Starting phenix.real_space_refine on Tue Jun 10 19:58:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yov_10864/06_2025/6yov_10864.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yov_10864/06_2025/6yov_10864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yov_10864/06_2025/6yov_10864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yov_10864/06_2025/6yov_10864.map" model { file = "/net/cci-nas-00/data/ceres_data/6yov_10864/06_2025/6yov_10864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yov_10864/06_2025/6yov_10864.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 3} 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-2': 2, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 2, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 7.25, per 1000 atoms: 0.59 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: 2.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.48 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: 4.22 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2001 1.32 - 1.45: 4464 1.45 - 1.57: 6014 1.57 - 1.69: 522 1.69 - 1.81: 34 Bond restraints: 13035 Sorted by residual: bond pdb=" CA ASN F 26 " pdb=" C ASN F 26 " ideal model delta sigma weight residual 1.522 1.601 -0.079 1.37e-02 5.33e+03 3.32e+01 bond pdb=" O3' DT J 84 " pdb=" P DG J 85 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.23e+01 bond pdb=" CD ARG B 40 " pdb=" NE ARG B 40 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.88e+00 bond pdb=" NE ARG B 24 " pdb=" CZ ARG B 24 " ideal model delta sigma weight residual 1.326 1.360 -0.034 1.10e-02 8.26e+03 9.81e+00 ... (remaining 13030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 16948 1.90 - 3.80: 1530 3.80 - 5.70: 145 5.70 - 7.60: 33 7.60 - 9.50: 5 Bond angle restraints: 18661 Sorted by residual: angle pdb=" N LYS L 42 " pdb=" CA LYS L 42 " pdb=" C LYS L 42 " ideal model delta sigma weight residual 110.53 120.03 -9.50 1.29e+00 6.01e-01 5.43e+01 angle pdb=" C HIS L 105 " pdb=" N PRO L 106 " pdb=" CA PRO L 106 " ideal model delta sigma weight residual 119.47 127.73 -8.26 1.16e+00 7.43e-01 5.07e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.56 126.55 -6.99 1.02e+00 9.61e-01 4.70e+01 angle pdb=" C HIS H 50 " pdb=" N PRO H 51 " pdb=" CA PRO H 51 " ideal model delta sigma weight residual 119.56 126.48 -6.92 1.02e+00 9.61e-01 4.61e+01 angle pdb=" C LEU H 103 " pdb=" N PRO H 104 " pdb=" CA PRO H 104 " ideal model delta sigma weight residual 120.31 126.68 -6.37 9.80e-01 1.04e+00 4.23e+01 ... (remaining 18656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5050 17.90 - 35.81: 948 35.81 - 53.71: 831 53.71 - 71.61: 260 71.61 - 89.52: 12 Dihedral angle restraints: 7101 sinusoidal: 4631 harmonic: 2470 Sorted by residual: dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C ASN F 26 " pdb=" N ASN F 26 " pdb=" CA ASN F 26 " pdb=" CB ASN F 26 " ideal model delta harmonic sigma weight residual -122.60 -131.46 8.86 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 7098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1339 0.060 - 0.120: 573 0.120 - 0.180: 133 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA GLN L 61 " pdb=" N GLN L 61 " pdb=" C GLN L 61 " pdb=" CB GLN L 61 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA LEU E 66 " pdb=" N LEU E 66 " pdb=" C LEU E 66 " pdb=" CB LEU E 66 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG L 88 " pdb=" N ARG L 88 " pdb=" C ARG L 88 " pdb=" CB ARG L 88 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2064 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 55 " 0.074 2.00e-02 2.50e+03 4.04e-02 3.27e+01 pdb=" CG TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 55 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 55 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 55 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 55 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 55 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 41 " 0.072 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR H 41 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 41 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR H 41 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR H 41 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR H 41 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 41 