Starting phenix.real_space_refine on Fri Sep 11 22:23:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_10864.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_10864.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_10864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_10864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_10864.map" model { file = "/net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_10864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yov_10864/09_2026/6yov_10864.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 2.70, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 455.6 milliseconds 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: 2.04 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: 2.51 Time building geometry restraints manager: 1.38 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 1.20e-02 6.94e+03 1.92e+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: 16963 1.90 - 3.80: 1525 3.80 - 5.70: 136 5.70 - 7.60: 32 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=" O5' DG J 85 " pdb=" C5' DG J 85 " pdb=" C4' DG J 85 " ideal model delta sigma weight residual 109.40 103.66 5.74 8.00e-01 1.56e+00 5.16e+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 ... (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: 1343 0.060 - 0.120: 558 0.120 - 0.180: 144 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.012 0.171 13051 Z= 0.858 Angle : 1.132 9.504 18661 Z= 0.858 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 are 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/Z covalent geometry : bond 0.01105 / 0.64 (13035) covalent geometry : angle 1.13175 / 0.86 (18661) hydrogen bonds : bond 0.17012 / 11.69 ( 807) hydrogen bonds : angle 5.74699 / 4.18 ( 2070) Misc. bond : bond 0.16313 / 12.43 ( 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 : 0.288 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 107 ASP cc_start: 0.8372 (m-30) cc_final: 0.8107 (m-30) REVERT: A 121 MET cc_start: 0.8920 (mmm) cc_final: 0.8649 (mmm) REVERT: A 124 ASP cc_start: 0.8083 (m-30) cc_final: 0.7835 (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: 0.8343 (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: 0.9157 (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: 0.0938 time to fit residues: 48.5888 Evaluate side-chains 251 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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: 20.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 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: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.070343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.047947 restraints weight = 56695.534| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.38 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13051 Z= 0.213 Angle : 0.774 12.067 18661 Z= 0.444 Chirality : 0.048 0.208 2067 Planarity : 0.006 0.046 1480 Dihedral : 28.721 78.392 3881 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 4.62 % Allowed : 17.49 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.27), residues: 878 helix: 1.90 (0.19), residues: 662 sheet: None (None), residues: 0 loop : 0.11 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 57 TYR 0.025 0.003 TYR G 40 PHE 0.024 0.003 PHE B 62 TRP 0.009 0.003 TRP L 51 HIS 0.015 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (13035) covalent geometry : angle 0.77364 / 0.44 (18661) hydrogen bonds : bond 0.07322 / 5.06 ( 807) hydrogen bonds : angle 3.97474 / 2.83 ( 2070) Misc. bond : bond 0.00890 / 0.59 ( 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 314 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 0.269 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: A 91 MET cc_start: 0.9304 (mmm) cc_final: 0.9059 (mmm) REVERT: A 121 MET cc_start: 0.9038 (mmm) cc_final: 0.8707 (mmm) REVERT: C 26 PHE cc_start: 0.8999 (m-10) cc_final: 0.8751 (m-80) REVERT: C 57 GLU cc_start: 0.8912 (tt0) cc_final: 0.8594 (tt0) REVERT: C 60 THR cc_start: 0.9654 (m) cc_final: 0.9454 (p) REVERT: C 102 THR cc_start: 0.8753 (m) cc_final: 0.8391 (p) REVERT: D 88 SER cc_start: 0.8616 (p) cc_final: 0.7648 (p) REVERT: D 94 GLU cc_start: 0.9456 (mp0) cc_final: 0.9124 (mp0) REVERT: E 59 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9026 (t) REVERT: E 77 GLN cc_start: 0.9331 (tt0) cc_final: 0.8916 (tp40) REVERT: E 91 MET cc_start: 0.9081 (mmm) cc_final: 0.8812 (mmt) REVERT: E 124 ASP cc_start: 0.8890 (m-30) cc_final: 0.8558 (m-30) REVERT: F 26 ASN cc_start: 0.8648 (m-40) cc_final: 0.8234 (m110) REVERT: F 58 VAL cc_start: 0.9603 (t) cc_final: 0.9329 (p) REVERT: G 57 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8625 (tt0) REVERT: G 102 THR cc_start: 0.8764 (m) cc_final: 0.8403 (p) REVERT: H 94 GLU cc_start: 0.9477 (mp0) cc_final: 0.9128 (mp0) outliers start: 32 outliers final: 13 residues processed: 294 average time/residue: 0.0897 time to fit residues: 39.6872 Evaluate side-chains 257 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 67 ILE 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 63 ILE Chi-restraints excluded: chain G residue 80 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 50.0000 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 82 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 2 optimal weight: 0.0870 chunk 93 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 overall best weight: 2.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN F 26 ASN ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.068767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046187 restraints weight = 58887.142| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.38 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13051 Z= 0.194 Angle : 0.700 9.826 18661 Z= 0.411 Chirality : 0.044 0.218 2067 Planarity : 0.005 0.044 1480 Dihedral : 28.876 74.256 3881 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.91 % Allowed : 20.23 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.27), residues: 878 helix: 1.93 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.19 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG L 53 TYR 0.019 0.002 TYR H 84 PHE 0.016 0.003 PHE E 68 TRP 0.010 0.003 TRP L 51 HIS 0.009 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (13035) covalent geometry : angle 0.70014 / 0.41 (18661) hydrogen bonds : bond 0.06152 / 4.29 ( 807) hydrogen bonds : angle 3.78219 / 2.68 ( 2070) Misc. bond : bond 0.00326 / 0.31 ( 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: 34 poor density : 268 time to evaluate : 0.333 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: symmetry clash REVERT: A 111 CYS cc_start: 0.9380 (m) cc_final: 0.9054 (m) REVERT: A 121 MET cc_start: 0.9051 (mmm) cc_final: 0.8738 (mmm) REVERT: B 98 LEU cc_start: 0.9529 (mm) cc_final: 0.9280 (mm) REVERT: C 60 THR cc_start: 0.9634 (m) cc_final: 0.9410 (p) REVERT: C 102 THR cc_start: 0.8805 (m) cc_final: 0.8583 (p) REVERT: D 48 GLN cc_start: 0.9406 (tp40) cc_final: 0.9021 (tm-30) REVERT: D 94 GLU cc_start: 0.9422 (mp0) cc_final: 0.8810 (mp0) REVERT: E 60 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: E 91 MET cc_start: 0.9164 (mmm) cc_final: 0.8770 (mmt) REVERT: E 124 ASP cc_start: 0.9039 (m-30) cc_final: 0.8696 (m-30) REVERT: F 25 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8716 (t0) REVERT: F 58 VAL cc_start: 0.9561 (t) cc_final: 0.9301 (p) REVERT: G 40 TYR cc_start: 0.9200 (m-80) cc_final: 0.8564 (m-80) REVERT: G 102 THR cc_start: 0.8888 (m) cc_final: 0.8444 (p) REVERT: H 69 ASP cc_start: 0.9445 (t0) cc_final: 0.9145 (t0) REVERT: H 106 GLU cc_start: 0.9262 (mp0) cc_final: 0.9048 (tt0) REVERT: H 114 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8971 (mm-30) outliers start: 34 outliers final: 20 residues processed: 280 average time/residue: 0.0910 time to fit residues: 38.3601 Evaluate side-chains 261 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 GLU 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 88 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 75 optimal weight: 50.0000 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 86 optimal weight: 50.0000 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.067671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.045220 restraints weight = 58580.253| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.28 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13051 Z= 0.189 Angle : 0.667 9.751 18661 Z= 0.391 Chirality : 0.041 0.162 2067 Planarity : 0.004 0.038 1480 Dihedral : 28.963 73.053 3881 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 