Starting phenix.real_space_refine on Sat Mar 16 05:13:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/03_2024/5kgf_8246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/03_2024/5kgf_8246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/03_2024/5kgf_8246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/03_2024/5kgf_8246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/03_2024/5kgf_8246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/03_2024/5kgf_8246_updated.pdb" } resolution = 4.54 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= 0.001 sd= 0.013 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 288 5.49 5 S 16 5.16 5 C 7741 2.51 5 N 2597 2.21 5 O 3140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13782 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 832 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "D" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 788 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N LYS C 9 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 9 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N GLU C 121 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU C 121 " occ=0.00 residue: pdb=" N LYS G 9 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS G 9 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 7.50, per 1000 atoms: 0.54 Number of scatterers: 13782 At special positions: 0 Unit cell: (120.35, 124.7, 116, 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 16 16.00 P 288 15.00 O 3140 8.00 N 2597 7.00 C 7741 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 8125 O4' DA I 17 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 2 sheets defined 56.2% alpha, 3.2% beta 118 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 8.26 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.913A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.710A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 removed outlier: 3.690A pdb=" N ARG B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.863A pdb=" N THR B 54 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 58 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.546A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.741A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.797A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.671A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 4.216A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.517A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.797A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 removed outlier: 4.225A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.912A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.712A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 40 removed outlier: 3.689A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.866A pdb=" N THR F 54 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 58 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.546A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 removed outlier: 3.742A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.797A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.671A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 4.218A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.518A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.796A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 119 removed outlier: 4.227A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 1624 through 1630 Processing helix chain 'O' and resid 23 through 34 Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 57 through 59 No H-bonds generated for 'chain 'O' and resid 57 through 59' Processing helix chain 'M' and resid 23 through 34 Processing helix chain 'M' and resid 38 through 40 No H-bonds generated for 'chain 'M' and resid 38 through 40' Processing helix chain 'M' and resid 57 through 59 No H-bonds generated for 'chain 'M' and resid 57 through 59' Processing helix chain 'K' and resid 1624 through 1630 Processing sheet with id= A, first strand: chain 'O' and resid 12 through 16 removed outlier: 3.634A pdb=" N VAL O 5 " --> pdb=" O ILE O 13 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.632A pdb=" N VAL M 5 " --> pdb=" O ILE M 13 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 8.