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 41 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 55 " -0.064 2.00e-02 2.50e+03 3.32e-02 2.20e+01 pdb=" CG TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 55 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 55 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 55 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 55 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 55 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 55 " -0.045 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 4200 2.90 - 3.40: 10733 3.40 - 3.90: 24145 3.90 - 4.40: 28333 4.40 - 4.90: 37125 Nonbonded interactions: 104536 Sorted by model distance: nonbonded pdb=" N GLU G 42 " pdb=" OE1 GLU G 42 " model vdw 2.395 3.120 nonbonded pdb=" O2 DT I 125 " pdb=" OG SER L 72 " model vdw 2.399 3.040 nonbonded pdb=" OG SER G 19 " pdb=" O PHE G 26 " model vdw 2.404 3.040 nonbonded pdb=" OG1 THR C 77 " pdb=" OP1 DG J 133 " model vdw 2.407 3.040 nonbonded pdb=" NH2 ARG A 54 " pdb=" OH TYR A 55 " model vdw 2.462 3.120 ... (remaining 104531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 23 through 102 or resid 201)) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 9 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 34 through 125 or resid 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.830 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.171 13051 Z= 0.827 Angle : 1.137 9.504 18661 Z= 0.776 Chirality : 0.067 0.300 2067 Planarity : 0.009 0.046 1480 Dihedral : 25.194 89.518 5551 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.007 TRP L 79 HIS 0.010 0.002 HIS D 110 PHE 0.046 0.010 PHE D 71 TYR 0.074 0.010 TYR A 55 ARG 0.010 0.001 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.17012 ( 807) hydrogen bonds : angle 5.74699 ( 2070) covalent geometry : bond 0.01127 (13035) covalent geometry : angle 1.13660 (18661) Misc. bond : bond 0.16313 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8372 (m-30) cc_final: 0.8108 (m-30) REVERT: A 121 MET cc_start: 0.8920 (mmm) cc_final: 0.8655 (mmm) REVERT: A 124 ASP cc_start: 0.8083 (m-30) cc_final: 0.7841 (m-30) REVERT: C 26 PHE cc_start: 0.8846 (m-10) cc_final: 0.8641 (m-80) REVERT: C 40 TYR cc_start: 0.8856 (m-80) cc_final: 0.8583 (m-80) REVERT: C 102 THR cc_start: 0.8545 (m) cc_final: 0.8342 (p) REVERT: D 72 GLU cc_start: 0.8602 (tt0) cc_final: 0.8346 (tp30) REVERT: E 94 GLN cc_start: 0.9044 (tt0) cc_final: 0.8801 (tt0) REVERT: E 120 ILE cc_start: 0.9443 (mm) cc_final: 0.9156 (mt) REVERT: G 74 ASN cc_start: 0.9213 (m-40) cc_final: 0.8900 (t0) REVERT: G 102 THR cc_start: 0.8998 (m) cc_final: 0.8769 (p) REVERT: H 52 ASP cc_start: 0.8663 (p0) cc_final: 0.8433 (p0) REVERT: H 106 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9135 (tt0) REVERT: H 114 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2261 time to fit residues: 113.6648 Evaluate side-chains 250 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.069541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046689 restraints weight = 57323.907| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.40 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13051 Z= 0.212 Angle : 0.646 9.993 18661 Z= 0.375 Chirality : 0.038 0.162 2067 Planarity : 0.005 0.053 1480 Dihedral : 28.429 74.014 3881 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.90 % Allowed : 17.77 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.27), residues: 878 helix: 2.26 (0.20), residues: 664 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.011 0.002 HIS B 76 PHE 0.027 0.002 PHE B 62 TYR 0.021 0.002 TYR H 41 ARG 0.009 0.001 ARG L 43 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 807) hydrogen bonds : angle 3.54657 ( 2070) covalent geometry : bond 0.00462 (13035) covalent geometry : angle 0.64587 (18661) Misc. bond : bond 0.00059 ( 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 307 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9129 (mt0) cc_final: 0.8830 (mt0) REVERT: A 121 MET cc_start: 0.9075 (mmm) cc_final: 0.8732 (mmm) REVERT: B 98 LEU cc_start: 0.9533 (mm) cc_final: 0.9293 (mm) REVERT: C 90 ASN cc_start: 0.7305 (m-40) cc_final: 0.7037 (m-40) REVERT: C 102 THR cc_start: 0.8899 (m) cc_final: 0.8551 (p) REVERT: D 94 GLU cc_start: 0.9417 (mp0) cc_final: 0.9071 (mp0) REVERT: E 91 MET cc_start: 0.9004 (mmm) cc_final: 0.8727 (mmt) REVERT: E 124 ASP cc_start: 0.9123 (m-30) cc_final: 0.8869 (m-30) REVERT: F 58 VAL cc_start: 0.9597 (t) cc_final: 0.9394 (p) REVERT: G 37 LYS cc_start: 0.7589 (ttpp) cc_final: 0.7273 (mtpt) REVERT: G 40 TYR cc_start: 0.9077 (m-80) cc_final: 0.8549 (m-80) REVERT: G 57 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8720 (tt0) REVERT: G 102 THR cc_start: 0.8891 (m) cc_final: 0.8476 (p) REVERT: H 69 ASP cc_start: 0.9544 (t0) cc_final: 0.9246 (t0) outliers start: 27 outliers final: 13 residues processed: 293 average time/residue: 0.2503 time to fit residues: 103.6240 Evaluate side-chains 254 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 125 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 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 17 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN E 94 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.087596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.069733 restraints weight = 90834.389| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.08 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4058 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= 0.157 Angle : 0.609 10.817 18661 Z= 0.352 Chirality : 0.035 0.170 2067 Planarity : 0.005 0.071 1480 Dihedral : 28.351 73.350 3881 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.18 % Allowed : 22.25 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.27), residues: 878 helix: 2.25 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 79 HIS 0.010 0.001 HIS L 101 PHE 0.014 0.002 PHE E 68 TYR 0.014 0.002 TYR B 89 ARG 0.011 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 807) hydrogen bonds : angle 3.34086 ( 2070) covalent geometry : bond 0.00337 (13035) covalent geometry : angle 0.60950 (18661) Misc. bond : bond 0.00048 ( 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 300 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9142 (mt0) cc_final: 0.8931 (mt0) REVERT: A 121 MET cc_start: 0.9127 (mmm) cc_final: 0.8544 (mmm) REVERT: A 124 ASP cc_start: 0.9305 (m-30) cc_final: 0.8908 (m-30) REVERT: A 126 GLN cc_start: 0.9376 (mt0) cc_final: 0.9092 (mt0) REVERT: B 85 MET cc_start: 0.8877 (mmm) cc_final: 0.8520 (mmm) REVERT: B 98 LEU cc_start: 0.9466 (mm) cc_final: 0.9161 (mm) REVERT: C 90 ASN cc_start: 0.7606 (m-40) cc_final: 0.7255 (m-40) REVERT: C 102 THR cc_start: 0.8851 (m) cc_final: 0.8634 (p) REVERT: D 48 GLN cc_start: 0.9311 (tm-30) cc_final: 0.9059 (tm-30) REVERT: D 94 GLU cc_start: 0.9336 (mp0) cc_final: 0.8793 (mp0) REVERT: E 60 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: E 77 GLN cc_start: 0.9375 (tt0) cc_final: 0.9037 (tp40) REVERT: E 91 MET cc_start: 0.9045 (mmm) cc_final: 0.8584 (mmt) REVERT: E 121 MET cc_start: 0.9156 (mmm) cc_final: 0.8612 (mmm) REVERT: E 124 ASP cc_start: 0.8973 (m-30) cc_final: 0.8732 (m-30) REVERT: F 25 ASP cc_start: 0.9093 (m-30) cc_final: 0.8884 (t0) REVERT: G 85 GLN cc_start: 0.9435 (tp-100) cc_final: 0.8978 (tp-100) REVERT: G 102 THR cc_start: 0.9009 (m) cc_final: 0.8513 (p) REVERT: H 69 ASP cc_start: 0.9500 (t0) cc_final: 0.9286 (t0) REVERT: H 106 GLU cc_start: 0.9164 (mp0) cc_final: 0.8949 (tt0) REVERT: H 107 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8788 (tt) outliers start: 22 outliers final: 9 residues processed: 284 average time/residue: 0.2322 time to fit residues: 95.2490 Evaluate side-chains 261 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 108 optimal weight: 40.0000 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN G 32 HIS G 74 ASN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.042422 restraints weight = 59452.931| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.23 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13051 Z= 0.264 Angle : 0.649 9.421 18661 Z= 0.376 Chirality : 0.039 0.165 2067 Planarity : 0.005 0.050 1480 Dihedral : 28.558 73.517 3881 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 5.35 % Allowed : 22.83 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.28), residues: 878 helix: 2.22 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.10 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP L 79 HIS 0.013 0.001 HIS F 76 PHE 0.022 0.002 PHE B 62 TYR 0.027 0.002 TYR B 89 ARG 0.008 0.001 ARG L 43 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 807) hydrogen bonds : angle 