Starting phenix.real_space_refine on Thu Sep 26 03:35:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/09_2024/6yov_10864.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/09_2024/6yov_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/09_2024/6yov_10864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/09_2024/6yov_10864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/09_2024/6yov_10864.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/09_2024/6yov_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.89, per 1000 atoms: 0.64 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: 3.16 Conformation dependent library (CDL) restraints added in 1.0 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: 5.79 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: 4.53 Time building geometry restraints manager: 3.76 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: 1.220 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.000 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.070 ------------------------------------------------------------------------------- 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 : 0.011 0.091 13035 Z= 0.703 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.079 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: 0.2216 time to fit residues: 111.3532 Evaluate side-chains 250 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 13035 Z= 0.267 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 *********************** 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 fitting. rotamer outliers: 27 poor density : 280 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASN cc_start: 0.7009 (m-40) cc_final: 0.6808 (m-40) REVERT: E 51 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8492 (mm-30) REVERT: E 91 MET cc_start: 0.8871 (mmm) cc_final: 0.8628 (mmt) REVERT: G 40 TYR cc_start: 0.8626 (m-80) cc_final: 0.8361 (m-80) REVERT: G 57 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8959 (tt0) REVERT: G 102 THR cc_start: 0.9122 (m) cc_final: 0.8816 (p) REVERT: H 69 ASP cc_start: 0.8590 (t0) cc_final: 0.8359 (t0) outliers start: 27 outliers final: 13 residues processed: 293 average time/residue: 0.2381 time to fit residues: 98.3158 Evaluate side-chains 251 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 57 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 76 HIS G 32 HIS G 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13035 Z= 0.273 Angle : 0.635 11.288 18661 Z= 0.366 Chirality : 0.037 0.160 2067 Planarity : 0.005 0.067 1480 Dihedral : 28.529 73.676 3881 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.34 % Allowed : 21.97 % Favored : 73.70 % 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: 2.20 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.07 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 79 HIS 0.009 0.001 HIS L 101 PHE 0.015 0.002 PHE E 68 TYR 0.024 0.002 TYR B 89 ARG 0.018 0.001 ARG L 53 *********************** 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 289 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8995 (mmm) cc_final: 0.8740 (mmm) REVERT: B 98 LEU cc_start: 0.9304 (mm) cc_final: 0.9020 (mm) REVERT: C 90 ASN cc_start: 0.7453 (m-40) cc_final: 0.7080 (m-40) REVERT: D 48 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8915 (tm-30) REVERT: E 52 ILE cc_start: 0.8948 (mt) cc_final: 0.8651 (mt) REVERT: E 91 MET cc_start: 0.8888 (mmm) cc_final: 0.8663 (mmt) REVERT: G 40 TYR cc_start: 0.8735 (m-80) cc_final: 0.8486 (m-80) REVERT: G 73 ASP cc_start: 0.8427 (m-30) cc_final: 0.8194 (m-30) REVERT: G 85 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8673 (tp-100) REVERT: G 102 THR cc_start: 0.9260 (m) cc_final: 0.8944 (p) REVERT: H 106 GLU cc_start: 0.9274 (mp0) cc_final: 0.9069 (tt0) outliers start: 30 outliers final: 14 residues processed: 270 average time/residue: 0.2232 time to fit residues: 87.1782 Evaluate side-chains 244 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 230 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN G 25 GLN G 74 ASN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13035 Z= 0.389 Angle : 0.686 10.075 18661 Z= 0.394 Chirality : 0.040 0.168 2067 Planarity : 0.005 0.057 1480 Dihedral : 28.683 74.068 3881 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.20 % Allowed : 22.54 % Favored : 72.25 % 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: 2.08 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -0.31 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP L 79 HIS 0.007 0.002 HIS F 76 PHE 0.027 0.002 PHE D 71 TYR 0.029 0.003 TYR B 89 ARG 0.005 0.001 ARG L 53 *********************** 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 269 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8642 (mmm) cc_final: 0.8219 (tpp) REVERT: D 48 GLN cc_start: 0.9261 (tm-30) cc_final: 0.8881 (tm-30) REVERT: D 72 GLU cc_start: 0.8760 (tt0) cc_final: 0.8519 (tp30) REVERT: D 116 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9086 (p) REVERT: E 124 ASP cc_start: 0.8205 (m-30) cc_final: 0.7943 (m-30) REVERT: G 40 TYR cc_start: 0.8917 (m-80) cc_final: 0.8667 (m-80) REVERT: G 85 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8934 (tp-100) outliers start: 36 outliers final: 24 residues processed: 251 average time/residue: 0.2256 time to