (0.34), residues: 213 loop : -1.15 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 73 TYR 0.021 0.001 TYR G 52 PHE 0.029 0.002 PHE H 16 TRP 0.010 0.001 TRP H 224 HIS 0.019 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00398 (12880) covalent geometry : angle 0.62131 (18164) hydrogen bonds : bond 0.03798 ( 608) hydrogen bonds : angle 4.28349 ( 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 175 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.387 Fit side-chains REVERT: C 42 GLU cc_start: 0.7983 (tt0) cc_final: 0.7754 (mt-10) REVERT: C 82 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8036 (tpp80) REVERT: E 1 MET cc_start: 0.6181 (mtm) cc_final: 0.5820 (mmp) REVERT: E 106 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8447 (mp) REVERT: G 14 VAL cc_start: 0.6883 (t) cc_final: 0.6654 (m) REVERT: H 263 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5801 (mtmt) outliers start: 45 outliers final: 24 residues processed: 159 average time/residue: 0.6705 time to fit residues: 115.0455 Evaluate side-chains 150 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 66 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 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 71 THR Chi-restraints excluded: chain G residue 72 MET 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 110 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 780 HIS Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.149284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129292 restraints weight = 14512.561| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 0.76 r_work: 0.3440 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12880 Z= 0.180 Angle : 0.627 14.816 18164 Z= 0.346 Chirality : 0.037 0.177 2016 Planarity : 0.004 0.051 1716 Dihedral : 27.410 174.735 3276 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.30 % Allowed : 20.31 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.25), residues: 1074 helix: 2.13 (0.24), residues: 461 sheet: 0.49 (0.34), residues: 213 loop : -1.17 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 262 TYR 0.012 0.001 TYR C 11 PHE 0.027 0.002 PHE H 16 TRP 0.010 0.001 TRP H 224 HIS 0.019 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00397 (12880) covalent geometry : angle 0.62698 (18164) hydrogen bonds : bond 0.03781 ( 608) hydrogen bonds : angle 4.27046 ( 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: 39 poor density : 124 time to evaluate : 0.405 Fit side-chains REVERT: C 42 GLU cc_start: 0.8014 (tt0) cc_final: 0.7776 (mt-10) REVERT: C 82 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.8034 (tpp80) REVERT: E 1 MET cc_start: 0.6207 (mtm) cc_final: 0.5830 (mmp) REVERT: E 106 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8443 (mp) REVERT: F 118 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5365 (ptm-80) REVERT: G 14 VAL cc_start: 0.6918 (t) cc_final: 0.6682 (m) REVERT: G 73 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5607 (ttm170) REVERT: H 263 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5842 (mtmt) outliers start: 39 outliers final: 26 residues processed: 150 average time/residue: 0.6751 time to fit residues: 109.0993 Evaluate side-chains 150 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 66 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 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 F residue 118 ARG Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET 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 110 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 780 HIS Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129413 restraints weight = 14626.358| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 0.72 r_work: 0.3439 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12880 Z= 0.196 Angle : 0.643 16.165 18164 Z= 0.353 Chirality : 0.038 0.177 2016 Planarity : 0.004 0.050 1716 Dihedral : 27.400 174.537 3276 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.86 % Allowed : 21.30 % Favored : 74.83 % 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 aren not related in a simple way. whole: 0.86 (0.25), residues: 1074 helix: 2.07 (0.24), residues: 462 sheet: 0.40 (0.34), residues: 215 loop : -1.16 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 262 TYR 0.024 0.001 TYR G 52 PHE 0.028 0.002 PHE H 16 TRP 0.010 0.001 TRP H 224 HIS 0.022 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00435 (12880) covalent geometry : angle 0.64263 (18164) hydrogen bonds : bond 0.03940 ( 608) hydrogen bonds : angle 4.30934 ( 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 161 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.393 Fit side-chains REVERT: C 42 GLU cc_start: 0.7969 (tt0) cc_final: 0.7751 (mt-10) REVERT: E 1 MET cc_start: 0.6283 (mtm) cc_final: 0.5937 (mmp) REVERT: E 106 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8414 (mp) REVERT: F 118 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5373 (ptm-80) REVERT: G 14 VAL cc_start: 0.6884 (t) cc_final: 0.6657 (m) REVERT: G 73 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.5703 (ttm170) outliers start: 35 outliers final: 24 residues processed: 151 average time/residue: 0.6452 time to fit residues: 105.2118 Evaluate side-chains 150 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 66 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 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 F residue 118 ARG Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 49 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 130 GLN H 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121495 restraints weight = 14446.650| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.24 r_work: 0.3406 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12880 Z= 0.182 Angle : 0.636 15.362 18164 Z= 0.351 Chirality : 0.037 0.174 2016 Planarity : 0.004 0.050 1716 Dihedral : 27.400 174.777 3276 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.31 % Allowed : 22.08 % Favored : 74.61 % 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 aren not related in a simple way. whole: 0.84 (0.25), residues: 1074 helix: 2.02 (0.24), residues: 462 sheet: 0.43 (0.34), residues: 215 loop : -1.16 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 262 TYR 0.014 0.001 TYR C 11 PHE 0.029 0.002 PHE H 16 TRP 0.010 0.001 TRP H 224 HIS 0.009 0.001 HIS H 780 Details of bonding type rmsd covalent geometry : bond 0.00402 (12880) covalent geometry : angle 0.63635 (18164) hydrogen bonds : bond 0.03839 ( 608) hydrogen bonds : angle 4.28787 ( 1605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5467.22 seconds wall clock time: 93 minutes 45.77 seconds (5625.77 seconds total)