3.61211 ( 2070) covalent geometry : bond 0.00580 (13035) covalent geometry : angle 0.64866 (18661) Misc. bond : bond 0.00201 ( 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 281 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 1.074 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 52 ILE cc_start: 0.9493 (mt) cc_final: 0.9244 (mm) REVERT: A 121 MET cc_start: 0.9078 (mmm) cc_final: 0.8850 (mmm) REVERT: A 126 GLN cc_start: 0.9361 (mt0) cc_final: 0.9142 (mt0) REVERT: B 85 MET cc_start: 0.9337 (mmm) cc_final: 0.8253 (mmm) REVERT: B 89 TYR cc_start: 0.9230 (m-80) cc_final: 0.8706 (m-80) REVERT: B 98 LEU cc_start: 0.9628 (mm) cc_final: 0.9186 (mm) REVERT: C 90 ASN cc_start: 0.8107 (m-40) cc_final: 0.7626 (m-40) REVERT: C 102 THR cc_start: 0.9245 (m) cc_final: 0.8964 (p) REVERT: D 48 GLN cc_start: 0.9460 (tm-30) cc_final: 0.9128 (tm-30) REVERT: D 94 GLU cc_start: 0.9239 (mp0) cc_final: 0.8758 (mp0) REVERT: E 60 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: E 77 GLN cc_start: 0.9357 (tt0) cc_final: 0.9003 (tm-30) REVERT: E 91 MET cc_start: 0.9030 (mmm) cc_final: 0.8662 (mmt) REVERT: G 25 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8818 (mp10) REVERT: G 31 VAL cc_start: 0.9782 (t) cc_final: 0.9563 (p) REVERT: G 40 TYR cc_start: 0.9337 (m-80) cc_final: 0.9056 (m-80) REVERT: G 73 ASP cc_start: 0.8961 (m-30) cc_final: 0.8663 (m-30) REVERT: G 85 GLN cc_start: 0.9524 (tp-100) cc_final: 0.8978 (tp-100) REVERT: G 102 THR cc_start: 0.9205 (m) cc_final: 0.8630 (p) REVERT: G 105 GLN cc_start: 0.9503 (mp10) cc_final: 0.9092 (mp10) REVERT: H 69 ASP cc_start: 0.9477 (t0) cc_final: 0.9246 (t0) REVERT: H 79 SER cc_start: 0.9807 (t) cc_final: 0.9513 (m) REVERT: H 94 GLU cc_start: 0.9327 (mp0) cc_final: 0.8977 (mp0) REVERT: H 106 GLU cc_start: 0.9301 (mp0) cc_final: 0.9094 (tt0) outliers start: 37 outliers final: 19 residues processed: 263 average time/residue: 0.2275 time to fit residues: 86.7518 Evaluate side-chains 241 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 26 ASN 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 108 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN F 26 ASN G 74 ASN H 50 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.066540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.044176 restraints weight = 58570.386| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.27 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13051 Z= 0.163 Angle : 0.617 13.526 18661 Z= 0.355 Chirality : 0.036 0.170 2067 Planarity : 0.005 0.064 1480 Dihedral : 28.420 73.705 3881 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.76 % Allowed : 26.59 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.28), residues: 878 helix: 2.13 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -0.10 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 79 HIS 0.008 0.001 HIS F 76 PHE 0.020 0.002 PHE B 62 TYR 0.018 0.002 TYR B 89 ARG 0.006 0.000 ARG L 96 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 807) hydrogen bonds : angle 3.27337 ( 2070) covalent geometry : bond 0.00356 (13035) covalent geometry : angle 0.61716 (18661) Misc. bond : bond 0.00034 ( 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 283 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 1.104 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: 0.9097 (mmm) cc_final: 0.8709 (mmm) REVERT: A 124 ASP cc_start: 0.9283 (m-30) cc_final: 0.8965 (m-30) REVERT: A 126 GLN cc_start: 0.9301 (mt0) cc_final: 0.9055 (mt0) REVERT: B 45 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8328 (mtpt) REVERT: B 85 MET cc_start: 0.9243 (mmm) cc_final: 0.8087 (mmm) REVERT: B 89 TYR cc_start: 0.8810 (m-80) cc_final: 0.8063 (m-80) REVERT: B 94 GLN cc_start: 0.9452 (mm-40) cc_final: 0.9248 (mm110) REVERT: C 90 ASN cc_start: 0.8235 (m-40) cc_final: 0.7752 (m-40) REVERT: C 102 THR cc_start: 0.9238 (m) cc_final: 0.8980 (p) REVERT: D 48 GLN cc_start: 0.9475 (tm-30) cc_final: 0.9018 (tm-30) REVERT: D 94 GLU cc_start: 0.9211 (mp0) cc_final: 0.8833 (mp0) REVERT: E 60 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: E 77 GLN cc_start: 0.9342 (tt0) cc_final: 0.9004 (tm-30) REVERT: E 91 MET cc_start: 0.8965 (mmm) cc_final: 0.8594 (mmt) REVERT: E 121 MET cc_start: 0.9151 (mmm) cc_final: 0.8943 (mmm) REVERT: E 124 ASP cc_start: 0.9288 (m-30) cc_final: 0.8668 (m-30) REVERT: E 127 