4.62 % Allowed : 20.23 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.28), residues: 878 helix: 1.90 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 129 TYR 0.017 0.002 TYR D 43 PHE 0.017 0.002 PHE F 101 TRP 0.008 0.002 TRP L 51 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 (13035) covalent geometry : angle 0.66708 / 0.39 (18661) hydrogen bonds : bond 0.05496 / 3.84 ( 807) hydrogen bonds : angle 3.67739 / 2.61 ( 2070) Misc. bond : bond 0.00305 / 0.30 ( 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 285 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 CYS cc_start: 0.9413 (m) cc_final: 0.9103 (m) REVERT: A 121 MET cc_start: 0.9104 (mmm) cc_final: 0.8764 (mmm) REVERT: A 126 GLN cc_start: 0.9394 (mt0) cc_final: 0.9134 (mt0) REVERT: C 57 GLU cc_start: 0.8956 (tt0) cc_final: 0.8754 (tt0) REVERT: C 90 ASN cc_start: 0.7709 (m-40) cc_final: 0.7355 (m-40) REVERT: C 102 THR cc_start: 0.9007 (m) cc_final: 0.8760 (p) REVERT: D 48 GLN cc_start: 0.9503 (tp40) cc_final: 0.9074 (tm-30) REVERT: D 94 GLU cc_start: 0.9396 (mp0) cc_final: 0.8836 (mp0) REVERT: E 51 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8784 (mm-30) REVERT: E 60 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8657 (pm20) REVERT: E 77 GLN cc_start: 0.9393 (tt0) cc_final: 0.8943 (tp40) REVERT: E 91 MET cc_start: 0.9159 (mmm) cc_final: 0.8708 (mmt) REVERT: E 95 GLU cc_start: 0.9517 (tp30) cc_final: 0.9194 (tt0) REVERT: E 124 ASP cc_start: 0.9026 (m-30) cc_final: 0.8770 (m-30) REVERT: G 40 TYR cc_start: 0.9283 (m-80) cc_final: 0.8730 (m-80) REVERT: H 69 ASP cc_start: 0.9502 (t0) cc_final: 0.9209 (t0) REVERT: H 114 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8985 (mm-30) outliers start: 32 outliers final: 22 residues processed: 267 average time/residue: 0.0857 time to fit residues: 34.2762 Evaluate side-chains 249 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 65 SER 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 90 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 59 LEU 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 80 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 50.0000 chunk 3 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 110 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.066982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.043832 restraints weight = 59368.727| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.30 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13051 Z= 0.216 Angle : 0.687 12.000 18661 Z= 0.401 Chirality : 0.042 0.251 2067 Planarity : 0.005 0.053 1480 Dihedral : 29.046 73.570 3881 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.77 % Allowed : 22.54 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.28), residues: 878 helix: 1.83 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.22 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 57 TYR 0.017 0.002 TYR B 89 PHE 0.023 0.002 PHE F 101 TRP 0.019 0.004 TRP L 51 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.22 (13035) covalent geometry : angle 0.68748 / 0.40 (18661) hydrogen bonds : bond 0.05474 / 3.80 ( 807) hydrogen bonds : angle 3.75337 / 2.65 ( 2070) Misc. bond : bond 0.00096 / 0.09 ( 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 272 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.340 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 111 CYS cc_start: 0.9375 (m) cc_final: 0.9069 (m) REVERT: A 121 MET cc_start: 0.9138 (mmm) cc_final: 0.8844 (mmm) REVERT: A 126 GLN cc_start: 0.9406 (mt0) cc_final: 0.9137 (mt0) REVERT: B 85 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8179 (tpp) REVERT: B 89 TYR cc_start: 0.9256 (m-80) cc_final: 0.8633 (m-80) REVERT: C 90 ASN cc_start: 0.7777 (m-40) cc_final: 0.7381 (m-40) REVERT: C 102 THR cc_start: 0.9150 (m) cc_final: 0.8915 (p) REVERT: C 116 LEU cc_start: 0.8824 (mm) cc_final: 0.8541 (mm) REVERT: D 48 GLN cc_start: 0.9506 (tp40) cc_final: 0.9082 (tm-30) REVERT: D 116 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8639 (p) REVERT: E 51 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8809 (mm-30) REVERT: E 60 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: E 77 GLN cc_start: 0.9396 (tt0) cc_final: 0.9000 (tp40) REVERT: E 91 MET cc_start: 0.9206 (mmm) cc_final: 0.8811 (mmt) REVERT: E 111 CYS cc_start: 0.9183 (m) cc_final: 0.8950 (t) REVERT: E 124 ASP cc_start: 0.9070 (m-30) cc_final: 0.8123 (m-30) REVERT: F 25 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8854 (t0) REVERT: G 25 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8703 (mp10) REVERT: G 31 VAL cc_start: 0.9722 (t) cc_final: 0.9426 (p) REVERT: G 40 TYR cc_start: 0.9310 (m-80) cc_final: 0.8830 (m-80) REVERT: G 65 GLU cc_start: 0.9248 (tm-30) cc_final: 0.9047 (pp20) REVERT: G 73 ASP cc_start: 0.8623 (m-30) cc_final: 0.8312 (m-30) REVERT: G 102 THR cc_start: 0.9069 (m) cc_final: 0.8601 (p) REVERT: H 69 ASP cc_start: 0.9494 (t0) cc_final: 0.9204 (t0) REVERT: H 106 GLU cc_start: 0.9264 (mp0) cc_final: 0.9041 (tt0) REVERT: H 114 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8970 (mm-30) outliers start: 33 outliers final: 22 residues processed: 257 average time/residue: 0.0858 time to fit residues: 33.3976 Evaluate side-chains 251 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER 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 C residue 63 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 102 LEU 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 90 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 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 80 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 68 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 70 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN E 94 GLN F 26 ASN F 28 GLN G 32 HIS G 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.066889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.044220 restraints weight = 59107.081| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.24 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13051 Z= 0.173 Angle : 0.667 9.444 18661 Z= 0.390 Chirality : 0.041 0.169 2067 Planarity : 0.004 0.051 1480 Dihedral : 29.015 73.787 3881 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.34 % Allowed : 24.86 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.28), residues: 878 helix: 1.87 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.25 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 88 TYR 0.019 0.002 TYR D 43 PHE 0.019 0.002 PHE F 62 TRP 0.012 0.003 TRP L 51 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (13035) covalent geometry : angle 0.66728 / 0.39 (18661) hydrogen bonds : bond 0.05059 / 3.50 ( 807) hydrogen bonds : angle 3.64359 / 2.58 ( 2070) Misc. bond : bond 0.00021 / 0.02 ( 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 279 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 0.313 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 121 MET cc_start: 0.9114 (mmm) cc_final: 0.8815 (mmm) REVERT: A 126 GLN cc_start: 0.9400 (mt0) cc_final: 0.9127 (mt0) REVERT: A 127 LEU cc_start: 0.9476 (tp) cc_final: 0.9270 (tp) REVERT: B 85 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.7702 (tpp) REVERT: B 89 TYR cc_start: 0.9233 (m-80) cc_final: 0.8373 (m-80) REVERT: C 90 ASN cc_start: 0.7887 (m-40) cc_final: 0.7472 (m-40) REVERT: C 102 THR cc_start: 0.9077 (m) cc_final: 0.8876 (p) REVERT: D 48 GLN cc_start: 0.9551 (tp40) cc_final: 0.9110 (tm-30) REVERT: D 84 TYR cc_start: 0.8310 (t80) cc_final: 0.7830 (t80) REVERT: E 51 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8803 (mm-30) REVERT: E 60 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: E 77 GLN cc_start: 0.9392 (tt0) cc_final: 0.8888 (tm-30) REVERT: E 91 MET cc_start: 0.9242 (mmm) cc_final: 0.8874 (mmt) REVERT: E 124 ASP cc_start: 0.9131 (m-30) cc_final: 0.8836 (m-30) REVERT: F 25 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8936 (t0) REVERT: G 31 VAL cc_start: 0.9720 (t) cc_final: 0.9441 (p) REVERT: G 40 TYR cc_start: 0.9270 (m-80) cc_final: 0.8756 (m-80) REVERT: G 73 ASP cc_start: 0.8671 (m-30) cc_final: 0.8378 (m-30) REVERT: G 102 THR cc_start: 0.8945 (m) cc_final: 0.8479 (p) REVERT: H 69 ASP cc_start: 0.9542 (t0) cc_final: 0.9235 (t0) REVERT: H 106 GLU cc_start: 0.9236 (mp0) cc_final: 0.9001 (tt0) REVERT: H 114 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8979 (mm-30) outliers start: 30 outliers final: 19 residues processed: 264 average time/residue: 0.0882 time to fit residues: 34.7818 Evaluate side-chains 250 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 