fit residues: 81.5896 Evaluate side-chains 232 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 50.0000 chunk 36 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13035 Z= 0.275 Angle : 0.652 11.262 18661 Z= 0.371 Chirality : 0.038 0.235 2067 Planarity : 0.005 0.051 1480 Dihedral : 28.618 74.376 3881 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.34 % Allowed : 24.57 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.30 (0.28), residues: 878 helix: 2.09 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 51 HIS 0.006 0.001 HIS E 114 PHE 0.012 0.002 PHE L 90 TYR 0.016 0.002 TYR D 84 ARG 0.008 0.000 ARG L 96 *********************** 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 261 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 0.996 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: B 85 MET cc_start: 0.8670 (mmm) cc_final: 0.8247 (tpp) REVERT: B 89 TYR cc_start: 0.8952 (m-80) cc_final: 0.8673 (m-80) REVERT: D 48 GLN cc_start: 0.9328 (tm-30) cc_final: 0.8851 (tm-30) REVERT: D 116 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9051 (p) REVERT: G 40 TYR cc_start: 0.8844 (m-80) cc_final: 0.8611 (m-80) REVERT: G 85 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8894 (tp-100) REVERT: G 105 GLN cc_start: 0.9205 (mp10) cc_final: 0.8963 (mp10) outliers start: 30 outliers final: 20 residues processed: 248 average time/residue: 0.2253 time to fit residues: 80.6614 Evaluate side-chains 235 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 109 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 105 optimal weight: 30.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN H 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13035 Z= 0.354 Angle : 0.667 12.359 18661 Z= 0.386 Chirality : 0.039 0.188 2067 Planarity : 0.005 0.055 1480 Dihedral : 28.673 74.093 3881 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.06 % Allowed : 26.45 % Favored : 68.50 % 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: 2.14 (0.28), residues: 878 helix: 1.95 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 51 HIS 0.006 0.001 HIS E 114 PHE 0.018 0.002 PHE L 90 TYR 0.032 0.002 TYR B 89 ARG 0.005 0.000 ARG L 57 *********************** 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 246 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 0.988 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 126 GLN cc_start: 0.8836 (mt0) cc_final: 0.8537 (mp10) REVERT: B 85 MET cc_start: 0.8728 (mmm) cc_final: 0.8285 (mmm) REVERT: B 89 TYR cc_start: 0.8535 (m-80) cc_final: 0.8180 (m-80) REVERT: D 48 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8911 (tm-30) REVERT: D 72 GLU cc_start: 0.8744 (tt0) cc_final: 0.8518 (tp30) REVERT: D 116 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9209 (p) REVERT: G 85 GLN cc_start: 0.9207 (tp-100) cc_final: 0.8900 (tp-100) REVERT: G 95 ASN cc_start: 0.9273 (m-40) cc_final: 0.8996 (m-40) outliers start: 35 outliers final: 25 residues processed: 232 average time/residue: 0.2268 time to fit residues: 75.7817 Evaluate side-chains 228 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13035 Z= 0.193 Angle : 0.648 12.887 18661 Z= 0.366 Chirality : 0.037 0.205 2067 Planarity : 0.005 0.058 1480 Dihedral : 28.497 73.794 3881 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.47 % Allowed : 28.32 % Favored : 68.21 % 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: 2.20 (0.28), residues: 878 helix: 1.99 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -0.08 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP L 79 HIS 0.005 0.001 HIS B 76 PHE 0.017 0.002 PHE E 79 TYR 0.015 0.002 TYR H 41 ARG 0.013 0.000 ARG L 88 *********************** 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 259 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.025 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 126 GLN cc_start: 0.8743 (mt0) cc_final: 0.8433 (mp10) REVERT: D 48 GLN cc_start: 0.9266 (tm-30) cc_final: 0.9021 (tm-30) REVERT: G 85 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8857 (tp-100) REVERT: G 95 ASN cc_start: 0.9169 (m-40) cc_final: 0.8888 (m110) REVERT: G 105 GLN cc_start: 0.9047 (mp10) cc_final: 0.8797 (mp10) outliers start: 24 outliers final: 15 residues processed: 248 average time/residue: 0.2268 time to fit residues: 80.6853 Evaluate side-chains 232 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 40.0000 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 104 optimal weight: 50.0000 chunk 95 optimal weight: 8.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13035 Z= 0.338 Angle : 0.692 13.502 18661 Z= 0.394 Chirality : 0.039 0.247 2067 Planarity : 0.005 0.051 1480 Dihedral : 28.553 74.895 3881 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.90 % Allowed : 29.19 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.29), residues: 878 helix: 1.86 (0.21), residues: 655 sheet: None (None), residues: 0 loop : -0.18 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP L 79 HIS 0.006 0.001 HIS E 114 PHE 0.023 0.002 PHE A 68 TYR 0.030 0.002 TYR B 89 ARG 0.008 0.000 ARG L 53 *********************** 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 239 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.174 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: B 89 TYR cc_start: 0.8200 (m-80) cc_final: 