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2701 1.33 - 1.45: 4263 1.45 - 1.57: 7028 1.57 - 1.68: 577 1.68 - 1.80: 26 Bond restraints: 14595 Sorted by residual: bond pdb=" SG M2L F 20 " pdb=" CD M2L F 20 " ideal model delta sigma weight residual 1.822 1.524 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" SG M2L B 20 " pdb=" CD M2L B 20 " ideal model delta sigma weight residual 1.822 1.525 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" CB M2L B 20 " pdb=" SG M2L B 20 " ideal model delta sigma weight residual 1.815 1.523 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" CB M2L F 20 " pdb=" SG M2L F 20 " ideal model delta sigma weight residual 1.815 1.525 0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" O5' DA I -72 " pdb=" C5' DA I -72 " ideal model delta sigma weight residual 1.423 1.649 -0.226 3.00e-02 1.11e+03 5.70e+01 ... (remaining 14590 not shown) Histogram of bond angle deviations from ideal: 81.26 - 91.70: 2 91.70 - 102.15: 316 102.15 - 112.60: 9251 112.60 - 123.04: 9453 123.04 - 133.49: 1896 Bond angle restraints: 20918 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 81.26 22.74 1.50e+00 4.44e-01 2.30e+02 angle pdb=" N ARG G 11 " pdb=" CA ARG G 11 " pdb=" C ARG G 11 " ideal model delta sigma weight residual 111.33 121.82 -10.49 1.21e+00 6.83e-01 7.51e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 83.14 24.86 3.00e+00 1.11e-01 6.87e+01 angle pdb=" C ASN K1621 " pdb=" CA ASN K1621 " pdb=" CB ASN K1621 " ideal model delta sigma weight residual 110.42 125.96 -15.54 1.99e+00 2.53e-01 6.10e+01 angle pdb=" C ASN L1621 " pdb=" CA ASN L1621 " pdb=" CB ASN L1621 " ideal model delta sigma weight residual 110.42 125.91 -15.49 1.99e+00 2.53e-01 6.06e+01 ... (remaining 20913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.73: 6394 31.73 - 63.46: 1621 63.46 - 95.19: 83 95.19 - 126.92: 14 126.92 - 158.65: 3 Dihedral angle restraints: 8115 sinusoidal: 5271 harmonic: 2844 Sorted by residual: dihedral pdb=" CA ARG H 28 " pdb=" C ARG H 28 " pdb=" N SER H 29 " pdb=" CA SER H 29 " ideal model delta harmonic sigma weight residual -180.00 -115.57 -64.43 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA GLY D 23 " pdb=" C GLY D 23 " pdb=" N LYS D 24 " pdb=" CA LYS D 24 " ideal model delta harmonic sigma weight residual 180.00 117.45 62.55 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA ASP L1620 " pdb=" C ASP L1620 " pdb=" N ASN L1621 " pdb=" CA ASN L1621 " ideal model delta harmonic sigma weight residual 180.00 118.72 61.28 0 5.00e+00 4.00e-02 1.50e+02 ... (remaining 8112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 2377 0.327 - 0.655: 2 0.655 - 0.982: 0 0.982 - 1.310: 0 1.310 - 1.637: 1 Chirality restraints: 2380 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.71 1.64 2.00e-01 2.50e+01 6.70e+01 chirality pdb=" CA ASN L1621 " pdb=" N ASN L1621 " pdb=" C ASN L1621 " pdb=" CB ASN L1621 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA ASN K1621 " pdb=" N ASN K1621 " pdb=" C ASN K1621 " pdb=" CB ASN K1621 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.57 2.00e-01 2.50e+01 7.99e+00 ... (remaining 2377 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 26 " 0.045 2.00e-02 2.50e+03 9.76e-02 9.52e+01 pdb=" C ARG D 26 " -0.168 2.00e-02 2.50e+03 pdb=" O ARG D 26 " 0.068 2.00e-02 2.50e+03 pdb=" N LYS D 27 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 26 " -0.027 2.00e-02 2.50e+03 5.26e-02 2.76e+01 pdb=" C ARG H 26 " 0.091 2.00e-02 2.50e+03 pdb=" O ARG H 26 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS H 27 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 23 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C GLY D 23 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY D 23 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS D 24 " -0.028 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 9 1.97 - 2.71: 936 2.71 - 3.44: 20345 3.44 - 4.17: 39435 4.17 - 4.90: 58567 Nonbonded interactions: 119292 Sorted by model distance: nonbonded pdb=" O ARG H 26 " pdb=" O3' DC J 30 " model vdw 1.243 3.040 nonbonded pdb=" CG1 VAL A 46 " pdb=" OP2 DT J 9 " model vdw 1.353 3.460 nonbonded pdb=" NH2 ARG E 63 " pdb=" C4' DA I 17 " model vdw 1.534 3.550 nonbonded pdb=" NH2 ARG E 63 " pdb=" O4' DA I 17 " model vdw 1.554 2.520 nonbonded pdb=" CD1 ILE L1617 " pdb=" CD2 HIS M 68 " model vdw 1.561 3.680 ... (remaining 119287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 36 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 122) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 1.420 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 47.110 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.009 0.298 14595 Z= 0.620 Angle : 1.372 24.863 20918 Z= 0.819 Chirality : 0.069 1.637 2380 Planarity : 0.006 0.098 1650 Dihedral : 27.921 158.653 6277 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.47 % Favored : 93.11 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.17 % 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: -4.86 (0.19), residues: 958 helix: -3.93 (0.13), residues: 498 sheet: -2.89 (0.53), residues: 38 loop : -2.12 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS O 68 PHE 0.014 0.002 PHE C 25 TYR 0.031 0.004 TYR H 37 ARG 0.011 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 424 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8571 (m-80) cc_final: 0.7127 (m-10) REVERT: A 55 GLN cc_start: 0.8695 (mt0) cc_final: 0.8442 (mt0) REVERT: A 60 LEU cc_start: 0.9132 (mt) cc_final: 0.7937 (mp) REVERT: A 112 ILE cc_start: 0.9268 (mt) cc_final: 0.8808 (mm) REVERT: B 58 LEU cc_start: 0.9354 (tp) cc_final: 0.9125 (tp) REVERT: B 64 ASN cc_start: 0.9159 (m-40) cc_final: 0.8905 (p0) REVERT: C 39 TYR cc_start: 0.8169 (m-80) cc_final: 0.7891 (m-80) REVERT: C 56 GLU cc_start: 0.8622 (tt0) cc_final: 0.8354 (tt0) REVERT: C 61 GLU cc_start: 0.8488 (tp30) cc_final: 0.8198 (tp30) REVERT: C 92 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6335 (tt0) REVERT: D 38 VAL cc_start: 0.9409 (t) cc_final: 0.9116 (t) REVERT: D 58 ILE cc_start: 0.8845 (mm) cc_final: 0.8636 (mt) REVERT: D 103 LEU cc_start: 0.9075 (tt) cc_final: 0.8487 (tp) REVERT: D 106 HIS cc_start: 0.8648 (m-70) cc_final: 0.7346 (m-70) REVERT: E 56 LYS cc_start: 0.9254 (tttt) cc_final: 0.8968 (tptm) REVERT: E 90 MET cc_start: 0.8530 (mmm) cc_final: 0.8183 (mmp) REVERT: E 94 GLU cc_start: 0.7782 (tp30) cc_final: 0.7561 (tp30) REVERT: E 112 ILE cc_start: 0.9266 (mt) cc_final: 0.8843 (mm) REVERT: E 119 ILE cc_start: 0.9248 (pt) cc_final: 0.8949 (pt) REVERT: E 125 GLN cc_start: 0.9201 (mt0) cc_final: 0.8958 (mm-40) REVERT: E 130 ILE cc_start: 0.9205 (mt) cc_final: 0.8915 (mt) REVERT: F 29 ILE cc_start: 0.9472 (mm) cc_final: 0.9217 (mm) REVERT: F 43 VAL cc_start: 0.9713 (t) cc_final: 0.9166 (p) REVERT: F 44 LYS cc_start: 0.9471 (tttt) cc_final: 0.9197 (ttpt) REVERT: F 84 MET cc_start: 0.8306 (mmm) cc_final: 0.8029 (tpp) REVERT: F 88 TYR cc_start: 0.9316 (m-10) cc_final: 0.8675 (m-80) REVERT: G 64 GLU cc_start: 0.8440 (tp30) cc_final: 0.8119 (tp30) REVERT: G 72 ASP cc_start: 0.9134 (m-30) cc_final: 0.8376 (m-30) REVERT: G 74 LYS cc_start: 0.8981 (mttp) cc_final: 0.8470 (tppt) REVERT: G 92 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7882 (tt0) REVERT: O 17 VAL cc_start: 0.6987 (m) cc_final: 0.5843 (m) REVERT: M 17 VAL cc_start: 0.8074 (m) cc_final: 0.7786 (p) REVERT: M 23 ILE cc_start: 0.7350 (mm) cc_final: 0.6876 (mm) REVERT: M 67 LEU cc_start: 0.8359 (mt) cc_final: 0.8020 (mp) REVERT: M 70 VAL cc_start: 0.4845 (t) cc_final: 0.4554 (t) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.3262 time to fit residues: 184.2610 Evaluate side-chains 281 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 31 HIS G 38 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14595 Z= 0.340 Angle : 0.858 13.417 20918 Z= 0.479 Chirality : 0.046 0.264 2380 Planarity : 0.008 0.154 1650 Dihedral : 32.184 158.819 4276 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.43 % Favored : 94.15 % Rotamer: Outliers : 0.24 % Allowed : 3.98 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.95 % 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: -2.29 (0.23), residues: 958 helix: -1.28 (0.18), residues: 564 sheet: -2.34 (0.51), residues: 50 loop : -1.50 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 31 PHE 0.013 0.002 PHE G 25 TYR 0.029 0.003 TYR G 39 ARG 0.017 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 385 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.5034 (t-90) cc_final: 0.4703 (t-90) REVERT: A 54 TYR cc_start: 0.8089 (m-80) cc_final: 0.7290 (m-10) REVERT: A 77 ASP cc_start: 0.8702 (m-30) cc_final: 0.8385 (m-30) REVERT: A 105 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8054 (tp30) REVERT: A 107 THR cc_start: 0.9279 (m) cc_final: 0.8901 (p) REVERT: A 119 ILE cc_start: 0.9214 (pt) cc_final: 0.8919 (mp) REVERT: B 30 THR cc_start: 0.9058 (p) cc_final: 0.8812 (p) REVERT: B 63 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8451 (mt-10) REVERT: C 56 GLU cc_start: 0.8507 (tt0) cc_final: 0.7959 (tt0) REVERT: C 65 LEU cc_start: 0.9114 (mt) cc_final: 0.8765 (mt) REVERT: D 58 ILE cc_start: 0.9332 (mm) cc_final: 0.9005 (mt) REVERT: D 83 ARG cc_start: 0.8487 (mmt-90) cc_final: 0.8004 (tpp80) REVERT: D 97 LEU cc_start: 0.9427 (mt) cc_final: 0.9207 (mt) REVERT: D 115 VAL cc_start: 0.9328 (t) cc_final: 0.9027 (p) REVERT: E 56 LYS cc_start: 0.9315 (tttt) cc_final: 0.9042 (tptp) REVERT: E 57 SER cc_start: 0.9097 (p) cc_final: 0.8266 (m) REVERT: E 70 LEU cc_start: 0.8861 (tp) cc_final: 0.8570 (tp) REVERT: E 80 THR cc_start: 0.8001 (p) cc_final: 0.7450 (p) REVERT: E 105 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7837 (mm-30) REVERT: E 125 GLN cc_start: 0.9111 (mt0) cc_final: 0.8909 (mt0) REVERT: F 34 ILE cc_start: 0.9402 (mp) cc_final: 0.8929 (mm) REVERT: F 43 VAL cc_start: 0.9597 (t) cc_final: 0.9129 (p) REVERT: F 64 ASN cc_start: 0.9110 (m-40) cc_final: 0.8884 (m-40) REVERT: F 96 THR cc_start: 0.8678 (m) cc_final: 0.8365 (m) REVERT: G 56 GLU cc_start: 0.8885 (tt0) cc_final: 0.8145 (tt0) REVERT: G 64 GLU cc_start: 0.8143 (tp30) cc_final: 0.7799 (tp30) REVERT: G 72 ASP cc_start: 0.9020 (m-30) cc_final: 0.8698 (m-30) REVERT: G 74 LYS cc_start: 0.9042 (mttp) cc_final: 0.8425 (tppt) REVERT: G 92 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7442 (mt-10) REVERT: H 49 THR cc_start: 0.8116 (m) cc_final: 0.7701 (p) REVERT: H 56 MET cc_start: 0.7131 (tpt) cc_final: 0.6917 (tpt) REVERT: H 92 GLN cc_start: 0.9036 (tt0) cc_final: 0.8620 (tt0) REVERT: H 108 VAL cc_start: 0.9512 (t) cc_final: 0.9251 (t) REVERT: O 17 VAL cc_start: 0.6769 (m) cc_final: 0.5779 (m) REVERT: M 68 HIS cc_start: 0.6528 (m90) cc_final: 0.6284 (m170) outliers start: 2 outliers final: 0 residues processed: 385 average time/residue: 0.2742 time to fit residues: 147.3014 Evaluate side-chains 282 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 106 HIS ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14595 Z= 0.309 Angle : 0.766 13.476 20918 Z= 0.433 Chirality : 0.042 0.226 2380 Planarity : 0.007 0.131 1650 Dihedral : 31.333 160.830 4276 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.95 % Favored : 93.74 % Rotamer: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: 958 helix: -0.06 (0.20), residues: 570 sheet: -1.98 (0.62), residues: 50 loop : -1.04 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 82 PHE 0.009 0.002 PHE G 25 TYR 0.019 0.002 TYR G 57 ARG 0.008 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7469 (tp30) cc_final: 0.7249 (mm-30) REVERT: A 54 TYR cc_start: 0.7917 (m-80) cc_final: 0.7522 (m-80) REVERT: A 80 THR cc_start: 0.7564 (p) cc_final: 0.6927 (p) REVERT: A 93 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 123 ASP cc_start: 0.7884 (t0) cc_final: 0.7592 (t0) REVERT: B 64 ASN cc_start: 0.9222 (m-40) cc_final: 0.8919 (m-40) REVERT: C 39 TYR cc_start: 0.8422 (m-80) cc_final: 0.8175 (m-80) REVERT: C 56 GLU cc_start: 0.8610 (tt0) cc_final: 0.8016 (tt0) REVERT: C 64 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7772 (tp30) REVERT: C 79 ILE cc_start: 0.9118 (tt) cc_final: 0.8872 (mm) REVERT: D 58 ILE cc_start: 0.9464 (mm) cc_final: 0.9210 (mt) REVERT: D 59 MET cc_start: 0.8577 (mmp) cc_final: 0.8341 (mmp) REVERT: D 83 ARG cc_start: 0.8867 (mmt-90) cc_final: 0.8492 (tpp80) REVERT: D 86 ILE cc_start: 0.9290 (tp) cc_final: 0.8763 (mt) REVERT: D 96 ARG cc_start: 0.8937 (mtt180) cc_final: 0.8649 (tpp80) REVERT: E 80 THR cc_start: 0.7732 (p) cc_final: 0.7070 (p) REVERT: E 84 PHE cc_start: 0.7413 (m-10) cc_final: 0.7191 (m-10) REVERT: E 123 ASP cc_start: 0.8167 (t0) cc_final: 0.7633 (t70) REVERT: F 34 ILE cc_start: 0.9449 (mp) cc_final: 0.9019 (mm) REVERT: G 39 TYR cc_start: 0.9243 (m-80) cc_final: 0.8963 (m-80) REVERT: G 50 TYR cc_start: 0.9252 (t80) cc_final: 0.8753 (t80) REVERT: G 56 GLU cc_start: 0.8971 (tt0) cc_final: 0.8291 (tt0) REVERT: G 64 GLU cc_start: 0.8174 (tp30) cc_final: 0.7904 (tp30) REVERT: G 72 ASP cc_start: 0.9144 (m-30) cc_final: 0.8816 (m-30) REVERT: G 74 LYS cc_start: 0.9067 (mttp) cc_final: 0.8454 (tppt) REVERT: G 92 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7679 (mt-10) REVERT: G 99 LYS cc_start: 0.8196 (mttt) cc_final: 0.7909 (mmtp) REVERT: H 49 THR cc_start: 0.8226 (m) cc_final: 0.8019 (p) REVERT: H 77 LEU cc_start: 0.9644 (mp) cc_final: 0.9429 (mp) REVERT: H 92 GLN cc_start: 0.9101 (tt0) cc_final: 0.8738 (tt0) REVERT: O 17 VAL cc_start: 0.6924 (m) cc_final: 0.5784 (m) REVERT: O 43 LEU cc_start: 0.7148 (mm) cc_final: 0.6920 (mm) REVERT: M 68 HIS cc_start: 0.6519 (m90) cc_final: 0.5993 (m170) outliers start: 1 outliers final: 1 residues processed: 358 average time/residue: 0.2936 time to fit residues: 144.1364 Evaluate side-chains 282 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14595 Z= 0.254 Angle : 0.706 11.926 20918 Z= 0.399 Chirality : 0.039 0.199 2380 Planarity : 0.006 0.131 1650 Dihedral : 30.899 157.581 4276 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.80 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -0.28 (0.27), residues: 958 helix: 0.50 (0.22), residues: 560 sheet: -1.83 (0.64), residues: 48 loop : -0.93 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 82 PHE 0.010 0.002 PHE G 25 TYR 0.016 0.002 TYR H 37 ARG 0.007 0.001 ARG O 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 39 HIS cc_start: 0.5056 (t-90) cc_final: 0.4822 (t70) REVERT: A 54 TYR cc_start: 0.7803 (m-80) cc_final: 0.7467 (m-80) REVERT: A 94 GLU cc_start: 0.7768 (tp30) cc_final: 0.7354 (tp30) REVERT: A 123 ASP cc_start: 0.7837 (t0) cc_final: 0.7312 (t0) REVERT: B 34 ILE cc_start: 0.9603 (mp) cc_final: 0.9240 (mm) REVERT: B 44 LYS cc_start: 0.9329 (mttt) cc_final: 0.9013 (mmtp) REVERT: B 49 LEU cc_start: 0.9254 (mt) cc_final: 0.9022 (mp) REVERT: C 56 GLU cc_start: 0.8446 (tt0) cc_final: 0.8062 (tt0) REVERT: D 86 ILE cc_start: 0.9286 (tp) cc_final: 0.8913 (tt) REVERT: D 96 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8767 (tpp80) REVERT: D 97 LEU cc_start: 0.9420 (mt) cc_final: 0.9143 (mt) REVERT: D 106 HIS cc_start: 0.7956 (m-70) cc_final: 0.7093 (m-70) REVERT: E 56 LYS cc_start: 0.9385 (tttt) cc_final: 0.9064 (tptp) REVERT: E 60 LEU cc_start: 0.8652 (pt) cc_final: 