Starting phenix.real_space_refine on Thu Jul 2 23:38:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3l_46537/07_2026/9d3l_46537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3l_46537/07_2026/9d3l_46537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3l_46537/07_2026/9d3l_46537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3l_46537/07_2026/9d3l_46537.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3l_46537/07_2026/9d3l_46537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3l_46537/07_2026/9d3l_46537.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 14 5.16 5 C 6135 2.51 5 N 2060 2.21 5 O 2537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 10994 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 90, 694 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 90, 694 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 693 Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 795 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 800 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 789 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 104, 789 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 787 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 684 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "J" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2564 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "I" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2520 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS D 82 " occ=0.57 ... (18 atoms not shown) pdb=" NE2BHIS D 82 " occ=0.43 residue: pdb=" N AARG G 32 " occ=0.58 ... (20 atoms not shown) pdb=" NH2BARG G 32 " occ=0.42 Time building chain proxies: 2.59, per 1000 atoms: 0.24 Number of scatterers: 10994 At special positions: 0 Unit cell: (89.76, 115.005, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 248 15.00 O 2537 8.00 N 2060 7.00 C 6135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 296.7 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 9 sheets defined 69.3% alpha, 2.9% beta 114 base pairs and 213 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.501A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.717A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.515A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 3.512A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.513A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.611A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.599A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.551A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.328A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.678A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.612A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.960A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.303A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.004A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.662A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.005A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.346A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 386 hydrogen bonds defined for protein. 1148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 291 hydrogen bonds 582 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 213 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.23 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: 2137 1.33 - 1.45: 3697 1.45 - 1.57: 5339 1.57 - 1.69: 494 1.69 - 1.81: 26 Bond restraints: 11693 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT I 71 " pdb=" C2' DT I 71 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" CA ASN C 73 " pdb=" C ASN C 73 " ideal model delta sigma weight residual 1.522 1.567 -0.044 1.37e-02 5.33e+03 1.05e+01 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT J 44 " pdb=" C2' DT J 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 11688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 15030 1.24 - 2.49: 1564 2.49 - 3.73: 234 3.73 - 4.98: 23 4.98 - 6.22: 10 Bond angle restraints: 16861 Sorted by residual: angle pdb=" O4' DG J -70 " pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 108.00 111.30 -3.30 7.00e-01 2.04e+00 2.22e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT J -59 " pdb=" C4 DT J -59 " pdb=" O4 DT J -59 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 16856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.68: 4661 28.68 - 57.36: 1602 57.36 - 86.04: 141 86.04 - 114.72: 1 114.72 - 143.40: 2 Dihedral angle restraints: 6407 sinusoidal: 4224 harmonic: 2183 Sorted by residual: dihedral pdb=" C4' DA I -45 " pdb=" C3' DA I -45 " pdb=" O3' DA I -45 " pdb=" P DA I -44 " ideal model delta sinusoidal sigma weight residual -140.00 3.40 -143.40 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DT J 44 " pdb=" C3' DT J 44 " pdb=" O3' DT J 44 " pdb=" P DT J 45 " ideal model delta sinusoidal sigma weight residual 220.00 89.31 130.69 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1228 0.040 - 0.079: 540 0.079 - 0.119: 139 0.119 - 0.158: 17 0.158 - 0.198: 2 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CB THR D 119 " pdb=" CA THR D 119 " pdb=" OG1 THR D 119 " pdb=" CG2 THR D 119 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" P DA I -44 " pdb=" OP1 DA I -44 " pdb=" OP2 DA I -44 " pdb=" O5' DA I -44 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1923 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO D 103 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 73 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ASN C 73 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN C 73 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS C 74 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -13 " 0.026 2.00e-02 2.50e+03 1.19e-02 3.89e+00 pdb=" N9 DA J -13 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DA J -13 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J -13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J -13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J -13 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J -13 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA J -13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J -13 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA J -13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA J -13 " -0.003 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 340 2.67 - 3.22: 8963 3.22 - 3.78: 20563 3.78 - 4.34: 27830 4.34 - 4.90: 39348 Nonbonded interactions: 97044 Sorted by model distance: nonbonded pdb=" OE2 GLU C 61 " pdb=" OG SER L 365 " model vdw 2.107 3.040 nonbonded pdb=" OE1 GLU C 61 " pdb=" NH1 ARG L 367 " model vdw 2.173 3.120 nonbonded pdb=" OH TYR G 39 " pdb=" OE2 GLU H 71 " model vdw 2.247 3.040 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 367 " model vdw 2.266 3.120 nonbonded pdb=" N ALA G 14 " pdb=" OP1 DT I -42 " model vdw 2.267 3.120 ... (remaining 97039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E' and resid 43 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 14 through 31 or resid 33 through 117)) selection = (chain 'G' and (resid 14 through 31 or resid 33 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 through 117)) } ncs_group { reference = (chain 'D' and (resid 36 through 81 or resid 83 through 123)) selection = (chain 'H' and (resid 36 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 81 or resid 83 through 123)) } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.570 Find NCS groups from input model: 0.150 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11693 Z= 0.520 Angle : 0.797 6.222 16861 Z= 0.687 Chirality : 0.045 0.198 1926 Planarity : 0.005 0.068 1278 Dihedral : 28.951 143.404 4999 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.93 % Allowed : 26.06 % Favored : 71.01 % 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: 0.69 (0.30), residues: 738 helix: 0.95 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.66 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 71 TYR 0.017 0.002 TYR D 40 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.52 (11693) covalent geometry : angle 0.79721 / 0.69 (16861) hydrogen bonds : bond 0.13150 / 8.51 ( 677) hydrogen bonds : angle 4.80314 / 3.43 ( 1730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.303 Fit side-chains REVERT: G 91 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: H 99 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8005 (mtt180) outliers start: 18 outliers final: 16 residues processed: 133 average time/residue: 0.8470 time to fit residues: 118.4603 Evaluate side-chains 132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.174012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119086 restraints weight = 27272.564| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.60 r_work: 0.3153 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11693 Z= 0.142 Angle : 0.645 6.558 16861 Z= 0.377 Chirality : 0.045 0.227 1926 Planarity : 0.005 0.053 1278 Dihedral : 30.972 142.043 3589 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.09 % Allowed : 25.08 % Favored : 71.82 % 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: 1.57 (0.31), residues: 738 helix: 1.58 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 71 TYR 0.014 0.001 TYR D 40 PHE 0.012 0.001 PHE A 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (11693) covalent geometry : angle 0.64481 / 0.38 (16861) hydrogen bonds : bond 0.04244 / 2.78 ( 677) hydrogen bonds : angle 3.18346 / 2.27 ( 1730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.238 Fit side-chains REVERT: A 65 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 95 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7536 (mtp-110) REVERT: C 73 ASN cc_start: 0.7883 (t0) cc_final: 0.7659 (m-40) REVERT: D 116 LYS cc_start: 0.8400 (tttp) cc_final: 0.7778 (tttm) REVERT: E 73 GLU cc_start: 0.8251 (tt0) cc_final: 0.7979 (tt0) REVERT: E 120 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8067 (mtt) REVERT: H 56 SER cc_start: 0.8907 (m) cc_final: 0.8638 (p) REVERT: H 99 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7946 (mtt180) REVERT: H 108 LYS cc_start: 0.8390 (tppt) cc_final: 0.8032 (mttt) outliers start: 19 outliers final: 8 residues processed: 124 average time/residue: 0.8010 time to fit residues: 104.6095 Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 104 GLN E 113 HIS H 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116563 restraints weight = 30889.856| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.70 r_work: 0.3097 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11693 Z= 0.196 Angle : 0.646 6.601 16861 Z= 0.376 Chirality : 0.046 0.226 1926 Planarity : 0.005 0.056 1278 Dihedral : 31.064 143.045 3568 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.42 % Allowed : 24.10 % Favored : 72.48 % 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: 1.68 (0.30), residues: 738 helix: 1.68 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.48 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 71 TYR 0.013 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (11693) covalent geometry : angle 0.64585 / 0.38 (16861) hydrogen bonds : bond 0.04807 / 3.21 ( 677) hydrogen bonds : angle 3.14924 / 2.24 ( 1730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.301 Fit side-chains REVERT: A 65 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 95 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7552 (mtp-110) REVERT: D 116 LYS cc_start: 0.8434 (tttp) cc_final: 0.7781 (tttm) REVERT: H 46 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7706 (mttt) REVERT: H 56 SER cc_start: 0.8972 (m) cc_final: 0.8711 (p) REVERT: H 99 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8045 (mtt180) REVERT: H 120 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (mtpt) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 0.8453 time to fit residues: 112.5757 Evaluate side-chains 122 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117308 restraints weight = 22696.565| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.46 r_work: 0.3130 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11693 Z= 0.154 Angle : 0.630 6.563 16861 Z= 0.368 Chirality : 0.045 0.225 1926 Planarity : 0.005 0.055 1278 Dihedral : 31.076 142.773 3567 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.58 % Allowed : 23.13 % Favored : 73.29 % 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: 