63 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 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 F residue 25 ASP Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 LEU 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 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 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.066923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044161 restraints weight = 59160.757| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.23 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13051 Z= 0.165 Angle : 0.683 12.121 18661 Z= 0.395 Chirality : 0.041 0.191 2067 Planarity : 0.004 0.053 1480 Dihedral : 28.988 73.839 3881 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.34 % Allowed : 26.30 % 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 are not related in a simple way. whole: 1.86 (0.28), residues: 878 helix: 1.77 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 88 TYR 0.017 0.002 TYR D 43 PHE 0.017 0.002 PHE F 62 TRP 0.017 0.004 TRP L 51 HIS 0.008 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (13035) covalent geometry : angle 0.68279 / 0.39 (18661) hydrogen bonds : bond 0.04887 / 3.37 ( 807) hydrogen bonds : angle 3.60866 / 2.55 ( 2070) Misc. bond : bond 0.00054 / 0.05 ( 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 270 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9112 (mmm) cc_final: 0.8807 (mmm) REVERT: A 126 GLN cc_start: 0.9393 (mt0) cc_final: 0.9103 (mt0) REVERT: B 85 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.7901 (tpp) REVERT: B 89 TYR cc_start: 0.9241 (m-80) cc_final: 0.8448 (m-80) REVERT: C 90 ASN cc_start: 0.7969 (m-40) cc_final: 0.7529 (m-40) REVERT: C 116 LEU cc_start: 0.8721 (mm) cc_final: 0.8449 (mm) REVERT: D 48 GLN cc_start: 0.9549 (tp40) cc_final: 0.9103 (tm-30) REVERT: D 94 GLU cc_start: 0.9301 (mp0) cc_final: 0.8838 (mp0) REVERT: E 51 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8820 (mm-30) REVERT: E 56 GLN cc_start: 0.9254 (mt0) cc_final: 0.8964 (mt0) REVERT: E 60 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8710 (pm20) REVERT: E 77 GLN cc_start: 0.9389 (tt0) cc_final: 0.8887 (tm-30) REVERT: E 91 MET cc_start: 0.9212 (mmm) cc_final: 0.8790 (mmt) REVERT: E 124 ASP cc_start: 0.9122 (m-30) cc_final: 0.8858 (m-30) REVERT: G 31 VAL cc_start: 0.9742 (t) cc_final: 0.9472 (p) REVERT: G 73 ASP cc_start: 0.8696 (m-30) cc_final: 0.8416 (m-30) REVERT: H 69 ASP cc_start: 0.9546 (t0) cc_final: 0.9216 (t0) REVERT: H 94 GLU cc_start: 0.9398 (mp0) cc_final: 0.8969 (mp0) REVERT: H 106 GLU cc_start: 0.9246 (mp0) cc_final: 0.9011 (tt0) REVERT: H 114 GLU cc_start: 0.9403 (mm-30) cc_final: 0.8948 (mm-30) outliers start: 30 outliers final: 21 residues processed: 256 average time/residue: 0.0921 time to fit residues: 35.4335 Evaluate side-chains 249 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 102 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 80 LYS Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 LEU 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 80 ILE Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.067032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045433 restraints weight = 57526.829| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.33 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13051 Z= 0.163 Angle : 0.684 11.102 18661 Z= 0.394 Chirality : 0.040 0.191 2067 Planarity : 0.004 0.053 1480 Dihedral : 28.959 73.757 3881 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.61 % Allowed : 28.47 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.28), residues: 878 helix: 1.68 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 57 TYR 0.015 0.002 TYR A 42 PHE 0.021 0.002 PHE D 71 TRP 0.018 0.003 TRP L 51 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (13035) covalent geometry : angle 0.68387 / 0.39 (18661) hydrogen bonds : bond 0.04769 / 3.29 ( 807) hydrogen bonds : angle 3.56935 / 2.52 ( 2070) Misc. bond : bond 0.00024 / 0.02 ( 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 256 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.327 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 121 MET cc_start: 0.9118 (mmm) cc_final: 0.8818 (mmm) REVERT: A 126 GLN cc_start: 0.9368 (mt0) cc_final: 0.9119 (mt0) REVERT: B 63 LEU