0.8237 (pt) REVERT: E 61 LEU cc_start: 0.9199 (mm) cc_final: 0.8874 (mm) REVERT: E 80 THR cc_start: 0.7885 (p) cc_final: 0.7552 (p) REVERT: E 97 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7195 (mm-30) REVERT: E 101 VAL cc_start: 0.9311 (t) cc_final: 0.9051 (p) REVERT: E 107 THR cc_start: 0.9154 (p) cc_final: 0.8847 (p) REVERT: E 123 ASP cc_start: 0.7988 (t0) cc_final: 0.7385 (t70) REVERT: F 30 THR cc_start: 0.8769 (p) cc_final: 0.8476 (t) REVERT: F 34 ILE cc_start: 0.9413 (mp) cc_final: 0.8943 (mm) REVERT: G 39 TYR cc_start: 0.9227 (m-80) cc_final: 0.8418 (m-80) REVERT: G 56 GLU cc_start: 0.9000 (tt0) cc_final: 0.8322 (tt0) REVERT: G 64 GLU cc_start: 0.8330 (tp30) cc_final: 0.7995 (tp30) REVERT: G 72 ASP cc_start: 0.9092 (m-30) cc_final: 0.8813 (m-30) REVERT: G 74 LYS cc_start: 0.8964 (mttp) cc_final: 0.8369 (tppt) REVERT: G 92 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7126 (mt-10) REVERT: G 116 LEU cc_start: 0.8828 (mm) cc_final: 0.8497 (mm) REVERT: H 92 GLN cc_start: 0.8946 (tt0) cc_final: 0.8677 (tt0) REVERT: H 103 LEU cc_start: 0.9020 (tp) cc_final: 0.8570 (mp) REVERT: H 106 HIS cc_start: 0.8600 (m-70) cc_final: 0.7693 (m170) REVERT: O 17 VAL cc_start: 0.7230 (m) cc_final: 0.6288 (m) REVERT: M 68 HIS cc_start: 0.6497 (m90) cc_final: 0.6174 (m170) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2915 time to fit residues: 142.8366 Evaluate side-chains 275 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.0370 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14595 Z= 0.226 Angle : 0.677 11.239 20918 Z= 0.384 Chirality : 0.037 0.198 2380 Planarity : 0.006 0.090 1650 Dihedral : 30.493 159.704 4276 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.85 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.28 (0.27), residues: 958 helix: 0.47 (0.22), residues: 565 sheet: -2.17 (0.77), residues: 36 loop : -0.91 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS D 106 PHE 0.015 0.002 PHE E 104 TYR 0.029 0.002 TYR F 88 ARG 0.008 0.001 ARG K1627 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 39 HIS cc_start: 0.4991 (t-90) cc_final: 0.4770 (t70) REVERT: A 80 THR cc_start: 0.7611 (p) cc_final: 0.7035 (p) REVERT: A 93 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 94 GLU cc_start: 0.7615 (tp30) cc_final: 0.7289 (tp30) REVERT: A 130 ILE cc_start: 0.8895 (tp) cc_final: 0.8688 (tp) REVERT: B 34 ILE cc_start: 0.9593 (mp) cc_final: 0.9237 (mm) REVERT: B 85 ASP cc_start: 0.8663 (m-30) cc_final: 0.8445 (m-30) REVERT: C 56 GLU cc_start: 0.8454 (tt0) cc_final: 0.7996 (tt0) REVERT: C 72 ASP cc_start: 0.9070 (m-30) cc_final: 0.8828 (m-30) REVERT: D 86 ILE cc_start: 0.9158 (tp) cc_final: 0.8865 (tt) REVERT: D 92 GLN cc_start: 0.9191 (tt0) cc_final: 0.8072 (tp40) REVERT: D 97 LEU cc_start: 0.9490 (mt) cc_final: 0.9010 (mt) REVERT: D 106 HIS cc_start: 0.7506 (m-70) cc_final: 0.6074 (m-70) REVERT: D 108 VAL cc_start: 0.9670 (t) cc_final: 0.9464 (t) REVERT: E 60 LEU cc_start: 0.8527 (pt) cc_final: 0.8034 (pt) REVERT: E 80 THR cc_start: 0.7823 (p) cc_final: 0.7312 (p) REVERT: E 90 MET cc_start: 0.8263 (mmm) cc_final: 0.8062 (mmt) REVERT: E 97 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7398 (mm-30) REVERT: E 107 THR cc_start: 0.9169 (p) cc_final: 0.8616 (t) REVERT: E 123 ASP cc_start: 0.8052 (t0) cc_final: 0.6882 (t0) REVERT: F 26 ILE cc_start: 0.8887 (tt) cc_final: 0.8620 (tt) REVERT: F 30 THR cc_start: 0.8573 (p) cc_final: 0.8364 (t) REVERT: F 34 ILE cc_start: 0.9344 (mp) cc_final: 0.8915 (mm) REVERT: F 37 LEU cc_start: 0.9575 (mp) cc_final: 0.9175 (mm) REVERT: F 88 TYR cc_start: 0.8951 (m-80) cc_final: 0.8549 (m-10) REVERT: G 39 TYR cc_start: 0.8907 (m-80) cc_final: 0.8438 (m-80) REVERT: G 41 GLU cc_start: 0.8461 (tt0) cc_final: 0.8231 (tt0) REVERT: G 54 VAL cc_start: 0.9413 (p) cc_final: 0.9189 (p) REVERT: G 56 GLU cc_start: 0.9023 (tt0) cc_final: 0.8449 (tt0) REVERT: G 57 TYR cc_start: 0.8602 (t80) cc_final: 0.8364 (t80) REVERT: G 64 GLU cc_start: 0.8288 (tp30) cc_final: 0.8042 (tp30) REVERT: G 72 ASP cc_start: 0.9045 (m-30) cc_final: 0.8766 (m-30) REVERT: G 74 LYS cc_start: 0.8923 (mttp) cc_final: 0.8153 (tppt) REVERT: G 92 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7830 (mt-10) REVERT: G 116 LEU cc_start: 0.8760 (mm) cc_final: 0.8518 (mm) REVERT: H 106 HIS cc_start: 0.8597 (m-70) cc_final: 0.8114 (m170) REVERT: O 17 VAL cc_start: 0.7102 (m) cc_final: 0.5971 (m) REVERT: M 68 HIS cc_start: 0.6369 (m90) cc_final: 0.6000 (m170) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2870 time to fit residues: 141.3932 Evaluate side-chains 280 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 0.2980 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 106 HIS ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14595 Z= 0.236 Angle : 0.662 11.212 20918 Z= 0.376 Chirality : 0.037 0.188 2380 Planarity : 0.005 0.082 1650 Dihedral : 30.249 