Starting phenix.real_space_refine on Wed Feb 4 13:07:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3l_46537/02_2026/9d3l_46537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3l_46537/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9d3l_46537/02_2026/9d3l_46537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3l_46537/02_2026/9d3l_46537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3l_46537/02_2026/9d3l_46537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3l_46537/02_2026/9d3l_46537.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 2.10, per 1000 atoms: 0.19 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: 0.69 Conformation dependent library (CDL) restraints added in 323.9 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: 1.46 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: 2.16 Time building geometry restraints manager: 0.90 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=" 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=" CG ARG G 71 " pdb=" CD ARG G 71 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" C3' DT J 44 " pdb=" O3' DT J 44 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CA ILE B 29 " pdb=" CB ILE B 29 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.02e+00 ... (remaining 11688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 15757 1.24 - 2.49: 982 2.49 - 3.73: 94 3.73 - 4.98: 18 4.98 - 6.22: 10 Bond angle restraints: 16861 Sorted by residual: angle pdb=" N SER K 366 " pdb=" CA SER K 366 " pdb=" C SER K 366 " ideal model delta sigma weight residual 113.72 108.74 4.98 1.30e+00 5.92e-01 1.47e+01 angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 115.78 -3.18 1.00e+00 1.00e+00 1.01e+01 angle pdb=" C ASP C 72 " pdb=" N ASN C 73 " pdb=" CA ASN C 73 " ideal model delta sigma weight residual 121.58 127.78 -6.20 1.95e+00 2.63e-01 1.01e+01 angle pdb=" CA ASN C 73 " pdb=" C ASN C 73 " pdb=" N LYS C 74 " ideal model delta sigma weight residual 118.41 114.17 4.24 1.34e+00 5.57e-01 1.00e+01 angle pdb=" C ASN C 73 " pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " ideal model delta sigma weight residual 109.95 116.17 -6.22 1.99e+00 2.53e-01 9.78e+00 ... (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: 1437 0.040 - 0.079: 416 0.079 - 0.119: 64 0.119 - 0.158: 7 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 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.38e-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: 0.580 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.004 0.044 11693 Z= 0.175 Angle : 0.659 6.222 16861 Z= 0.417 Chirality : 0.037 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 covalent geometry : bond 0.00368 (11693) covalent geometry : angle 0.65927 (16861) hydrogen bonds : bond 0.13150 ( 677) hydrogen bonds : angle 4.80314 ( 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 : 0.210 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: 0.7944 time to fit residues: 110.6698 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 : 0.210 ------------------------------------------------------------------------------- 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: 7.9990 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: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 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 = 0.3980 r_free = 0.3980 target = 0.176769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122603 restraints weight = 27292.452| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.66 r_work: 0.3184 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11693 Z= 0.149 Angle : 0.550 5.537 16861 Z= 0.334 Chirality : 0.033 0.143 1926 Planarity : 0.005 0.057 1278 Dihedral : 30.369 143.001 3589 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.77 % Allowed : 25.24 % Favored : 71.99 % 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: 1.81 (0.30), residues: 738 helix: 1.75 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.013 0.001 TYR D 40 PHE 0.012 0.001 PHE A 67 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00324 (11693) covalent geometry : angle 0.54986 (16861) hydrogen bonds : bond 0.03345 ( 677) hydrogen bonds : angle 2.97452 ( 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 132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.214 Fit side-chains REVERT: A 65 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 95 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7653 (mtp-110) REVERT: D 116 LYS cc_start: 0.8455 (tttp) cc_final: 0.7839 (tttm) REVERT: E 56 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8216 (ttmm) REVERT: E 120 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: F 35 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8276 (ttm110) REVERT: G 71 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7085 (tmm-80) REVERT: H 40 TYR cc_start: 0.8731 (m-80) cc_final: 0.8475 (m-80) REVERT: H 46 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7866 (mtpp) REVERT: H 56 SER cc_start: 0.8931 (m) cc_final: 0.8678 (p) REVERT: H 99 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7947 (mtt180) REVERT: H 108 LYS cc_start: 0.8269 (mppt) cc_final: 0.7962 (mttt) outliers start: 17 outliers final: 4 residues processed: 128 average time/residue: 0.8492 time to fit residues: 113.8807 Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR 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: 0.8980 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 84 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 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 = 0.4045 r_free = 0.4045 target = 0.180942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128573 restraints weight = 30023.025| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.74 r_work: 0.3165 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11693 Z= 0.148 Angle : 0.528 5.347 16861 Z= 0.322 Chirality : 0.033 0.129 1926 Planarity : 0.004 0.058 1278 Dihedral : 30.313 141.246 3563 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.12 % Allowed : 25.24 % 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: 2.38 (0.31), residues: 738 helix: 2.19 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.011 0.001 TYR D 40 PHE 0.010 0.001 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00327 (11693) covalent geometry : angle 0.52807 (16861) hydrogen bonds : bond 0.03316 ( 677) hydrogen bonds : angle 2.83966 ( 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 119 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.272 Fit side-chains REVERT: A 65 