Starting phenix.real_space_refine on Sat Aug 23 12:15:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yov_10864/08_2025/6yov_10864.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yov_10864/08_2025/6yov_10864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yov_10864/08_2025/6yov_10864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yov_10864/08_2025/6yov_10864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yov_10864/08_2025/6yov_10864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yov_10864/08_2025/6yov_10864.map" } resolution = 3.42 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= 0.005 sd= 0.044 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 261 5.49 5 S 19 5.16 5 C 6892 2.51 5 N 2327 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12298 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2662 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2706 Classifications: {'DNA': 131} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 130} Chain: "K" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 272 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 625 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.54, per 1000 atoms: 0.29 Number of scatterers: 12298 At special positions: 0 Unit cell: (104.06, 116.96, 129.86, 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 19 16.00 P 261 15.00 O 2799 8.00 N 2327 7.00 C 6892 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 567.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1550 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 72.0% alpha, 2.7% beta 129 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.511A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.504A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.247A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.961A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 160 Processing helix chain 'K' and resid 163 through 176 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 193 through 208 Proline residue: K 202 - end of helix Processing helix chain 'L' and resid 46 through 61 removed outlier: 3.566A pdb=" N GLY L 54 " --> pdb=" O VAL L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 81 Processing helix chain 'L' and resid 83 through 105 Proline residue: L 89 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.769A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.880A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.800A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.855A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.218A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 477 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 330 hydrogen bonds 660 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2001 1.32 - 1.45: 4464 1.45 - 1.57: 6014 1.57 - 1.69: 522 1.69 - 1.81: 34 Bond restraints: 13035 Sorted by residual: bond pdb=" CA ASN F 26 " pdb=" C ASN F 26 " ideal model delta sigma weight residual 1.522 1.601 -0.079 1.37e-02 5.33e+03 3.32e+01 bond pdb=" O3' DT J 84 " pdb=" P DG J 85 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.23e+01 bond pdb=" CD ARG B 40 " pdb=" NE ARG B 40 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.88e+00 bond pdb=" NE ARG B 24 " pdb=" CZ ARG B 24 " ideal model delta sigma weight residual 1.326 1.360 -0.034 1.10e-02 8.26e+03 9.81e+00 ... (remaining 13030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 16948 1.90 - 3.80: 1530 3.80 - 5.70: 145 5.70 - 7.60: 33 7.60 - 9.50: 5 Bond angle restraints: 18661 Sorted by residual: angle pdb=" N LYS L 42 " pdb=" CA LYS L 42 " pdb=" C LYS L 42 " ideal model delta sigma weight residual 110.53 120.03 -9.50 1.29e+00 6.01e-01 5.43e+01 angle pdb=" C HIS L 105 " pdb=" N PRO L 106 " pdb=" CA PRO L 106 " ideal model delta sigma weight residual 119.47 127.73 -8.26 1.16e+00 7.43e-01 5.07e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.56 126.55 -6.99 1.02e+00 9.61e-01 4.70e+01 angle pdb=" C HIS H 50 " pdb=" N PRO H 51 " pdb=" CA PRO H 51 " ideal model delta sigma weight residual 119.56 126.48 -6.92 1.02e+00 9.61e-01 4.61e+01 angle pdb=" C LEU H 103 " pdb=" N PRO H 104 " pdb=" CA PRO H 104 " ideal model delta sigma weight residual 120.31 126.68 -6.37 9.80e-01 1.04e+00 4.23e+01 ... (remaining 18656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5050 17.90 - 35.81: 948 35.81 - 53.71: 831 53.71 - 71.61: 260 71.61 - 89.52: 12 Dihedral angle restraints: 7101 sinusoidal: 4631 harmonic: 2470 Sorted by residual: dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C ASN F 26 " pdb=" N ASN F 26 " pdb=" CA ASN F 26 " pdb=" CB ASN