159.093 4276 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.43 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -0.08 (0.27), residues: 958 helix: 0.68 (0.22), residues: 565 sheet: -2.06 (0.63), residues: 50 loop : -0.85 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS D 106 PHE 0.009 0.001 PHE G 25 TYR 0.031 0.002 TYR F 88 ARG 0.007 0.000 ARG K1627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.4884 (t-90) cc_final: 0.4609 (t70) REVERT: A 50 GLU cc_start: 0.7387 (tp30) cc_final: 0.6792 (mm-30) REVERT: A 80 THR cc_start: 0.7503 (p) cc_final: 0.6855 (p) REVERT: A 94 GLU cc_start: 0.7569 (tp30) cc_final: 0.7117 (tp30) REVERT: A 107 THR cc_start: 0.9219 (m) cc_final: 0.9000 (p) REVERT: B 30 THR cc_start: 0.8589 (p) cc_final: 0.8265 (t) REVERT: B 34 ILE cc_start: 0.9600 (mp) cc_final: 0.9191 (mm) REVERT: B 97 LEU cc_start: 0.9170 (tp) cc_final: 0.8870 (tt) REVERT: C 56 GLU cc_start: 0.8617 (tt0) cc_final: 0.8186 (tt0) REVERT: D 56 MET cc_start: 0.7593 (tpp) cc_final: 0.7344 (tpp) REVERT: D 83 ARG cc_start: 0.8840 (tpp80) cc_final: 0.8502 (mmm-85) REVERT: D 86 ILE cc_start: 0.9022 (tp) cc_final: 0.8731 (tt) REVERT: D 97 LEU cc_start: 0.9411 (mt) cc_final: 0.8992 (mt) REVERT: E 54 TYR cc_start: 0.7660 (m-10) cc_final: 0.7391 (m-10) REVERT: E 60 LEU cc_start: 0.8434 (pt) cc_final: 0.8081 (pt) REVERT: E 61 LEU cc_start: 0.9183 (mm) cc_final: 0.8913 (mm) REVERT: E 80 THR cc_start: 0.7745 (p) cc_final: 0.7002 (p) REVERT: E 97 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7314 (mm-30) REVERT: E 107 THR cc_start: 0.9213 (p) cc_final: 0.8950 (t) REVERT: E 123 ASP cc_start: 0.7879 (t0) cc_final: 0.6673 (t0) REVERT: F 30 THR cc_start: 0.8526 (p) cc_final: 0.8324 (t) REVERT: F 34 ILE cc_start: 0.9273 (mp) cc_final: 0.8893 (mm) REVERT: F 37 LEU cc_start: 0.9472 (mp) cc_final: 0.9229 (mm) REVERT: F 62 LEU cc_start: 0.9219 (mp) cc_final: 0.9004 (mp) REVERT: F 88 TYR cc_start: 0.8663 (m-80) cc_final: 0.8164 (m-80) REVERT: G 39 TYR cc_start: 0.8630 (m-80) cc_final: 0.8342 (m-80) REVERT: G 56 GLU cc_start: 0.8945 (tt0) cc_final: 0.8653 (tt0) REVERT: G 64 GLU cc_start: 0.8288 (tp30) cc_final: 0.8045 (tp30) REVERT: G 72 ASP cc_start: 0.9034 (m-30) cc_final: 0.8734 (m-30) REVERT: G 74 LYS cc_start: 0.8937 (mttp) cc_final: 0.8265 (tppt) REVERT: G 92 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7650 (mt-10) REVERT: G 116 LEU cc_start: 0.8725 (mm) cc_final: 0.8511 (mm) REVERT: H 92 GLN cc_start: 0.8951 (tt0) cc_final: 0.8644 (tt0) REVERT: H 102 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6229 (tm-30) REVERT: O 17 VAL cc_start: 0.7557 (m) cc_final: 0.7013 (p) REVERT: O 51 GLU cc_start: 0.7251 (pm20) cc_final: 0.6930 (pm20) REVERT: M 39 ASP cc_start: 0.7222 (p0) cc_final: 0.6870 (p0) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2842 time to fit residues: 136.5410 Evaluate side-chains 268 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.0670 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 92 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14595 Z= 0.190 Angle : 0.640 8.648 20918 Z= 0.365 Chirality : 0.036 0.204 2380 Planarity : 0.005 0.058 1650 Dihedral : 30.056 160.297 4276 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.11 % Favored : 94.47 % Rotamer: Outliers : 0.12 % Allowed : 2.41 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.31 (0.27), residues: 958 helix: 0.51 (0.22), residues: 576 sheet: -2.12 (0.62), residues: 50 loop : -1.00 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 31 PHE 0.014 0.001 PHE A 78 TYR 0.018 0.002 TYR A 54 ARG 0.012 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.4817 (t-90) cc_final: 0.4432 (t70) REVERT: A 76 GLN cc_start: 0.8791 (pm20) cc_final: 0.8186 (pm20) REVERT: A 80 THR cc_start: 0.7990 (p) cc_final: 0.7454 (p) REVERT: A 86 SER cc_start: 0.8792 (m) cc_final: 0.8526 (m) REVERT: A 94 GLU cc_start: 0.7481 (tp30) cc_final: 0.7227 (tp30) REVERT: B 30 THR cc_start: 0.8186 (p) cc_final: 0.7966 (t) REVERT: B 34 ILE cc_start: 0.9586 (mp) cc_final: 0.9215 (mm) REVERT: C 56 GLU cc_start: 0.8403 (tt0) cc_final: 0.7934 (tt0) REVERT: C 89 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8093 (t0) REVERT: D 56 MET cc_start: 0.7595 (tpp) cc_final: 0.7301 (tpp) REVERT: D 83 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8480 (mmm-85) REVERT: D 86 ILE cc_start: 0.8952 (tp) cc_final: 0.8748 (tt) REVERT: E 60 LEU cc_start: 0.8318 (pt) cc_final: 0.7886 (pt) REVERT: E 61 LEU cc_start: 0.9032 (mm) cc_final: 0.8827 (mm) REVERT: E 97 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7041 (mm-30) REVERT: E 107 THR cc_start: 0.9351 (p) cc_final: 0.8914 (t) REVERT: E 123 ASP cc_start: 0.7773 (t0) cc_final: 0.6451 (t0) REVERT: E 125 GLN cc_start: 0.8920 (mt0) cc_final: 0.8500 (mm-40) REVERT: F 26 ILE cc_start: 0.8741 (tt) cc_final: 0.8441 (tt) REVERT: F 30 THR cc_start: 0.8273 (p) cc_final: 0.8038 (t) REVERT: F 34 ILE cc_start: 0.9180 (mp) cc_final: 0.8823 (mm) REVERT: F 37 LEU cc_start: 0.9388 (mp) cc_final: 0.9139 (mm) REVERT: G 39 TYR cc_start: 0.8719 (m-80) cc_final: 0.8356 (m-80) REVERT: G 56 GLU cc_start: 0.8866 (tt0) cc_final: 0.8648 (mt-10) REVERT: G 72 ASP cc_start: 0.9013 (m-30) cc_final: 0.8765 (m-30) REVERT: G 74 LYS cc_start: 0.8815 (mttp) cc_final: 0.8214 (tppt) REVERT: G 92 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7226 (mt-10) REVERT: H 51 ILE cc_start: 0.8675 (mm) cc_final: 0.8453 (tp) REVERT: O 17 VAL cc_start: 0.7570 (m) cc_final: 0.7234 (p) REVERT: O 43 LEU cc_start: 0.7129 (mm) cc_final: 0.6372 (mm) REVERT: M 20 SER cc_start: 0.6433 (p) cc_final: 0.6163 (t) REVERT: M 39 ASP cc_start: 0.7024 (p0) cc_final: 0.6622 (p0) REVERT: M 72 ARG cc_start: 0.7447 (ttp80) cc_final: 0.6816 (ttp80) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.2802 time to fit residues: 137.5096 Evaluate side-chains 274 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 113 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 76 GLN E 85 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14595 Z= 0.210 Angle : 0.650 9.887 20918 Z= 0.367 Chirality : 0.037 0.235 2380 Planarity : 0.005 0.076 1650 Dihedral : 29.893 162.167 4276 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.91 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.30 (0.27), residues: 958 helix: 0.54 (0.22), residues: 575 sheet: -2.38 (0.60), residues: 52 loop : -0.99 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 31 PHE 0.008 0.001 PHE G 25 TYR 0.035 0.002 TYR M 59 ARG 0.015 0.001 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.4695 (t-90) cc_final: 0.4445 (t70) REVERT: A 80 THR cc_start: 0.7668 (p) cc_final: 0.6956 (p) REVERT: A 94 GLU cc_start: 0.7615 (tp30) cc_final: 0.7292 (tp30) REVERT: A 97 GLU cc_start: 0.7739 (mt-10) cc_final: 0.6639 (mm-30) REVERT: B 34 ILE cc_start: 0.9663 (mp) cc_final: 0.9243 (mm) REVERT: B 52 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 53 GLU cc_start: 0.8544 (pm20) cc_final: 0.7874 (pm20) REVERT: C 56 GLU cc_start: 0.8615 (tt0) cc_final: 0.8360 (tt0) REVERT: D 56 MET cc_start: 0.7607 (tpp) cc_final: 0.7298 (tpp) REVERT: D 83 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8496 (mmm-85) REVERT: D 86 ILE cc_start: 0.8913 (tp) cc_final: 0.8680 (tp) REVERT: D 92 GLN cc_start: 0.9104 (tt0) cc_final: 0.8055 (tp40) REVERT: D 103 LEU cc_start: 0.8791 (mm) cc_final: 0.8541 (mm) REVERT: E 57 SER cc_start: 0.9111 (m) cc_final: 0.8909 (m) REVERT: E 68 GLN cc_start: 0.8656 (tt0) cc_final: 0.8240 (tm-30) REVERT: E 80 THR cc_start: 0.7833 (p) cc_final: 0.7264 (p) REVERT: E 90 MET cc_start: 0.8386 (mmm) cc_final: 0.8182 (mmp) REVERT: E 97 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7048 (mm-30) REVERT: E 123 ASP cc_start: 0.7887 (t0) cc_final: 0.7358 (t0) REVERT: E 125 GLN cc_start: 0.8848 (mt0) cc_final: 0.8336 (mm-40) REVERT: F 30 THR cc_start: 0.8309 (p) cc_final: 0.8033 (t) REVERT: F 34 ILE cc_start: 0.9240 (mp) cc_final: 0.8844 (mm) REVERT: F 37 LEU cc_start: 0.9435 (mp) cc_final: 0.9110 (mm) REVERT: G 39 TYR cc_start: 0.8674 (m-80) cc_final: 0.8223 (m-80) REVERT: G 50 TYR cc_start: 0.9153 (t80) cc_final: 0.7776 (t80) REVERT: G 56 GLU cc_start: 0.8869 (tt0) cc_final: 0.8365 (tt0) REVERT: G 64 GLU cc_start: 0.8520 (tp30) cc_final: 0.8281 (tp30) REVERT: G 72 ASP cc_start: 0.9050 (m-30) cc_final: 0.8773 (m-30) REVERT: G 74 LYS cc_start: 0.8784 (mttp) cc_final: 0.8175 (tppt) REVERT: G 116 LEU cc_start: 0.8651 (mm) cc_final: 0.8416 (mm) REVERT: G 118 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8211 (mmmt) REVERT: H 92 GLN cc_start: 0.9121 (tt0) cc_final: 0.8195 (tp-100) REVERT: H 108 VAL cc_start: 0.9475 (t) cc_final: 0.8845 (t) REVERT: M 39 ASP cc_start: 0.7391 (p0) cc_final: 0.7038 (p0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2820 time to fit residues: 129.5814 Evaluate side-chains 268 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 0.0970 chunk 113 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 92 GLN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14595 Z= 0.215 Angle : 0.646 10.877 20918 Z= 0.365 Chirality : 0.037 0.238 2380 Planarity : 0.005 0.097 1650 Dihedral : 29.796 164.554 4276 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.53 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -0.28 (0.27), residues: 958 helix: 0.62 (0.22), residues: 570 sheet: -2.34 (0.61), residues: 52 loop : -1.10 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS O 68 PHE 0.011 0.001 PHE H 62 TYR 0.043 0.003 TYR F 88 ARG 0.009 0.000 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7946 (m-10) cc_final: 0.7268 (m-10) REVERT: A 80 THR cc_start: 0.7681 (p) cc_final: 0.7036 (p) REVERT: A 86 SER cc_start: 0.8698 (m) cc_final: 0.8438 (m) REVERT: A 94 GLU cc_start: 0.7646 (tp30) cc_final: 0.7262 (tp30) REVERT: A 97 GLU