LEU cc_start: 0.9722 (tp) cc_final: 0.9479 (tt) REVERT: F 26 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.7859 (t0) REVERT: G 31 VAL cc_start: 0.9781 (t) cc_final: 0.9546 (p) REVERT: G 73 ASP cc_start: 0.8932 (m-30) cc_final: 0.8618 (m-30) REVERT: G 85 GLN cc_start: 0.9555 (tp-100) cc_final: 0.9184 (tp-100) REVERT: G 95 ASN cc_start: 0.9463 (t0) cc_final: 0.8997 (m-40) REVERT: G 102 THR cc_start: 0.9204 (m) cc_final: 0.8575 (p) REVERT: G 105 GLN cc_start: 0.9464 (mp10) cc_final: 0.9052 (mp10) REVERT: H 69 ASP cc_start: 0.9449 (t0) cc_final: 0.9201 (t0) REVERT: H 79 SER cc_start: 0.9780 (t) cc_final: 0.9460 (m) REVERT: H 94 GLU cc_start: 0.9359 (mp0) cc_final: 0.8980 (mp0) outliers start: 26 outliers final: 16 residues processed: 270 average time/residue: 0.2186 time to fit residues: 86.1518 Evaluate side-chains 245 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 102 LEU 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 26 ASN 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 108 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.066033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.044573 restraints weight = 57942.150| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.38 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13051 Z= 0.199 Angle : 0.642 9.022 18661 Z= 0.366 Chirality : 0.037 0.216 2067 Planarity : 0.005 0.060 1480 Dihedral : 28.379 73.649 3881 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.61 % Allowed : 26.59 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 878 helix: 2.18 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP L 51 HIS 0.007 0.001 HIS F 76 PHE 0.028 0.002 PHE D 71 TYR 0.026 0.002 TYR B 89 ARG 0.009 0.000 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 807) hydrogen bonds : angle 3.27287 ( 2070) covalent geometry : bond 0.00442 (13035) covalent geometry : angle 0.64210 (18661) Misc. bond : bond 0.00100 ( 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 261 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 1.105 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 121 MET cc_start: 0.9071 (mmm) cc_final: 0.8770 (mmm) REVERT: A 124 ASP cc_start: 0.9237 (m-30) cc_final: 0.8945 (m-30) REVERT: A 126 GLN cc_start: 0.9296 (mt0) cc_final: 0.9040 (mt0) REVERT: B 45 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8169 (mtpp) REVERT: B 89 TYR cc_start: 0.8770 (m-80) cc_final: 0.8256 (m-80) REVERT: B 94 GLN cc_start: 0.9485 (mm-40) cc_final: 0.9228 (mm110) REVERT: C 102 THR cc_start: 0.9213 (m) cc_final: 0.8952 (p) REVERT: D 48 GLN cc_start: 0.9492 (tm-30) cc_final: 0.9101 (tm-30) REVERT: D 94 GLU cc_start: 0.9199 (mp0) cc_final: 0.8805 (mp0) REVERT: E 60 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8569 (pm20) REVERT: E 77 GLN cc_start: 0.9348 (tt0) cc_final: 0.8971 (tm-30) REVERT: E 91 MET cc_start: 0.9045 (mmm) cc_final: 0.8664 (mmt) REVERT: E 121 MET cc_start: 0.9098 (mmm) cc_final: 0.8702 (mmm) REVERT: G 31 VAL cc_start: 0.9794 (t) cc_final: 0.9578 (p) REVERT: G 73 ASP cc_start: 0.9006 (m-30) cc_final: 0.8701 (m-30) REVERT: G 85 GLN cc_start: 0.9576 (tp-100) cc_final: 0.9240 (tp-100) REVERT: G 95 ASN cc_start: 0.9461 (t0) cc_final: 0.9037 (m-40) REVERT: G 105 GLN cc_start: 0.9513 (mp10) cc_final: 0.9089 (mp10) REVERT: H 69 ASP cc_start: 0.9469 (t0) cc_final: 0.9210 (t0) REVERT: H 79 SER cc_start: 0.9792 (t) cc_final: 0.9502 (m) REVERT: H 94 GLU cc_start: 0.9329 (mp0) cc_final: 0.8919 (mp0) REVERT: H 106 GLU cc_start: 0.9258 (mp0) cc_final: 0.9035 (tt0) outliers start: 25 outliers final: 17 residues processed: 250 average time/residue: 0.2222 time to fit residues: 81.7286 Evaluate side-chains 243 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain 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 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN E 94 GLN F 26 ASN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.082878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.064467 restraints weight = 90623.056| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.03 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13051 Z= 0.178 Angle : 0.630 9.013 18661 Z= 0.360 Chirality : 0.036 0.189 2067 Planarity : 0.005 0.069 1480 Dihedral : 28.350 74.126 3881 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.90 % Allowed : 27.75 