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8778 (mp) REVERT: D 116 LYS cc_start: 0.8558 (tttp) cc_final: 0.8021 (tttm) REVERT: H 40 TYR cc_start: 0.8870 (m-80) cc_final: 0.8658 (m-80) REVERT: H 99 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.8062 (mtt180) outliers start: 13 outliers final: 5 residues processed: 117 average time/residue: 0.7213 time to fit residues: 88.6644 Evaluate side-chains 109 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 113 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.174277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118847 restraints weight = 23105.051| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.47 r_work: 0.3177 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- 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 = 0.46 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11693 Z= 0.173 Angle : 0.542 5.237 16861 Z= 0.328 Chirality : 0.034 0.129 1926 Planarity : 0.004 0.056 1278 Dihedral : 30.409 141.856 3559 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 24.76 % Favored : 73.13 % 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: 2.39 (0.31), residues: 738 helix: 2.20 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.012 0.001 TYR D 40 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (11693) covalent geometry : angle 0.54245 (16861) hydrogen bonds : bond 0.03574 ( 677) hydrogen bonds : angle 2.87628 ( 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 121 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.284 Fit side-chains REVERT: A 65 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8571 (mp) REVERT: C 73 ASN cc_start: 0.8069 (t160) cc_final: 0.7753 (m-40) REVERT: D 116 LYS cc_start: 0.8497 (tttp) cc_final: 0.7876 (tttm) REVERT: E 120 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8154 (mtt) REVERT: H 99 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.8105 (mtt180) outliers start: 13 outliers final: 5 residues processed: 115 average time/residue: 0.7860 time to fit residues: 95.0296 Evaluate side-chains 111 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.174535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119101 restraints weight = 23059.317| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.47 r_work: 0.3180 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11693 Z= 0.165 Angle : 0.537 5.234 16861 Z= 0.326 Chirality : 0.034 0.160 1926 Planarity : 0.005 0.055 1278 Dihedral : 30.390 141.613 3559 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.28 % Allowed : 24.92 % 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: 2.50 (0.31), residues: 738 helix: 2.25 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.18 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 71 TYR 0.012 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00371 (11693) covalent geometry : angle 0.53737 (16861) hydrogen bonds : bond 0.03489 ( 677) hydrogen bonds : angle 2.85811 ( 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 117 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.282 Fit side-chains REVERT: A 65 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8577 (mp) REVERT: C 73 ASN cc_start: 0.8089 (t160) cc_final: 0.7761 (m-40) REVERT: D 116 LYS cc_start: 0.8506 (tttp) cc_final: 0.7844 (tttm) REVERT: G 71 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7011 (tmm-80) REVERT: G 77 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6618 (ttt-90) REVERT: H 99 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8113 (mtt180) outliers start: 14 outliers final: 6 residues processed: 114 average time/residue: 0.8400 time to fit residues: 100.4307 Evaluate side-chains 109 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 96 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 73 ASN C 104 GLN H 84 ASN H 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113956 restraints weight = 22614.616| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.45 r_work: 0.3107 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11693 Z= 0.307 Angle : 0.634 5.347 16861 Z= 0.373 Chirality : 0.041 0.158 1926 Planarity : 0.005 0.056 1278 Dihedral : 30.852 144.160 3559 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.77 % Allowed : 23.94 % 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: 1.83 (0.30), residues: 738 helix: 1.78 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 71 TYR 0.014 0.002 TYR B 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00720 (11693) covalent geometry : angle 0.63443 (16861) hydrogen bonds : bond 0.04876 ( 677) hydrogen bonds : angle 3.11092 ( 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 127 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 133 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8304 (mt-10) REVERT: C 73 ASN cc_start: 0.8087 (t0) cc_final: 0.7665 (m110) REVERT: D 116 LYS cc_start: 0.8549 (tttp) cc_final: 0.7818 (tttm) REVERT: E 120 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8263 (mtt) REVERT: G 77 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6447 (ttt-90) REVERT: H 99 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8152 (mtt180) outliers start: 17 outliers final: 7 residues processed: 123 average time/residue: 0.8751 time to fit residues: 112.6951 Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 364 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116859 restraints weight = 28958.365| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.65 r_work: 0.3104 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1304 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= 0.173 Angle : 0.582 5.502 16861 Z= 0.350 Chirality : 0.036 0.157 1926 Planarity : 0.005 0.071 1278 Dihedral : 30.849 144.068 3559 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.44 % Allowed : 23.29 % Favored : 74.27 % 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: 1.99 (0.30), residues: 738 helix: 1.90 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 71 TYR 0.014 0.002 TYR D 40 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00392 (11693) covalent geometry : angle 0.58211 (16861) hydrogen bonds : bond 0.04102 ( 677) hydrogen bonds : angle 3.04815 ( 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 126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 73 ASN cc_start: 0.7983 (t0) cc_final: 0.7587 (m110) REVERT: D 116 LYS cc_start: 0.8455 (tttp) cc_final: 0.7762 (tttm) REVERT: G 77 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6258 (ttt-90) REVERT: H 99 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.8016 (mtt180) outliers start: 15 outliers final: 8 residues processed: 124 average time/residue: 0.8285 time to fit residues: 107.7063 Evaluate side-chains 115 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 364 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115645 restraints weight = 27010.964| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.59 r_work: 0.3101 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 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 = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11693 Z= 0.222 Angle : 0.585 5.694 16861 Z= 0.349 Chirality : 0.037 0.167 1926 Planarity : 0.005 0.055 1278 Dihedral : 30.725 142.681 3559 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.12 % Allowed : 23.78 % Favored : 74.10 % 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: 1.96 (0.30), residues: 738 helix: 1.87 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 71 TYR 0.015 0.002 TYR H 40 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00514 (11693) covalent geometry : angle 0.58542 (16861) hydrogen bonds : bond 0.04087 ( 677) hydrogen bonds : angle 2.99813 ( 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 117 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.297 Fit side-chains REVERT: A 65 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 73 ASN cc_start: 0.7999 (t0) cc_final: 0.7600 (m110) REVERT: D 116 LYS cc_start: 0.8480 (tttp) cc_final: 0.7785 (tttm) REVERT: G 77 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6159 (ttt-90) REVERT: H 99 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.8046 (mtt180) REVERT: L 364 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6288 (mpp-170) outliers start: 13 outliers final: 6 residues processed: 116 average time/residue: 0.8340 time to fit residues: 101.4723 Evaluate side-chains 112 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 364 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 84 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 = 0.172291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116832 restraints weight = 24557.201| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.53 r_work: 0.3143 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11693 Z= 0.153 Angle : 0.565 5.344 16861 Z= 0.340 Chirality : 0.035 0.172 1926 Planarity : 0.005 0.055 1278 Dihedral : 30.743 142.554 3559 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.12 % Allowed : 23.62 % Favored : 74.27 % 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: 2.26 (0.31), residues: 738 helix: 2.10 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 71 TYR 0.014 0.002 TYR H 40 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (11693) covalent geometry : angle 0.56479 (16861) hydrogen bonds : bond 0.03695 ( 677) hydrogen bonds : angle 2.97145 ( 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 117 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.289 Fit side-chains REVERT: A 65 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8550 (mp) REVERT: C 73 ASN cc_start: 0.8008 (t0) cc_final: 0.7577 (m110) REVERT: D 116 LYS cc_start: 0.8482 (tttp) cc_final: 0.7790 (tttm) REVERT: G 77 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6136 (ttt-90) REVERT: H 99 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8104 (mtt90) REVERT: L 364 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6292 (mpp-170) outliers start: 13 outliers final: 7 residues processed: 114 average time/residue: 0.7922 time to fit residues: 94.7373 Evaluate side-chains 113 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 96 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 364 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.171740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116440 restraints weight = 26538.688| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.56 r_work: 0.3131 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 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 = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11693 Z= 0.196 Angle : 0.566 5.282 16861 Z= 0.340 Chirality : 0.035 0.166 1926 Planarity : 0.005 0.055 1278 Dihedral : 30.626 140.842 3559 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 23.78 % Favored : 74.10 % 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: 2.24 (0.30), residues: 738 helix: 2.07 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.28 (0.41), residues: 185 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 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (11693) covalent geometry : angle 0.56580 (16861) hydrogen bonds : bond 0.03823 ( 677) hydrogen bonds : angle 2.94849 ( 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 117 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.284 Fit side-chains REVERT: A 65 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 73 ASN cc_start: 0.8067 (t0) cc_final: 0.7675 (m110) REVERT: D 116 LYS cc_start: 0.8550 (tttp) cc_final: 0.7881 (tttm) REVERT: G 77 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6176 (ttt-90) REVERT: H 99 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8165 (mtt180) REVERT: L 364 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6274 (mpp-170) outliers start: 13 outliers final: 7 residues processed: 114 average time/residue: 0.8106 time to fit residues: 97.0077 Evaluate side-chains 115 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 96 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 364 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 44 optimal weight: 0.0670 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 84 ASN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116485 restraints weight = 21623.158| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.43 r_work: 0.3161 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11693 Z= 0.199 Angle : 0.565 5.272 16861 Z= 0.339 Chirality : 0.036 0.164 1926 Planarity : 0.005 0.055 1278 Dihedral : 30.578 139.589 3559 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.95 % Allowed : 23.78 % Favored : 74.27 % 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: 2.24 (0.30), residues: 738 helix: 2.06 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 71 TYR 0.016 0.002 TYR H 40 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (11693) covalent geometry : angle 0.56504 (16861) hydrogen bonds : bond 0.03803 ( 677) hydrogen bonds : angle 2.94781 ( 1730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.74 seconds wall clock time: 65 minutes 28.38 seconds (3928.38 seconds total)