1.95 (0.30), residues: 738 helix: 1.89 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 71 TYR 0.014 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (11693) covalent geometry : angle 0.63022 / 0.37 (16861) hydrogen bonds : bond 0.04359 / 2.90 ( 677) hydrogen bonds : angle 3.09541 / 2.20 ( 1730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.292 Fit side-chains REVERT: A 65 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8614 (mp) REVERT: B 95 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7650 (mtp-110) REVERT: D 116 LYS cc_start: 0.8498 (tttp) cc_final: 0.7882 (tttm) REVERT: E 120 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: H 56 SER cc_start: 0.9029 (m) cc_final: 0.8749 (p) REVERT: H 99 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8139 (mtt180) REVERT: H 120 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7763 (mtpt) outliers start: 22 outliers final: 13 residues processed: 129 average time/residue: 0.7785 time to fit residues: 105.5799 Evaluate side-chains 123 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118540 restraints weight = 22737.795| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.47 r_work: 0.3134 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11693 Z= 0.142 Angle : 0.621 6.405 16861 Z= 0.364 Chirality : 0.045 0.222 1926 Planarity : 0.005 0.054 1278 Dihedral : 31.062 142.515 3567 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.77 % Allowed : 24.59 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.31), residues: 738 helix: 2.05 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG K 367 TYR 0.013 0.001 TYR D 40 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (11693) covalent geometry : angle 0.62117 / 0.36 (16861) hydrogen bonds : bond 0.04118 / 2.73 ( 677) hydrogen bonds : angle 3.06044 / 2.17 ( 1730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.302 Fit side-chains REVERT: A 65 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8629 (mp) REVERT: B 95 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7691 (mtp-110) REVERT: D 116 LYS cc_start: 0.8542 (tttp) cc_final: 0.7906 (tttm) REVERT: H 56 SER cc_start: 0.9030 (m) cc_final: 0.8747 (p) REVERT: H 99 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8136 (mtt180) REVERT: H 108 LYS cc_start: 0.8544 (mppt) cc_final: 0.7927 (ttpt) REVERT: H 120 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7708 (mtpt) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 0.8563 time to fit residues: 110.8173 Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 51 optimal weight: 0.0570 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118278 restraints weight = 22920.227| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.51 r_work: 0.3123 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11693 Z= 0.162 Angle : 0.617 6.407 16861 Z= 0.361 Chirality : 0.044 0.222 1926 Planarity : 0.005 0.057 1278 Dihedral : 31.044 142.096 3567 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.75 % Allowed : 23.29 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.30), residues: 738 helix: 2.07 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 71 TYR 0.015 0.002 TYR H 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (11693) covalent geometry : angle 0.61708 / 0.36 (16861) hydrogen bonds : bond 0.04172 / 2.77 ( 677) hydrogen bonds : angle 3.01336 / 2.14 ( 1730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.349 Fit side-chains REVERT: A 65 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 122 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8303 (ptpp) REVERT: B 95 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7836 (mmm160) REVERT: D 116 LYS cc_start: 0.8477 (tttp) cc_final: 0.7840 (tttm) REVERT: F 84 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: G 77 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6034 (ttt-90) REVERT: H 56 SER cc_start: 0.8963 (m) cc_final: 0.8692 (p) REVERT: H 99 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8031 (mtt180) REVERT: H 108 LYS cc_start: 0.8460 (mppt) cc_final: 0.8061 (mttt) outliers start: 23 outliers final: 9 residues processed: 125 average time/residue: 0.7864 time to fit residues: 103.0836 Evaluate side-chains 120 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117218 restraints weight = 30452.327| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.71 r_work: 0.3123 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11693 Z= 0.140 Angle : 0.609 6.415 16861 Z= 0.358 Chirality : 0.044 0.222 1926 Planarity : 0.004 0.053 1278 Dihedral : 31.045 142.059 3565 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.75 % Allowed : 22.96 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.31), residues: 738 helix: 2.13 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 71 TYR 0.013 0.001 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (11693) covalent geometry : angle 0.60881 / 0.36 (16861) hydrogen bonds : bond 0.04051 / 2.69 ( 677) hydrogen bonds : angle 3.00411 / 2.13 ( 1730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.280 Fit side-chains REVERT: A 65 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 122 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8269 (ptpp) REVERT: B 95 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7818 (mmm160) REVERT: D 116 LYS cc_start: 0.8441 (tttp) cc_final: 0.7796 (tttm) REVERT: F 84 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8679 (mmm) REVERT: G 77 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6000 (ttt-90) REVERT: H 56 SER cc_start: 0.8977 (m) cc_final: 0.8695 (p) REVERT: H 84 ASN cc_start: 0.8356 (m-40) cc_final: 0.8149 (m-40) REVERT: H 93 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: H 99 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8021 (mtt90) REVERT: H 108 LYS cc_start: 0.8440 (mppt) cc_final: 0.8018 (mttp) REVERT: H 120 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7612 (mtpt) outliers start: 23 outliers final: 12 residues processed: 122 average time/residue: 0.8115 time to fit residues: 104.1965 Evaluate side-chains 123 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 76 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 50.0000 