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.28), residues: 878 helix: 2.08 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.09 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP L 51 HIS 0.006 0.001 HIS F 76 PHE 0.025 0.002 PHE F 101 TYR 0.020 0.001 TYR H 41 ARG 0.011 0.000 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 807) hydrogen bonds : angle 3.18012 ( 2070) covalent geometry : bond 0.00392 (13035) covalent geometry : angle 0.62964 (18661) Misc. bond : bond 0.00047 ( 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 265 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 1.142 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: 0.9042 (mmm) cc_final: 0.8732 (mmm) REVERT: A 124 ASP cc_start: 0.9230 (m-30) cc_final: 0.8901 (m-30) REVERT: A 126 GLN cc_start: 0.9278 (mt0) cc_final: 0.9037 (mt0) REVERT: B 45 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8300 (mtpt) REVERT: B 85 MET cc_start: 0.9146 (mmm) cc_final: 0.8047 (mmm) REVERT: B 89 TYR cc_start: 0.8651 (m-80) cc_final: 0.7697 (m-80) REVERT: B 94 GLN cc_start: 0.9508 (mm-40) cc_final: 0.8950 (mm110) REVERT: C 102 THR cc_start: 0.9216 (m) cc_final: 0.8981 (p) REVERT: D 48 GLN cc_start: 0.9442 (tm-30) cc_final: 0.9012 (tm-30) REVERT: D 63 MET cc_start: 0.9512 (mmm) cc_final: 0.9184 (mmm) REVERT: D 94 GLU cc_start: 0.9193 (mp0) cc_final: 0.8806 (mp0) REVERT: E 51 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8708 (tp30) REVERT: E 60 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: E 77 GLN cc_start: 0.9368 (tt0) cc_final: 0.8978 (tm-30) REVERT: E 91 MET cc_start: 0.8966 (mmm) cc_final: 0.8604 (mmt) REVERT: E 111 CYS cc_start: 0.8603 (t) cc_final: 0.8378 (t) REVERT: E 121 MET cc_start: 0.9027 (mmm) cc_final: 0.8774 (mmm) REVERT: E 124 ASP cc_start: 0.8794 (m-30) cc_final: 0.8433 (m-30) REVERT: F 25 ASP cc_start: 0.9016 (t0) cc_final: 0.8809 (t0) REVERT: F 26 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.7781 (t0) REVERT: G 31 VAL cc_start: 0.9789 (t) cc_final: 0.9565 (p) REVERT: G 40 TYR cc_start: 0.9302 (m-80) cc_final: 0.9030 (m-80) REVERT: G 73 ASP cc_start: 0.9068 (m-30) cc_final: 0.8769 (m-30) REVERT: G 85 GLN cc_start: 0.9543 (tp-100) cc_final: 0.9167 (tp-100) REVERT: G 95 ASN cc_start: 0.9442 (t0) cc_final: 0.9010 (m-40) REVERT: G 105 GLN cc_start: 0.9490 (mp10) cc_final: 0.9075 (mp10) REVERT: H 69 ASP cc_start: 0.9436 (t0) cc_final: 0.9160 (t0) REVERT: H 79 SER cc_start: 0.9777 (t) cc_final: 0.9504 (m) REVERT: H 94 GLU cc_start: 0.9264 (mp0) cc_final: 0.8886 (mp0) REVERT: H 106 GLU cc_start: 0.9305 (mp0) cc_final: 0.9081 (tt0) outliers start: 27 outliers final: 17 residues processed: 252 average time/residue: 0.2167 time to fit residues: 81.0103 Evaluate side-chains 246 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 26 ASN 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 44 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.0370 chunk 85 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.063042 restraints weight = 91226.870| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.07 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13051 Z= 0.214 Angle : 0.654 9.996 18661 Z= 0.373 Chirality : 0.038 0.214 2067 Planarity : 0.005 0.052 1480 Dihedral : 28.383 74.993 3881 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.34 % Allowed : 27.31 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.28), residues: 878 helix: 2.02 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 79 HIS 0.005 0.001 HIS F 76 PHE 0.033 0.002 PHE F 101 TYR 0.020 0.002 TYR B 89 ARG 0.008 0.000 ARG L 96 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 807) hydrogen bonds : angle 3.31532 ( 2070) covalent geometry : bond 0.00476 (13035) covalent geometry : angle 0.65361 (18661) Misc. bond : bond 0.00051 ( 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 268 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 1.080 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: 0.9003 (mmm) cc_final: 0.8709 (mmm) REVERT: A 124 ASP cc_start: 0.9167 (m-30) cc_final: 0.8858 (m-30) REVERT: A 126 GLN cc_start: 0.9278 (mt0) cc_final: 0.9069 (mt0) REVERT: B 45 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8471 (mtpt) REVERT: B 85 MET cc_start: 0.9140 (mmm) cc_final: 0.8063 (mmm) REVERT: B 89 TYR cc_start: 0.8791 (m-80) cc_final: 0.7915 (m-80) REVERT: B 94 GLN cc_start: 