F 26 " ideal model delta harmonic sigma weight residual -122.60 -131.46 8.86 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 7098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1339 0.060 - 0.120: 573 0.120 - 0.180: 133 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA GLN L 61 " pdb=" N GLN L 61 " pdb=" C GLN L 61 " pdb=" CB GLN L 61 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA LEU E 66 " pdb=" N LEU E 66 " pdb=" C LEU E 66 " pdb=" CB LEU E 66 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG L 88 " pdb=" N ARG L 88 " pdb=" C ARG L 88 " pdb=" CB ARG L 88 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2064 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 55 " 0.074 2.00e-02 2.50e+03 4.04e-02 3.27e+01 pdb=" CG TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 55 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 55 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 55 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 55 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 55 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 41 " 0.072 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR H 41 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 41 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR H 41 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR H 41 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR H 41 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 41 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 41 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 55 " -0.064 2.00e-02 2.50e+03 3.32e-02 2.20e+01 pdb=" CG TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 55 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 55 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 55 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 55 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 55 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 55 " -0.045 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 4200 2.90 - 3.40: 10733 3.40 - 3.90: 24145 3.90 - 4.40: 28333 4.40 - 4.90: 37125 Nonbonded interactions: 104536 Sorted by model distance: nonbonded pdb=" N GLU G 42 " pdb=" OE1 GLU G 42 " model vdw 2.395 3.120 nonbonded pdb=" O2 DT I 125 " pdb=" OG SER L 72 " model vdw 2.399 3.040 nonbonded pdb=" OG SER G 19 " pdb=" O PHE G 26 " model vdw 2.404 3.040 nonbonded pdb=" OG1 THR C 77 " pdb=" OP1 DG J 133 " model vdw 2.407 3.040 nonbonded pdb=" NH2 ARG A 54 " pdb=" OH TYR A 55 " model vdw 2.462 3.120 ... (remaining 104531 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 23 through 102 or resid 201)) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 9 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 201) selection = (chain 'H' and (resid 34 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201)) } 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=0.00 max=1.00 mean=0.95 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: 1.470 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.750 Find NCS groups from input model: 0.160 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.013 0.171 13051 Z= 0.827 Angle : 1.137 9.504 18661 Z= 0.776 Chirality : 0.067 0.300 2067 Planarity : 0.009 0.046 1480 Dihedral : 25.194 89.518 5551 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.25), residues: 878 helix: 0.78 (0.18), residues: 650 sheet: None (None), residues: 0 loop : 0.34 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 80 TYR 0.074 0.010 TYR A 55 PHE 0.046 0.010 PHE D 71 TRP 0.017 0.007 TRP L 79 HIS 0.010 0.002 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.01127 (13035) covalent geometry : angle 1.13660 (18661) hydrogen bonds : bond 0.17012 ( 807) hydrogen bonds : angle 5.74699 ( 2070) Misc. bond : bond 0.16313 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8372 (m-30) cc_final: 0.8108 (m-30) REVERT: A 121 MET cc_start: 0.8920 (mmm) cc_final: 0.8655 (mmm) REVERT: A 124 ASP cc_start: 0.8083 (m-30) cc_final: 0.7841 (m-30) REVERT: C 26 PHE cc_start: 0.8846 (m-10) cc_final: 0.8641 (m-80) REVERT: C 40 TYR cc_start: 0.8856 (m-80) cc_final: 0.8583 (m-80) REVERT: C 102 THR cc_start: 0.8545 (m) cc_final: 0.8342 (p) REVERT: D 72 GLU cc_start: 0.8602 (tt0) cc_final: 0.8346 (tp30) REVERT: E 94 GLN cc_start: 0.9044 (tt0) cc_final: 0.8801 (tt0) REVERT: E 120 ILE cc_start: 0.9443 (mm) cc_final: 0.9156 (mt) REVERT: G 74 ASN cc_start: 0.9213 (m-40) cc_final: 0.8900 (t0) REVERT: G 102 THR cc_start: 0.8998 (m) cc_final: 0.8769 (p) REVERT: H 52 ASP cc_start: 0.8663 (p0) cc_final: 0.8433 (p0) REVERT: H 