0.7919 (m-80) REVERT: D 48 GLN cc_start: 0.9303 (tm-30) cc_final: 0.9073 (tm-30) REVERT: D 116 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9251 (p) REVERT: E 51 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8483 (tp30) REVERT: E 124 ASP cc_start: 0.8285 (m-30) cc_final: 0.8023 (m-30) REVERT: G 74 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8788 (t0) REVERT: G 85 GLN cc_start: 0.9250 (tp-100) cc_final: 0.8937 (tp-100) REVERT: G 95 ASN cc_start: 0.9213 (m-40) cc_final: 0.8901 (m-40) REVERT: G 105 GLN cc_start: 0.9165 (mp10) cc_final: 0.8924 (mp10) REVERT: H 114 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8433 (tp30) outliers start: 27 outliers final: 16 residues processed: 228 average time/residue: 0.2289 time to fit residues: 74.9758 Evaluate side-chains 228 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- 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** G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13035 Z= 0.262 Angle : 0.711 19.970 18661 Z= 0.393 Chirality : 0.038 0.230 2067 Planarity : 0.005 0.052 1480 Dihedral : 28.492 74.414 3881 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.32 % Allowed : 29.91 % Favored : 66.76 % 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: 1.83 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP L 79 HIS 0.005 0.001 HIS B 76 PHE 0.016 0.002 PHE L 90 TYR 0.022 0.002 TYR B 89 ARG 0.012 0.000 ARG L 88 *********************** 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 241 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8745 (mmm) cc_final: 0.8544 (mmt) REVERT: A 126 GLN cc_start: 0.8757 (mt0) cc_final: 0.8513 (mp10) REVERT: B 85 MET cc_start: 0.8458 (mmm) cc_final: 0.6205 (tmm) REVERT: B 89 TYR cc_start: 0.8133 (m-80) cc_final: 0.7870 (m-80) REVERT: D 48 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9133 (tm-30) REVERT: D 116 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9131 (p) REVERT: E 51 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8160 (tp30) REVERT: E 124 ASP cc_start: 0.8247 (m-30) cc_final: 0.7999 (m-30) REVERT: G 85 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8885 (tp-100) REVERT: G 95 ASN cc_start: 0.9217 (m-40) cc_final: 0.8889 (m-40) REVERT: G 105 GLN cc_start: 0.9106 (mp10) cc_final: 0.8851 (mp10) REVERT: H 114 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8435 (tp30) outliers start: 23 outliers final: 17 residues processed: 230 average time/residue: 0.2274 time to fit residues: 75.8699 Evaluate side-chains 231 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 40.0000 chunk 112 optimal weight: 40.0000 chunk 103 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 overall best weight: 5.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13035 Z= 0.405 Angle : 0.768 18.409 18661 Z= 0.423 Chirality : 0.042 0.275 2067 Planarity : 0.005 0.050 1480 Dihedral : 28.647 74.488 3881 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.47 % Allowed : 29.62 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.28), residues: 878 helix: 1.66 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP L 51 HIS 0.007 0.002 HIS B 76 PHE 0.018 0.002 PHE L 90 TYR 0.030 0.002 TYR B 89 ARG 0.011 0.001 ARG L 88 ********************** 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 231 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 0.946 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: 0.8757 (mmm) cc_final: 0.8435 (mmm) REVERT: A 126 GLN cc_start: 0.8795 (mt0) cc_final: 0.8542 (mp10) REVERT: B 85 MET cc_start: 0.8611 (mmm) cc_final: 0.7976 (tmm) REVERT: B 89 TYR cc_start: 0.8521 (m-80) cc_final: 0.8189 (m-80) REVERT: D 48 GLN cc_start: 0.9430 (tm-30) cc_final: 0.9050 (tm-30) REVERT: D 116 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9281 (p) REVERT: E 51 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: E 124 ASP cc_start: 0.8311 (m-30) cc_final: 0.8057 (m-30) REVERT: G 85 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8937 (tp-100) REVERT: G 95 ASN cc_start: 0.9290 (m-40) cc_final: 0.8944 (m-40) REVERT: H 114 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8490 (tp30) outliers start: 24 outliers final: 20 residues processed: 221 average time/residue: 0.2338 time to fit residues: 73.3883 Evaluate side-chains 223 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** H 85 ASN ** 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 = 0.3729 r_free = 0.3729 target = 0.081250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.062511 restraints weight = 90680.203| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.12 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13035 Z= 0.236 Angle : 0.718 14.212 18661 Z= 0.398 Chirality : 0.039 0.248 2067 Planarity : 0.005 0.053 1480 Dihedral : 28.547 74.338 3881 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.89 % Allowed : 31.07 % Favored : 66.04 % 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: 1.98 (0.29), residues: 878 helix: 1.86 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -0.23 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP L 51 HIS 0.005 0.001 HIS B 76 PHE 0.014 0.002 PHE L 90 TYR 0.019 0.002 TYR B 89 ARG 0.009 0.000 ARG L 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.27 seconds wall clock time: 44 minutes 54.57 seconds (2694.57 seconds total)