0.9521 (mm-40) cc_final: 0.9204 (mm110) REVERT: C 39 ASN cc_start: 0.8962 (m-40) cc_final: 0.7831 (t0) REVERT: C 102 THR cc_start: 0.9349 (m) cc_final: 0.9139 (p) REVERT: D 48 GLN cc_start: 0.9446 (tm-30) cc_final: 0.9030 (tm-30) REVERT: D 94 GLU cc_start: 0.9151 (mp0) cc_final: 0.8777 (mp0) REVERT: E 51 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8742 (tp30) REVERT: E 60 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: E 77 GLN cc_start: 0.9395 (tt0) cc_final: 0.9050 (tm-30) REVERT: E 91 MET cc_start: 0.8976 (mmm) cc_final: 0.8638 (mmt) REVERT: E 124 ASP cc_start: 0.8873 (m-30) cc_final: 0.8298 (m-30) REVERT: F 26 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.7790 (t0) REVERT: F 35 ILE cc_start: 0.9741 (mm) cc_final: 0.9525 (tp) REVERT: G 31 VAL cc_start: 0.9820 (t) cc_final: 0.9615 (p) REVERT: G 73 ASP cc_start: 0.9151 (m-30) cc_final: 0.8842 (m-30) REVERT: G 74 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8622 (t0) REVERT: G 85 GLN cc_start: 0.9559 (tp-100) cc_final: 0.9190 (tp-100) REVERT: G 95 ASN cc_start: 0.9465 (t0) cc_final: 0.9009 (m-40) REVERT: G 105 GLN cc_start: 0.9517 (mp10) cc_final: 0.9099 (mp10) REVERT: H 69 ASP cc_start: 0.9378 (t0) cc_final: 0.9103 (t0) REVERT: H 79 SER cc_start: 0.9776 (t) cc_final: 0.9502 (m) REVERT: H 94 GLU cc_start: 0.9222 (mp0) cc_final: 0.8865 (mp0) REVERT: H 106 GLU cc_start: 0.9385 (mp0) cc_final: 0.9149 (tt0) outliers start: 30 outliers final: 21 residues processed: 256 average time/residue: 0.2313 time to fit residues: 85.3677 Evaluate side-chains 249 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 26 ASN 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 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 0.0970 chunk 95 optimal weight: 7.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.063080 restraints weight = 90515.473| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.05 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13051 Z= 0.208 Angle : 0.676 16.364 18661 Z= 0.382 Chirality : 0.037 0.207 2067 Planarity : 0.005 0.066 1480 Dihedral : 28.389 74.836 3881 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.90 % Allowed : 28.47 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.28), residues: 878 helix: 1.97 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -0.18 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP L 79 HIS 0.007 0.001 HIS F 76 PHE 0.025 0.002 PHE F 101 TYR 0.018 0.002 TYR B 89 ARG 0.006 0.000 ARG L 96 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 807) hydrogen bonds : angle 3.28844 ( 2070) covalent geometry : bond 0.00465 (13035) covalent geometry : angle 0.67565 (18661) Misc. bond : bond 0.00029 ( 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 255 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 1.073 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 59 THR cc_start: 0.9614 (p) cc_final: 0.9381 (t) REVERT: A 121 MET cc_start: 0.9003 (mmm) cc_final: 0.8722 (mmm) REVERT: A 124 ASP cc_start: 0.9177 (m-30) cc_final: 0.8867 (m-30) REVERT: A 126 GLN cc_start: 0.9242 (mt0) cc_final: 0.9019 (mt0) REVERT: B 85 MET cc_start: 0.9124 (mmm) cc_final: 0.8102 (mmm) REVERT: B 89 TYR cc_start: 0.8772 (m-80) cc_final: 0.7963 (m-80) REVERT: C 39 ASN cc_start: 0.8924 (m-40) cc_final: 0.7830 (t0) REVERT: C 102 THR cc_start: 0.9362 (m) cc_final: 0.9143 (p) REVERT: D 48 GLN cc_start: 0.9476 (tm-30) cc_final: 0.9044 (tm-30) REVERT: D 94 GLU cc_start: 0.9162 (mp0) cc_final: 0.8799 (mp0) REVERT: E 51 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8314 (tp30) REVERT: E 60 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: E 77 GLN cc_start: 0.9391 (tt0) cc_final: 0.9025 (tm-30) REVERT: E 83 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9249 (mp) REVERT: E 91 MET cc_start: 0.8957 (mmm) cc_final: 0.8628 (mmt) REVERT: E 124 ASP cc_start: 0.8813 (m-30) cc_final: 0.8122 (m-30) REVERT: F 26 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.7908 (t0) REVERT: F 35 ILE cc_start: 0.9744 (mm) cc_final: 0.9524 (tp) REVERT: G 31 VAL cc_start: 0.9815 (t) cc_final: 0.9606 (p) REVERT: G 73 ASP cc_start: 0.9146 (m-30) cc_final: 0.8852 (m-30) REVERT: G 85 GLN cc_start: 0.9558 (tp-100) cc_final: 0.9172 (tp-100) REVERT: G 95 ASN cc_start: 0.9452 (t0) cc_final: 0.8985 (m-40) REVERT: G 105 GLN cc_start: 0.9543 (mp10) cc_final: 0.8991 (mp10) REVERT: H 69 ASP cc_start: 0.9387 (t0) cc_final: 0.9124 (t0) REVERT: H 79 SER cc_start: 0.9781 (t) cc_final: 0.9510 (m) REVERT: H 94 GLU cc_start: 0.9249 (mp0) cc_final: 0.8886 (mp0) REVERT: H 106 GLU cc_start: 0.9398 (mp0) cc_final: 0.9159 (tt0) outliers start: 27 outliers final: 19 residues processed: 246 average time/residue: 0.2349 time to fit residues: 83.2017 Evaluate side-chains 245 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 26 ASN 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 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.079197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060253 restraints weight = 91214.246| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.03 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 13051 Z= 0.321 Angle : 0.756 10.973 18661 Z= 0.427 Chirality : 0.041 0.223 2067 Planarity : 0.006 0.064 1480 Dihedral : 28.619 74.755 3881 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.48 % Allowed : 28.90 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.28), residues: 878 helix: 1.80 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.009 TRP L 79 HIS 0.007 0.002 HIS B 76 PHE 0.029 0.002 PHE F 101 TYR 0.027 0.002 TYR B 89 ARG 0.007 0.001 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 807) hydrogen bonds : angle 3.71209 ( 2070) covalent geometry : bond 0.00713 (13035) covalent geometry : angle 0.75596 (18661) Misc. bond : bond 0.00043 ( 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 244 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.905 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 59 THR cc_start: 0.9658 (p) cc_final: 0.9413 (t) REVERT: A 121 MET cc_start: 0.8969 (mmm) cc_final: 0.8727 (mmm) REVERT: A 124 ASP cc_start: 0.9199 (m-30) cc_final: 0.8907 (m-30) REVERT: A 126 GLN cc_start: 0.9279 (mt0) cc_final: 0.9018 (mt0) REVERT: B 85 MET cc_start: 0.9184 (mmm) cc_final: 0.8241 (mmm) REVERT: B 89 TYR cc_start: 0.8994 (m-80) cc_final: 0.8315 (m-80) REVERT: C 102 THR cc_start: 0.9486 (m) cc_final: 0.9243 (p) REVERT: C 116 LEU cc_start: 0.8588 (mm) cc_final: 0.8240 (mm) REVERT: D 48 GLN cc_start: 0.9521 (tm-30) cc_final: 0.9075 (tm-30) REVERT: D 94 GLU cc_start: 0.9165 (mp0) cc_final: 0.8793 (mp0) REVERT: E 51 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8401 (tp30) REVERT: E 60 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: E 77 GLN cc_start: 0.9408 (tt0) cc_final: 0.9097 (tm-30) REVERT: E 91 MET cc_start: 0.9026 (mmm) cc_final: 0.8666 (mmt) REVERT: E 124 ASP cc_start: 0.8962 (m-30) cc_final: 0.8333 (m-30) REVERT: F 26 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.7858 (t0) REVERT: F 35 ILE cc_start: 0.9764 (mm) cc_final: 0.9513 (tp) REVERT: G 40 TYR cc_start: 0.9446 (m-80) cc_final: 0.9178 (m-80) REVERT: G 73 ASP cc_start: 0.9274 (m-30) cc_final: 0.8993 (m-30) REVERT: G 85 GLN cc_start: 0.9581 (tp-100) cc_final: 0.9200 (tp-100) REVERT: G 105 GLN cc_start: 0.9623 (mp10) cc_final: 0.8970 (mp10) REVERT: H 69 ASP cc_start: 0.9403 (t0) cc_final: 0.9131 (t0) REVERT: H 94 GLU cc_start: 0.9248 (mp0) cc_final: 0.8905 (mp0) REVERT: H 106 GLU cc_start: 0.9439 (mp0) cc_final: 0.9188 (tt0) outliers start: 31 outliers final: 23 residues processed: 234 average time/residue: 0.2376 time to fit residues: 79.8408 Evaluate side-chains 228 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.080812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.062027 restraints weight = 91072.789| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.04 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13051 Z= 0.215 Angle : 0.710 10.998 18661 Z= 0.401 Chirality : 0.038 0.220 2067 Planarity : 0.005 0.061 1480 Dihedral : 28.545 74.708 3881 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.76 % Allowed : 29.77 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 878 helix: 1.88 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.008 TRP L 79 HIS 0.006 0.001 HIS F 76 PHE 0.024 0.002 PHE F 101 TYR 0.019 0.002 TYR B 89 ARG 0.007 0.001 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 807) hydrogen bonds : angle 3.36472 ( 2070) covalent geometry : bond 0.00481 (13035) covalent geometry : angle 0.71035 (18661) Misc. bond : bond 0.00029 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5104.31 seconds wall clock time: 88 minutes 12.82 seconds (5292.82 seconds total)