106 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9135 (tt0) REVERT: H 114 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1018 time to fit residues: 51.7549 Evaluate side-chains 250 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.070856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048296 restraints weight = 57151.774| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.43 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13051 Z= 0.183 Angle : 0.636 10.200 18661 Z= 0.369 Chirality : 0.037 0.163 2067 Planarity : 0.005 0.057 1480 Dihedral : 28.345 73.827 3881 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.47 % Allowed : 18.50 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.27), residues: 878 helix: 2.23 (0.20), residues: 664 sheet: None (None), residues: 0 loop : 0.20 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 43 TYR 0.020 0.002 TYR H 41 PHE 0.025 0.002 PHE B 62 TRP 0.006 0.002 TRP L 51 HIS 0.011 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00394 (13035) covalent geometry : angle 0.63637 (18661) hydrogen bonds : bond 0.05266 ( 807) hydrogen bonds : angle 3.46917 ( 2070) Misc. bond : bond 0.00169 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8937 (mt0) cc_final: 0.8715 (mt0) REVERT: A 121 MET cc_start: 0.9055 (mmm) cc_final: 0.8722 (mmm) REVERT: B 98 LEU cc_start: 0.9499 (mm) cc_final: 0.9251 (mm) REVERT: C 26 PHE cc_start: 0.8987 (m-10) cc_final: 0.8782 (m-80) REVERT: C 57 GLU cc_start: 0.8976 (tt0) cc_final: 0.8687 (tt0) REVERT: C 60 THR cc_start: 0.9627 (m) cc_final: 0.9417 (p) REVERT: C 62 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8842 (mm-30) REVERT: C 102 THR cc_start: 0.8783 (m) cc_final: 0.8445 (p) REVERT: D 94 GLU cc_start: 0.9427 (mp0) cc_final: 0.9064 (mp0) REVERT: E 51 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8621 (mm-30) REVERT: E 91 MET cc_start: 0.8968 (mmm) cc_final: 0.8690 (mmt) REVERT: E 124 ASP cc_start: 0.9027 (m-30) cc_final: 0.8752 (m-30) REVERT: F 58 VAL cc_start: 0.9581 (t) cc_final: 0.9337 (p) REVERT: G 57 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8706 (tt0) REVERT: G 102 THR cc_start: 0.8797 (m) cc_final: 0.8399 (p) REVERT: H 69 ASP cc_start: 0.9533 (t0) cc_final: 0.9241 (t0) outliers start: 24 outliers final: 10 residues processed: 295 average time/residue: 0.0987 time to fit residues: 41.7441 Evaluate side-chains 254 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 40.0000 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 0.0000 chunk 93 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 HIS G 32 HIS G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.084378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.065832 restraints weight = 91933.606| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.05 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13051 Z= 0.214 Angle : 0.631 11.866 18661 Z= 0.366 Chirality : 0.037 0.165 2067 Planarity : 0.005 0.050 1480 Dihedral : 28.587 73.674 3881 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 5.06 % Allowed : 20.23 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.28), residues: 878 helix: 2.28 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 88 TYR 0.023 0.002 TYR D 84 PHE 0.025 0.002 PHE H 71 TRP 0.006 0.002 TRP L 79 HIS 0.010 0.001 HIS L 101 Details of bonding type rmsd covalent geometry : bond 0.00467 (13035) covalent geometry : angle 0.63073 (18661) hydrogen bonds : bond 0.04721 ( 807) hydrogen bonds : angle 3.52639 ( 2070) Misc. bond : bond 0.00073 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9421 (tt0) cc_final: 0.8810 (tp-100) REVERT: A 121 MET cc_start: 0.9097 (mmm) cc_final: 0.8501 (mmm) REVERT: A 124 ASP cc_start: 0.9347 (m-30) cc_final: 0.9054 (m-30) REVERT: A 126 GLN cc_start: 0.9409 (mt0) cc_final: 0.9112 (mt0) REVERT: B 85 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8822 (tpp) REVERT: B 98 LEU cc_start: 0.9516 (mm) cc_final: 0.9135 (mm) REVERT: C 60 THR cc_start: 0.9684 (m) cc_final: 0.9479 (p) REVERT: C 88 ILE cc_start: 0.9329 (tp) cc_final: 0.9118 (tp) REVERT: C 90 ASN cc_start: 0.7760 (m-40) cc_final: 0.7331 (m-40) REVERT: C 102 THR cc_start: 0.9116 (m) cc_final: 0.8862 (p) REVERT: D 48 GLN cc_start: 0.9440 (tm-30) cc_final: 0.9173 (tm-30) REVERT: D 94 GLU cc_start: 0.9309 (mp0) cc_final: 0.8799 (mp0) REVERT: D 122 TYR cc_start: 0.8877 (t80) cc_final: 0.8669 (t80) REVERT: E 51 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8880 (mm-30) REVERT: E 60 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: E 77 GLN cc_start: 0.9376 (tt0) cc_final: 0.8901 (tm-30) REVERT: E 91 MET