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115263 restraints weight = 28594.578| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.74 r_work: 0.3103 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11693 Z= 0.190 Angle : 0.632 6.905 16861 Z= 0.366 Chirality : 0.045 0.222 1926 Planarity : 0.005 0.054 1278 Dihedral : 31.081 142.118 3565 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.42 % Allowed : 23.78 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.30), residues: 738 helix: 2.01 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 71 TYR 0.013 0.002 TYR D 40 PHE 0.013 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (11693) covalent geometry : angle 0.63248 / 0.37 (16861) hydrogen bonds : bond 0.04451 / 2.96 ( 677) hydrogen bonds : angle 3.03885 / 2.16 ( 1730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.348 Fit side-chains REVERT: A 65 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 122 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8319 (ptpp) REVERT: B 95 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7824 (mmm160) REVERT: D 116 LYS cc_start: 0.8437 (tttp) cc_final: 0.7798 (tttm) REVERT: F 84 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8713 (mmm) REVERT: G 77 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6067 (ttt-90) REVERT: H 56 SER cc_start: 0.8951 (m) cc_final: 0.8679 (p) REVERT: H 84 ASN cc_start: 0.8427 (m-40) cc_final: 0.8221 (m-40) REVERT: H 99 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.8061 (mtt180) REVERT: H 120 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7660 (mtpt) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.7939 time to fit residues: 105.1314 Evaluate side-chains 125 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.172358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118599 restraints weight = 24636.739| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.32 r_work: 0.3165 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11693 Z= 0.142 Angle : 0.618 6.880 16861 Z= 0.361 Chirality : 0.044 0.218 1926 Planarity : 0.005 0.053 1278 Dihedral : 31.079 142.119 3565 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.93 % Allowed : 24.43 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.30), residues: 738 helix: 2.07 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 71 TYR 0.013 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (11693) covalent geometry : angle 0.61823 / 0.36 (16861) hydrogen bonds : bond 0.04243 / 2.82 ( 677) hydrogen bonds : angle 3.03020 / 2.15 ( 1730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.189 Fit side-chains REVERT: A 65 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 122 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8402 (ptpp) REVERT: B 95 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7953 (mmm160) REVERT: D 116 LYS cc_start: 0.8526 (tttp) cc_final: 0.7881 (tttm) REVERT: E 56 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8362 (ttmm) REVERT: G 77 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6154 (ttt-90) REVERT: H 56 SER cc_start: 0.8995 (m) cc_final: 0.8718 (p) REVERT: H 99 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8141 (mtt180) REVERT: H 120 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7661 (mtpt) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 0.8278 time to fit residues: 103.4456 Evaluate side-chains 120 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 20.0000 chunk 52 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 64 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 50.0000 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.172233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116028 restraints weight = 26723.594| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.65 r_work: 0.3117 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11693 Z= 0.155 Angle : 0.619 6.912 16861 Z= 0.360 Chirality : 0.044 0.219 1926 Planarity : 0.005 0.058 1278 Dihedral : 31.078 142.036 3565 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.77 % Allowed : 24.76 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.30), residues: 738 helix: 2.09 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 71 TYR 0.013 0.002 TYR D 40 PHE 0.012 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (11693) covalent geometry : angle 0.61931 / 0.36 (16861) hydrogen bonds : bond 0.04178 / 2.77 ( 677) hydrogen bonds : angle 3.02389 / 2.14 ( 1730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.286 Fit side-chains REVERT: A 65 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8520 (mp) REVERT: A 122 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8290 (ptpp) REVERT: B 95 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7861 (mmm160) REVERT: D 116 LYS cc_start: 0.8436 (tttp) cc_final: 0.7777 (tttm) REVERT: E 56 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8246 (ttmm) REVERT: G 77 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6017 (ttt-90) REVERT: H 56 SER cc_start: 0.8936 (m) cc_final: 0.8658 (p) REVERT: H 99 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8028 (mtt180) outliers start: 17 outliers final: 10 residues processed: 119 average time/residue: 0.7926 time to fit residues: 98.9154 Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 50.0000 chunk 67 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116610 restraints weight = 21592.544| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.40 r_work: 0.3154 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11693 Z= 0.173 Angle : 0.624 6.922 16861 Z= 0.361 Chirality : 0.044 0.220 1926 Planarity : 0.005 0.063 1278 Dihedral : 31.073 141.944 3565 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.61 % Allowed : 24.76 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.30), residues: 738 helix: 2.02 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 71 TYR 0.012 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (11693) covalent geometry : angle 0.62394 / 0.36 (16861) hydrogen bonds : bond 0.04199 / 2.78 ( 677) hydrogen bonds : angle 3.01711 / 2.14 ( 1730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3741.49 seconds wall clock time: 64 minutes 11.93 seconds (3851.93 seconds total)