cc_start: 0.9399 (tt) cc_final: 0.9151 (tt) REVERT: B 85 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: B 89 TYR cc_start: 0.8920 (m-80) cc_final: 0.8391 (m-80) REVERT: C 90 ASN cc_start: 0.8063 (m-40) cc_final: 0.7572 (m-40) REVERT: C 116 LEU cc_start: 0.8725 (mm) cc_final: 0.8448 (mm) REVERT: D 48 GLN cc_start: 0.9535 (tp40) cc_final: 0.9118 (tm-30) REVERT: D 84 TYR cc_start: 0.7987 (t80) cc_final: 0.7339 (t80) REVERT: D 94 GLU cc_start: 0.9281 (mp0) cc_final: 0.8837 (mp0) REVERT: E 51 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8868 (tp30) REVERT: E 60 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8715 (pm20) REVERT: E 77 GLN cc_start: 0.9375 (tt0) cc_final: 0.8928 (tm-30) REVERT: E 91 MET cc_start: 0.9187 (mmm) cc_final: 0.8743 (mmt) REVERT: E 124 ASP cc_start: 0.9098 (m-30) cc_final: 0.8812 (m-30) REVERT: G 31 VAL cc_start: 0.9747 (t) cc_final: 0.9484 (p) REVERT: G 65 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8962 (pp20) REVERT: G 73 ASP cc_start: 0.8684 (m-30) cc_final: 0.8377 (m-30) REVERT: G 85 GLN cc_start: 0.9549 (tp-100) cc_final: 0.9005 (tp-100) REVERT: H 69 ASP cc_start: 0.9526 (t0) cc_final: 0.9201 (t0) REVERT: H 106 GLU cc_start: 0.9245 (mp0) cc_final: 0.9006 (tt0) REVERT: H 114 GLU cc_start: 0.9389 (mm-30) cc_final: 0.8939 (mm-30) outliers start: 25 outliers final: 17 residues processed: 244 average time/residue: 0.0878 time to fit residues: 32.1771 Evaluate side-chains 243 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 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 97 CYS Chi-restraints excluded: chain F residue 50 LEU 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 H residue 47 LYS 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: 1.9990 chunk 112 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043317 restraints weight = 59876.906| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.33 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13051 Z= 0.216 Angle : 0.714 11.425 18661 Z= 0.411 Chirality : 0.041 0.192 2067 Planarity : 0.005 0.052 1480 Dihedral : 29.017 73.474 3881 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.90 % Allowed : 28.03 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.28), residues: 878 helix: 1.63 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.15 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 88 TYR 0.021 0.002 TYR C 40 PHE 0.021 0.002 PHE F 62 TRP 0.010 0.002 TRP L 51 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 (13035) covalent geometry : angle 0.71383 / 0.41 (18661) hydrogen bonds : bond 0.05101 / 3.52 ( 807) hydrogen bonds : angle 3.76698 / 2.66 ( 2070) Misc. bond : bond 0.00023 / 0.02 ( 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 245 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.313 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 121 MET cc_start: 0.9119 (mmm) cc_final: 0.8874 (mmm) REVERT: A 126 GLN cc_start: 0.9368 (mt0) cc_final: 0.9095 (mt0) REVERT: B 63 LEU cc_start: 0.9455 (tt) cc_final: 0.9227 (tt) REVERT: B 85 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.7899 (tpp) REVERT: B 89 TYR cc_start: 0.8990 (m-80) cc_final: 0.8343 (m-80) REVERT: C 90 ASN cc_start: 0.8300 (m-40) cc_final: 0.7788 (m-40) REVERT: C 116 LEU cc_start: 0.8788 (mm) cc_final: 0.8534 (mm) REVERT: D 48 GLN cc_start: 0.9535 (tp40) cc_final: 0.9114 (tm-30) REVERT: D 84 TYR cc_start: 0.8135 (t80) cc_final: 0.7544 (t80) REVERT: D 94 GLU cc_start: 0.9260 (mp0) cc_final: 0.8812 (mp0) REVERT: E 51 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8952 (tp30) REVERT: E 60 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8691 (pm20) REVERT: E 77 GLN cc_start: 0.9384 (tt0) cc_final: 0.8901 (tm-30) REVERT: E 91 MET cc_start: 0.9111 (mmm) cc_final: 0.8800 (mmt) REVERT: E 124 ASP cc_start: 0.9131 (m-30) cc_final: 0.8874 (m-30) REVERT: G 65 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8877 (pp20) REVERT: G 73 ASP cc_start: 0.8811 (m-30) cc_final: 0.8524 (m-30) REVERT: G 85 GLN cc_start: 0.9556 (tp-100) cc_final: 0.9004 (tp-100) REVERT: G 95 ASN cc_start: 0.9462 (t0) cc_final: 0.9057 (m-40) REVERT: H 69 ASP cc_start: 0.9541 (t0) cc_final: 0.9328 (t0) REVERT: H 106 GLU cc_start: 0.9273 (mp0) cc_final: 0.9033 (tt0) REVERT: H 114 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8930 (tp30) outliers start: 27 outliers final: 19 residues processed: 234 average time/residue: 0.0886 time to fit residues: 30.8702 Evaluate side-chains 234 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 50 LEU 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 H residue 47 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.066404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.045333 restraints weight = 58917.999| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.38 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13051 Z= 0.164 Angle : 0.706 11.362 18661 Z= 0.405 Chirality : 0.041 0.205 2067 Planarity : 0.004 0.053 1480 Dihedral : 28.985 73.895 3881 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.75 % Allowed : 30.20 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.28), residues: 878 helix: 1.57 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 88 TYR 0.019 0.002 TYR C 40 PHE 0.031 0.002 PHE D 71 TRP 0.018 0.003 TRP L 51 HIS 0.006 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (13035) covalent geometry : angle 0.70584 / 0.41 (18661) hydrogen bonds : bond 0.04780 / 3.27 ( 807) hydrogen bonds : angle 3.61961 / 2.55 ( 2070) Misc. bond : bond 0.00010 / 0.01 ( 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 250 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9108 (mmm) cc_final: 0.8801 (mmm) REVERT: A 126 GLN cc_start: 0.9352 (mt0) cc_final: 0.9080 (mt0) REVERT: B 45 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8210 (mtpt) REVERT: B 63 LEU cc_start: 0.9404 (tt) cc_final: 0.9188 (tt) REVERT: B 85 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.7843 (tpp) REVERT: B 89 TYR cc_start: 0.8938 (m-80) cc_final: 0.8256 (m-80) REVERT: C 90 ASN cc_start: 0.8386 (m-40) cc_final: 0.7893 (m-40) REVERT: C 116 LEU cc_start: 0.8727 (mm) cc_final: 0.8474 (mm) REVERT: D 48 GLN cc_start: 0.9545 (tp40) cc_final: 0.9143 (tm-30) REVERT: D 84 TYR cc_start: 0.8075 (t80) cc_final: 0.7554 (t80) REVERT: D 94 GLU cc_start: 0.9249 (mp0) cc_final: 0.8815 (mp0) REVERT: E 51 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8924 (tp30) REVERT: E 60 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: E 77 GLN cc_start: 0.9373 (tt0) cc_final: 0.8916 (tm-30) REVERT: E 91 MET cc_start: 0.9169 (mmm) cc_final: 0.8812 (mmt) REVERT: E 124 ASP cc_start: 0.9114 (m-30) cc_final: 0.8843 (m-30) REVERT: G 65 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8841 (pp20) REVERT: G 73 ASP cc_start: 0.8800 (m-30) cc_final: 0.8515 (m-30) REVERT: G 85 GLN cc_start: 0.9552 (tp-100) cc_final: 0.9222 (tp-100) REVERT: G 95 ASN cc_start: 0.9445 (t0) cc_final: 0.9023 (m-40) REVERT: H 69 ASP cc_start: 0.9544 (t0) cc_final: 0.9340 (t0) REVERT: H 94 GLU cc_start: 0.9364 (mp0) cc_final: 0.8972 (mp0) REVERT: H 106 GLU cc_start: 0.9249 (mp0) cc_final: 0.9012 (tt0) REVERT: H 114 GLU cc_start: 0.9415 (mm-30) cc_final: 0.8905 (tp30) outliers start: 19 outliers final: 14 residues processed: 241 average time/residue: 0.0898 time to fit residues: 32.5235 Evaluate side-chains 237 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 50 LEU 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 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: 3.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.066613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.043827 restraints weight = 58866.041| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.34 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13051 Z= 0.197 Angle : 0.728 13.813 18661 Z= 0.415 Chirality : 0.041 0.227 2067 Planarity : 0.005 0.053 1480 Dihedral : 28.993 73.583 3881 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.89 % Allowed : 29.91 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.28), residues: 878 helix: 1.55 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 88 TYR 0.038 0.002 TYR E 100 PHE 0.027 0.002 PHE F 62 TRP 0.016 0.003 TRP L 51 HIS 0.014 0.002 HIS L 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (13035) covalent geometry : angle 0.72826 / 0.41 (18661) hydrogen bonds : bond 0.04912 / 3.38 ( 807) hydrogen bonds : angle 3.70956 / 2.62 ( 2070) Misc. bond : bond 0.00018 / 0.01 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.20 seconds wall clock time: 36 minutes 12.17 seconds (2172.17 seconds total)