cc_start: 0.9108 (mmm) cc_final: 0.8711 (mmt) REVERT: E 95 GLU cc_start: 0.9394 (tp30) cc_final: 0.8808 (tt0) REVERT: E 121 MET cc_start: 0.9291 (mmp) cc_final: 0.8720 (mmm) REVERT: F 85 MET cc_start: 0.9417 (mmm) cc_final: 0.9153 (mmm) REVERT: G 31 VAL cc_start: 0.9721 (t) cc_final: 0.9437 (p) REVERT: G 40 TYR cc_start: 0.9306 (m-80) cc_final: 0.8876 (m-80) REVERT: G 73 ASP cc_start: 0.8754 (m-30) cc_final: 0.8439 (m-30) REVERT: G 85 GLN cc_start: 0.9480 (tp-100) cc_final: 0.8976 (tp-100) REVERT: G 102 THR cc_start: 0.9105 (m) cc_final: 0.8574 (p) REVERT: G 105 GLN cc_start: 0.9389 (mp10) cc_final: 0.9040 (mp10) REVERT: H 69 ASP cc_start: 0.9488 (t0) cc_final: 0.9265 (t0) REVERT: H 106 GLU cc_start: 0.9218 (mp0) cc_final: 0.8989 (tt0) outliers start: 35 outliers final: 20 residues processed: 281 average time/residue: 0.0925 time to fit residues: 37.5552 Evaluate side-chains 256 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.065955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.043300 restraints weight = 58683.998| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.29 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13051 Z= 0.210 Angle : 0.625 10.279 18661 Z= 0.362 Chirality : 0.037 0.178 2067 Planarity : 0.005 0.064 1480 Dihedral : 28.439 73.547 3881 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.05 % Allowed : 24.71 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.28), residues: 878 helix: 2.38 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -0.12 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 30 TYR 0.013 0.002 TYR C 40 PHE 0.014 0.001 PHE H 71 TRP 0.006 0.002 TRP L 51 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00458 (13035) covalent geometry : angle 0.62510 (18661) hydrogen bonds : bond 0.04417 ( 807) hydrogen bonds : angle 3.36105 ( 2070) Misc. bond : bond 0.00044 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9276 (tt0) cc_final: 0.8859 (tp-100) REVERT: A 121 MET cc_start: 0.9096 (mmm) cc_final: 0.8483 (mmm) REVERT: A 126 GLN cc_start: 0.9312 (mt0) cc_final: 0.9070 (mt0) REVERT: B 89 TYR cc_start: 0.9276 (m-80) cc_final: 0.8838 (m-80) REVERT: B 98 LEU cc_start: 0.9576 (mm) cc_final: 0.9105 (mm) REVERT: C 90 ASN cc_start: 0.8261 (m-40) cc_final: 0.7793 (m-40) REVERT: C 102 THR cc_start: 0.9197 (m) cc_final: 0.8932 (p) REVERT: D 48 GLN cc_start: 0.9504 (tm-30) cc_final: 0.9133 (tm-30) REVERT: D 94 GLU cc_start: 0.9240 (mp0) cc_final: 0.8802 (mp0) REVERT: E 51 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8885 (tp30) REVERT: E 60 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: E 77 GLN cc_start: 0.9378 (tt0) cc_final: 0.8978 (tm-30) REVERT: E 91 MET cc_start: 0.9068 (mmm) cc_final: 0.8648 (mmt) REVERT: E 124 ASP cc_start: 0.9261 (m-30) cc_final: 0.8976 (m-30) REVERT: F 44 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8564 (p) REVERT: G 25 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8837 (mp10) REVERT: G 31 VAL cc_start: 0.9756 (t) cc_final: 0.9499 (p) REVERT: G 40 TYR cc_start: 0.9283 (m-80) cc_final: 0.8931 (m-80) REVERT: G 73 ASP cc_start: 0.8954 (m-30) cc_final: 0.8652 (m-30) REVERT: G 85 GLN cc_start: 0.9545 (tp-100) cc_final: 0.9192 (tp-100) REVERT: G 95 ASN cc_start: 0.9522 (t0) cc_final: 0.9126 (m-40) REVERT: G 102 THR cc_start: 0.9258 (m) cc_final: 0.8694 (p) REVERT: G 105 GLN cc_start: 0.9482 (mp10) cc_final: 0.9042 (mp10) REVERT: H 69 ASP cc_start: 0.9466 (t0) cc_final: 0.9234 (t0) REVERT: H 79 SER cc_start: 0.9802 (t) cc_final: 0.9511 (m) REVERT: H 94 GLU cc_start: 0.9351 (mp0) cc_final: 0.8998 (mp0) REVERT: H 106 GLU cc_start: 0.9257 (mp0) cc_final: 0.9023 (tt0) outliers start: 28 outliers final: 18 residues processed: 263 average time/residue: 0.0885 time to fit residues: 34.0850 Evaluate side-chains 250 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.066083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.043665 restraints weight = 58447.156| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.28 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13051 Z= 0.185 Angle : 0.625 14.350 18661 Z= 0.356 Chirality : 0.036 0.172 2067 Planarity : 0.005 0.054 1480 Dihedral : 28.384 73.693 3881 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.05 % Allowed : 25.29 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.28), residues: 878 helix: 2.25 (0.20), residues: 657 sheet: None (None), residues: 0 loop : 0.06 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 88 TYR 0.015 0.001 TYR C 40 PHE 0.028 0.002 PHE D 71 TRP 0.011 0.002 TRP L 51 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00406 (13035) covalent geometry : angle 0.62492 (18661) hydrogen bonds : bond 0.04180 ( 807) hydrogen bonds : angle 3.25221 ( 2070) Misc. bond : bond 0.00020 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9296 (tt0) cc_final: 0.8928 (tp-100) REVERT: A 120 ILE cc_start: 0.9034 (mm) cc_final: 0.8822 (mm) REVERT: A 121 MET cc_start: 0.9007 (mmm) cc_final: 0.8666 (mmm) REVERT: A 126 GLN cc_start: 0.9306 (mt0) cc_final: 0.8973 (mt0) REVERT: B 45 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8207 (mtpt) REVERT: B 85 MET cc_start: 0.9170 (tpp) cc_final: 0.8589 (mmm) REVERT: B 89 TYR cc_start: 0.8926 (m-80) cc_final: 0.8269 (m-80) REVERT: B 94 GLN cc_start: 0.9488 (mm-40) cc_final: 0.9009 (mm110) REVERT: C 39 ASN cc_start: 0.8944 (m-40) cc_final: 0.7659 (t0) REVERT: C 102 THR cc_start: 0.9207 (m) cc_final: 0.8952 (p) REVERT: D 48 GLN cc_start: 0.9525 (tm-30) cc_final: 0.9068 (tm-30) REVERT: D 60 MET cc_start: 0.9189 (tpp) cc_final: 0.8893 (tpp) REVERT: D 94 GLU cc_start: 0.9226 (mp0) cc_final: 0.8797 (mp0) REVERT: E 51 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8923 (tp30) REVERT: E 60 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8633 (pm20) REVERT: E 77 GLN cc_start: 0.9390 (tt0) cc_final: 0.8959 (tm-30) REVERT: E 91 MET cc_start: 0.9017 (mmm) cc_final: 0.8551 (mmt) REVERT: E 95 GLU cc_start: 0.9360 (tp30) cc_final: 0.9157 (tt0) REVERT: E 121 MET cc_start: 0.9168 (mmm) cc_final: 0.8748 (mmp) REVERT: F 44 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8696 (m) REVERT: G 31 VAL cc_start: 0.9720 (t) cc_final: 0.9461 (p) REVERT: G 40 TYR cc_start: 0.9283 (m-80) cc_final: 0.8923 (m-80) REVERT: G 73 ASP cc_start: 0.8987 (m-30) cc_final: 0.8676 (m-30) REVERT: G 85 GLN cc_start: 0.9575 (tp-100) cc_final: 0.9173 (tp-100) REVERT: G 95 ASN cc_start: 0.9488 (t0) cc_final: 0.9068 (m-40) REVERT: G 102 THR cc_start: 0.9224 (m) cc_final: 0.8567 (p) REVERT: G 105 GLN cc_start: 0.9475 (mp10) cc_final: 0.9065 (mp10) REVERT: H 69 ASP cc_start: 0.9460 (t0) cc_final: 0.9194 (t0) REVERT: H 79 SER cc_start: 0.9791 (t) cc_final: 0.9510 (m) REVERT: H 106 GLU cc_start: 0.9253 (mp0) cc_final: 0.9022 (tt0) outliers start: 28 outliers final: 21 residues processed: 272 average time/residue: 0.0871 time to fit residues: 34.7737 Evaluate side-chains 254 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.042290 restraints weight = 59247.655| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.25 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13051 Z= 0.237 Angle : 0.642 11.088 18661 Z= 0.372 Chirality : 0.038 0.183 2067 Planarity : 0.004 0.050 1480 Dihedral : 28.461 74.279 3881 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 5.06 % Allowed : 25.58 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.28), residues: 878 helix: 2.17 (0.20), residues: 655 sheet: None (None), residues: 0 loop : 0.05 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.022 0.002 TYR H 41 PHE 0.016 0.002 PHE L 90 TRP 0.013 0.002 TRP L 51 HIS 0.007 0.001 HIS L 105 Details of bonding type rmsd covalent geometry : bond 0.00526 (13035) covalent geometry : angle 0.64225 (18661) hydrogen bonds : bond 0.04564 ( 807) hydrogen bonds : angle 3.45916 ( 2070) Misc. bond : bond 0.00028 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9306 (tt0) cc_final: 0.8894 (tp-100) REVERT: A 126 GLN cc_start: 0.9310 (mt0) cc_final: 0.9089 (mt0) REVERT: B 45 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8577 (mtpt) REVERT: B 85 MET cc_start: 0.9194 (tpp) cc_final: 0.8603 (mmm) REVERT: B 89 TYR cc_start: 0.8807 (m-80) cc_final: 0.8003 (m-80) REVERT: B 94 GLN cc_start: 0.9497 (mm-40) cc_final: 0.8967 (mm110) REVERT: C 102 THR cc_start: 0.9304 (m) cc_final: 0.9014 (p) REVERT: D 48 GLN cc_start: 0.9567 (tm-30) cc_final: 0.9088 (tm-30) REVERT: D 94 GLU cc_start: 0.9204 (mp0) cc_final: 0.8784 (mp0) REVERT: D 114 GLU cc_start: 0.9435 (tp30) cc_final: 0.9197 (tp30) REVERT: D 116 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9028 (p) REVERT: E 51 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9089 (tp30) REVERT: E 60 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8573 (pm20) REVERT: E 77 GLN cc_start: 0.9396 (tt0) cc_final: 0.9012 (tm-30) REVERT: E 91 MET cc_start: 0.9025 (mmm) cc_final: 0.8767 (mmt) REVERT: E 121 MET cc_start: 0.9189 (mmm) cc_final: 0.8600 (mmp) REVERT: E 124 ASP cc_start: 0.9341 (m-30) cc_final: 0.8877 (m-30) REVERT: G 31 VAL cc_start: 0.9751 (t) cc_final: 0.9523 (p) REVERT: G 40 TYR cc_start: 0.9359 (m-80) cc_final: 0.9132 (m-80) REVERT: G 73 ASP cc_start: 0.9131 (m-30) cc_final: 0.8842 (m-30) REVERT: G 85 GLN cc_start: 0.9586 (tp-100) cc_final: 0.9232 (tp-100) REVERT: G 95 ASN cc_start: 0.9509 (t0) cc_final: 0.9079 (m-40) REVERT: G 105 GLN cc_start: 0.9518 (mp10) cc_final: 0.9077 (mp10) REVERT: H 69 ASP cc_start: 0.9456 (t0) cc_final: 0.9204 (t0) REVERT: H 79 SER cc_start: 0.9797 (t) cc_final: 0.9526 (m) REVERT: H 106 GLU cc_start: 0.9304 (mp0) cc_final: 0.9070 (tt0) outliers start: 35 outliers final: 22 residues processed: 243 average time/residue: 0.0971 time to fit residues: 34.4539 Evaluate side-chains 233 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 GLN G 74 ASN H 50 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043120 restraints weight = 58621.522| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.28 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13051 Z= 0.183 Angle : 0.623 10.189 18661 Z= 0.360 Chirality : 0.036 0.190 2067 Planarity : 0.004 0.058 1480 Dihedral : 28.409 74.720 3881 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.34 % Allowed : 27.89 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.28), residues: 878 helix: 2.14 (0.20), residues: 659 sheet: None (None), residues: 0 loop : 0.05 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 78 TYR 0.013 0.001 TYR H 43 PHE 0.014 0.001 PHE L 90 TRP 0.016 0.002 TRP L 51 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00407 (13035) covalent geometry : angle 0.62252 (18661) hydrogen bonds : bond 0.03980 ( 807) hydrogen bonds : angle 3.22362 ( 2070) Misc. bond : bond 0.00015 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9298 (tt0) cc_final: 0.8887 (tp-100) REVERT: A 126 GLN cc_start: 0.9237 (mt0) cc_final: 0.8979 (mt0) REVERT: B 45 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8363 (mtpt) REVERT: B 85 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8589 (mmm) REVERT: B 89 TYR cc_start: 0.8612 (m-80) cc_final: 0.7736 (m-80) REVERT: B 94 GLN cc_start: 0.9522 (mm-40) cc_final: 0.8982 (mm110) REVERT: C 102 THR cc_start: 0.9301 (m) cc_final: 0.9007 (p) REVERT: D 48 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9073 (tm-30) REVERT: D 60 MET cc_start: 0.9210 (tpp) cc_final: 0.8910 (tpp) REVERT: D 94 GLU cc_start: 0.9191 (mp0) cc_final: 0.8786 (mp0) REVERT: D 114 GLU cc_start: 0.9413 (tp30) cc_final: 0.9191 (tp30) REVERT: E 51 GLU cc_start: 0.9261 (mm-30) cc_final: 0.9002 (tp30) REVERT: E 60 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8537 (pm20) REVERT: E 77 GLN cc_start: 0.9381 (tt0) cc_final: 0.9041 (tm-30) REVERT: E 91 MET cc_start: 0.9031 (mmm) cc_final: 0.8539 (mmt) REVERT: E 95 GLU cc_start: 0.9347 (tp30) cc_final: 0.9121 (tt0) REVERT: E 121 MET cc_start: 0.9142 (mmm) cc_final: 0.8913 (mmm) REVERT: G 31 VAL cc_start: 0.9757 (t) cc_final: 0.9522 (p) REVERT: G 40 TYR cc_start: 0.9324 (m-80) cc_final: 0.9075 (m-80) REVERT: G 73 ASP cc_start: 0.9121 (m-30) cc_final: 0.8822 (m-30) REVERT: G 74 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8649 (t0) REVERT: G 85 GLN cc_start: 0.9593 (tp-100) cc_final: 0.9229 (tp-100) REVERT: G 95 ASN cc_start: 0.9510 (t0) cc_final: 0.9067 (m-40) REVERT: G 105 GLN cc_start: 0.9506 (mp10) cc_final: 0.9053 (mp10) REVERT: H 69 ASP cc_start: 0.9468 (t0) cc_final: 0.9182 (t0) REVERT: H 79 SER cc_start: 0.9792 (t) cc_final: 0.9527 (m) REVERT: H 94 GLU cc_start: 0.9297 (mp0) cc_final: 0.8945 (mp0) REVERT: H 106 GLU cc_start: 0.9283 (mp0) cc_final: 0.9051 (tt0) outliers start: 30 outliers final: 21 residues processed: 248 average time/residue: 0.0925 time to fit residues: 33.4351 Evaluate side-chains 245 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN H 50 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.081376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.062615 restraints weight = 90707.703| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.01 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13051 Z= 0.219 Angle : 0.646 10.503 18661 Z= 0.372 Chirality : 0.037 0.200 2067 Planarity : 0.004 0.054 1480 Dihedral : 28.404 74.866 3881 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.91 % Allowed : 28.18 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.28), residues: 878 helix: 2.11 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.00 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 78 TYR 0.014 0.001 TYR F 89 PHE 0.014 0.002 PHE L 90 TRP 0.014 0.002 TRP L 51 HIS 0.006 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00488 (13035) covalent geometry : angle 0.64584 (18661) hydrogen bonds : bond 0.04364 ( 807) hydrogen bonds : angle 3.39364 ( 2070) Misc. bond : bond 0.00018 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9311 (tt0) cc_final: 0.8911 (tp-100) REVERT: A 126 GLN cc_start: 0.9251 (mt0) cc_final: 0.8991 (mt0) REVERT: B 45 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8605 (mtpt) REVERT: B 85 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8539 (mmm) REVERT: B 89 TYR cc_start: 0.8610 (m-80) cc_final: 0.7716 (m-80) REVERT: B 94 GLN cc_start: 0.9498 (mm-40) cc_final: 0.8952 (mm110) REVERT: C 39 ASN cc_start: 0.8927 (m-40) cc_final: 0.7853 (t0) REVERT: C 102 THR cc_start: 0.9438 (m) cc_final: 0.9169 (p) REVERT: D 48 GLN cc_start: 0.9477 (tm-30) cc_final: 0.9188 (tm-30) REVERT: D 94 GLU cc_start: 0.9134 (mp0) cc_final: 0.8761 (mp0) REVERT: D 114 GLU cc_start: 0.9311 (tp30) cc_final: 0.9100 (tp30) REVERT: E 51 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8975 (tp30) REVERT: E 60 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: E 77 GLN cc_start: 0.9391 (tt0) cc_final: 0.9102 (tm-30) REVERT: E 91 MET cc_start: 0.8958 (mmm) cc_final: 0.8555 (mmt) REVERT: E 95 GLU cc_start: 0.9279 (tp30) cc_final: 0.8687 (tt0) REVERT: E 124 ASP cc_start: 0.8764 (m-30) cc_final: 0.8162 (m-30) REVERT: G 31 VAL cc_start: 0.9792 (t) cc_final: 0.9573 (p) REVERT: G 40 TYR cc_start: 0.9322 (m-80) cc_final: 0.9056 (m-80) REVERT: G 73 ASP cc_start: 0.9123 (m-30) cc_final: 0.8821 (m-30) REVERT: G 74 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8880 (t0) REVERT: G 85 GLN cc_start: 0.9574 (tp-100) cc_final: 0.9188 (tp-100) REVERT: G 95 ASN cc_start: 0.9508 (t0) cc_final: 0.9067 (m-40) REVERT: G 105 GLN cc_start: 0.9526 (mp10) cc_final: 0.9093 (mp10) REVERT: H 69 ASP cc_start: 0.9370 (t0) cc_final: 0.9087 (t0) REVERT: H 79 SER cc_start: 0.9780 (t) cc_final: 0.9527 (m) REVERT: H 94 GLU cc_start: 0.9225 (mp0) cc_final: 0.8911 (mp0) REVERT: H 106 GLU cc_start: 0.9398 (mp0) cc_final: 0.9154 (tt0) REVERT: H 114 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8820 (tp30) outliers start: 34 outliers final: 24 residues processed: 240 average time/residue: 0.0949 time to fit residues: 33.3967 Evaluate side-chains 239 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 56 GLN G 74 ASN H 50 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.082406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063906 restraints weight = 89998.139| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.01 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13051 Z= 0.175 Angle : 0.673 18.925 18661 Z= 0.379 Chirality : 0.037 0.204 2067 Planarity : 0.005 0.056 1480 Dihedral : 28.327 74.418 3881 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.34 % Allowed : 28.76 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.28), residues: 878 helix: 1.98 (0.20), residues: 665 sheet: None (None), residues: 0 loop : 0.09 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 88 TYR 0.014 0.001 TYR F 89 PHE 0.015 0.002 PHE L 90 TRP 0.011 0.002 TRP L 51 HIS 0.006 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00387 (13035) covalent geometry : angle 0.67341 (18661) hydrogen bonds : bond 0.03996 ( 807) hydrogen bonds : angle 3.19127 ( 2070) Misc. bond : bond 0.00011 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9294 (tt0) cc_final: 0.8870 (tp-100) REVERT: A 126 GLN cc_start: 0.9211 (mt0) cc_final: 0.8923 (mt0) REVERT: B 45 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8473 (mtpt) REVERT: B 85 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8593 (mmm) REVERT: B 89 TYR cc_start: 0.8494 (m-80) cc_final: 0.7526 (m-80) REVERT: C 39 ASN cc_start: 0.8850 (m-40) cc_final: 0.7867 (t0) REVERT: C 102 THR cc_start: 0.9407 (m) cc_final: 0.9133 (p) REVERT: D 48 GLN cc_start: 0.9486 (tm-30) cc_final: 0.9210 (tm-30) REVERT: D 94 GLU cc_start: 0.9149 (mp0) cc_final: 0.8788 (mp0) REVERT: E 51 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8630 (tp30) REVERT: E 60 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: E 77 GLN cc_start: 0.9368 (tt0) cc_final: 0.9138 (tm-30) REVERT: E 91 MET cc_start: 0.8910 (mmm) cc_final: 0.8525 (mmt) REVERT: E 95 GLU cc_start: 0.9242 (tp30) cc_final: 0.8688 (tt0) REVERT: E 121 MET cc_start: 0.9104 (mmm) cc_final: 0.8813 (mmp) REVERT: E 124 ASP cc_start: 0.8739 (m-30) cc_final: 0.8082 (m-30) REVERT: F 72 THR cc_start: 0.9651 (m) cc_final: 0.9447 (p) REVERT: G 31 VAL cc_start: 0.9784 (t) cc_final: 0.9558 (p) REVERT: G 73 ASP cc_start: 0.9130 (m-30) cc_final: 0.8839 (m-30) REVERT: G 74 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8888 (t0) REVERT: G 85 GLN cc_start: 0.9575 (tp-100) cc_final: 0.9175 (tp-100) REVERT: G 95 ASN cc_start: 0.9484 (t0) cc_final: 0.9029 (m-40) REVERT: G 105 GLN cc_start: 0.9504 (mp10) cc_final: 0.9071 (mp10) REVERT: H 69 ASP cc_start: 0.9386 (t0) cc_final: 0.9103 (t0) REVERT: H 79 SER cc_start: 0.9769 (t) cc_final: 0.9495 (m) REVERT: H 94 GLU cc_start: 0.9237 (mp0) cc_final: 0.8913 (mp0) REVERT: H 106 GLU cc_start: 0.9401 (mp0) cc_final: 0.9157 (tt0) REVERT: H 114 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8833 (tp30) outliers start: 30 outliers final: 22 residues processed: 247 average time/residue: 0.0982 time to fit residues: 35.6457 Evaluate side-chains 248 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 50 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.081651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.062840 restraints weight = 91044.889| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.06 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13051 Z= 0.210 Angle : 0.694 18.981 18661 Z= 0.392 Chirality : 0.038 0.253 2067 Planarity : 0.005 0.085 1480 Dihedral : 28.309 75.189 3881 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.05 % Allowed : 29.62 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.29), residues: 878 helix: 1.96 (0.20), residues: 664 sheet: None (None), residues: 0 loop : 0.02 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG L 57 TYR 0.017 0.002 TYR F 89 PHE 0.020 0.002 PHE L 48 TRP 0.019 0.003 TRP L 51 HIS 0.006 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00473 (13035) covalent geometry : angle 0.69418 (18661) hydrogen bonds : bond 0.04322 ( 807) hydrogen bonds : angle 3.30209 ( 2070) Misc. bond : bond 0.00016 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9245 (tt0) cc_final: 0.8871 (tp-100) REVERT: A 126 GLN cc_start: 0.9230 (mt0) cc_final: 0.8938 (mt0) REVERT: B 45 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8610 (mtpt) REVERT: B 85 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8557 (mmm) REVERT: B 89 TYR cc_start: 0.8548 (m-80) cc_final: 0.7590 (m-80) REVERT: C 102 THR cc_start: 0.9451 (m) cc_final: 0.9171 (p) REVERT: D 48 GLN cc_start: 0.9516 (tm-30) cc_final: 0.9251 (tm-30) REVERT: D 94 GLU cc_start: 0.9162 (mp0) cc_final: 0.8733 (mp0) REVERT: E 51 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8682 (tp30) REVERT: E 60 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: E 77 GLN cc_start: 0.9314 (tt0) cc_final: 0.9090 (tm-30) REVERT: E 91 MET cc_start: 0.8951 (mmm) cc_final: 0.8516 (mmt) REVERT: E 121 MET cc_start: 0.9106 (mmm) cc_final: 0.8880 (mmp) REVERT: E 124 ASP cc_start: 0.8766 (m-30) cc_final: 0.8144 (m-30) REVERT: F 72 THR cc_start: 0.9636 (m) cc_final: 0.9432 (p) REVERT: G 31 VAL cc_start: 0.9806 (t) cc_final: 0.9596 (p) REVERT: G 73 ASP cc_start: 0.9110 (m-30) cc_final: 0.8808 (m-30) REVERT: G 74 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8800 (t0) REVERT: G 85 GLN cc_start: 0.9579 (tp-100) cc_final: 0.9180 (tp-100) REVERT: G 95 ASN cc_start: 0.9482 (t0) cc_final: 0.8995 (m-40) REVERT: G 105 GLN cc_start: 0.9544 (mp10) cc_final: 0.9071 (mp10) REVERT: H 69 ASP cc_start: 0.9419 (t0) cc_final: 0.9133 (t0) REVERT: H 79 SER cc_start: 0.9789 (t) cc_final: 0.9535 (m) REVERT: H 94 GLU cc_start: 0.9240 (mp0) cc_final: 0.8894 (mp0) REVERT: H 114 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8842 (tp30) outliers start: 28 outliers final: 21 residues processed: 245 average time/residue: 0.0993 time to fit residues: 36.1197 Evaluate side-chains 245 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 74 optimal weight: 40.0000 chunk 111 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN H 50 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.082662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064152 restraints weight = 89351.357| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.05 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13051 Z= 0.173 Angle : 0.697 18.431 18661 Z= 0.387 Chirality : 0.037 0.204 2067 Planarity : 0.005 0.078 1480 Dihedral : 28.237 75.290 3881 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.61 % Allowed : 30.49 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.28), residues: 878 helix: 1.87 (0.20), residues: 664 sheet: None (None), residues: 0 loop : 0.02 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 57 TYR 0.013 0.001 TYR H 41 PHE 0.018 0.002 PHE L 90 TRP 0.015 0.003 TRP L 51 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00386 (13035) covalent geometry : angle 0.69685 (18661) hydrogen bonds : bond 0.03952 ( 807) hydrogen bonds : angle 3.18247 ( 2070) Misc. bond : bond 0.00008 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.77 seconds wall clock time: 38 minutes 48.85 seconds (2328.85 seconds total)