cc_start: 0.7784 (mt-10) cc_final: 0.6655 (mm-30) REVERT: A 110 CYS cc_start: 0.8202 (p) cc_final: 0.7795 (p) REVERT: B 34 ILE cc_start: 0.9651 (mp) cc_final: 0.9247 (mm) REVERT: B 52 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7959 (tm-30) REVERT: C 56 GLU cc_start: 0.8599 (tt0) cc_final: 0.8365 (tt0) REVERT: D 56 MET cc_start: 0.7626 (tpp) cc_final: 0.7259 (tpp) REVERT: D 83 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8512 (mmm-85) REVERT: D 86 ILE cc_start: 0.8815 (tp) cc_final: 0.8548 (tp) REVERT: D 92 GLN cc_start: 0.9098 (tt0) cc_final: 0.8310 (tt0) REVERT: D 103 LEU cc_start: 0.8844 (mm) cc_final: 0.8509 (mm) REVERT: E 60 LEU cc_start: 0.8530 (pt) cc_final: 0.7942 (pt) REVERT: E 80 THR cc_start: 0.7852 (p) cc_final: 0.7314 (p) REVERT: E 90 MET cc_start: 0.8435 (mmm) cc_final: 0.8166 (mmp) REVERT: E 97 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7003 (mm-30) REVERT: E 105 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6342 (tm-30) REVERT: E 123 ASP cc_start: 0.8131 (t0) cc_final: 0.7491 (t70) REVERT: F 30 THR cc_start: 0.8259 (p) cc_final: 0.7945 (t) REVERT: F 34 ILE cc_start: 0.9288 (mp) cc_final: 0.8929 (mm) REVERT: F 37 LEU cc_start: 0.9434 (mp) cc_final: 0.9091 (mp) REVERT: G 39 TYR cc_start: 0.8594 (m-80) cc_final: 0.8307 (m-80) REVERT: G 50 TYR cc_start: 0.9136 (t80) cc_final: 0.7659 (t80) REVERT: G 64 GLU cc_start: 0.8659 (tp30) cc_final: 0.8327 (tp30) REVERT: G 72 ASP cc_start: 0.9034 (m-30) cc_final: 0.8692 (m-30) REVERT: G 74 LYS cc_start: 0.8713 (mttp) cc_final: 0.8186 (tppt) REVERT: G 116 LEU cc_start: 0.8710 (mm) cc_final: 0.8457 (mm) REVERT: G 118 LYS cc_start: 0.8349 (mmmt) cc_final: 0.7938 (mmmt) REVERT: H 54 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8794 (mmmm) REVERT: H 86 ILE cc_start: 0.8734 (tp) cc_final: 0.8413 (tt) REVERT: H 92 GLN cc_start: 0.9083 (tt0) cc_final: 0.8021 (tp40) REVERT: H 108 VAL cc_start: 0.9571 (t) cc_final: 0.8879 (t) REVERT: H 110 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8664 (mm-30) REVERT: M 39 ASP cc_start: 0.7428 (p0) cc_final: 0.7023 (p0) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2574 time to fit residues: 120.8587 Evaluate side-chains 286 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 68 GLN E 85 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14595 Z= 0.246 Angle : 0.671 10.507 20918 Z= 0.377 Chirality : 0.037 0.238 2380 Planarity : 0.005 0.067 1650 Dihedral : 29.738 167.073 4276 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.95 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -0.37 (0.27), residues: 958 helix: 0.48 (0.22), residues: 577 sheet: -2.02 (0.62), residues: 50 loop : -1.10 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 106 PHE 0.023 0.002 PHE G 25 TYR 0.024 0.003 TYR M 59 ARG 0.012 0.001 ARG M 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.230 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 68 GLN cc_start: 0.8534 (tt0) cc_final: 0.8046 (tm-30) REVERT: A 94 GLU cc_start: 0.7602 (tp30) cc_final: 0.7371 (tp30) REVERT: A 97 GLU cc_start: 0.7895 (mt-10) cc_final: 0.6728 (mm-30) REVERT: B 34 ILE cc_start: 0.9663 (mp) cc_final: 0.9239 (mm) REVERT: B 52 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 56 GLU cc_start: 0.8687 (tt0) cc_final: 0.8396 (tt0) REVERT: D 56 MET cc_start: 0.7696 (tpp) cc_final: 0.7448 (tpp) REVERT: D 86 ILE cc_start: 0.8879 (tp) cc_final: 0.8676 (tt) REVERT: D 92 GLN cc_start: 0.9029 (tt0) cc_final: 0.8006 (tp40) REVERT: D 103 LEU cc_start: 0.8852 (mm) cc_final: 0.8507 (mm) REVERT: E 57 SER cc_start: 0.9171 (m) cc_final: 0.8932 (p) REVERT: E 60 LEU cc_start: 0.8587 (pt) cc_final: 0.8088 (pt) REVERT: E 80 THR cc_start: 0.8050 (p) cc_final: 0.7375 (p) REVERT: E 90 MET cc_start: 0.8431 (mmm) cc_final: 0.8209 (mmp) REVERT: E 97 GLU cc_start: 0.8190 (mt-10) cc_final: 0.6985 (mm-30) REVERT: E 107 THR cc_start: 0.9365 (p) cc_final: 0.9101 (p) REVERT: E 123 ASP cc_start: 0.7774 (t0) cc_final: 0.7302 (t0) REVERT: F 30 THR cc_start: 0.8202 (p) cc_final: 0.7887 (t) REVERT: F 34 ILE cc_start: 0.9288 (mp) cc_final: 0.8929 (mm) REVERT: F 37 LEU cc_start: 0.9483 (mp) cc_final: 0.9077 (mp) REVERT: F 52 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7674 (tm-30) REVERT: F 53 GLU cc_start: 0.7433 (tp30) cc_final: 0.7059 (tp30) REVERT: F 84 MET cc_start: 0.7987 (tpp) cc_final: 0.7768 (tpt) REVERT: F 88 TYR cc_start: 0.8315 (m-80) cc_final: 0.8083 (m-80) REVERT: G 39 TYR cc_start: 0.8595 (m-80) cc_final: 0.8345 (m-80) REVERT: G 56 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8672 (mt-10) REVERT: G 64 GLU cc_start: 0.8615 (tp30) cc_final: 0.8319 (tp30) REVERT: G 72 ASP cc_start: 0.9042 (m-30) cc_final: 0.8714 (m-30) REVERT: G 74 LYS cc_start: 0.8811 (mttp) cc_final: 0.8180 (tppt) REVERT: G 118 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7929 (mmmt) REVERT: H 86 ILE cc_start: 0.8759 (tp) cc_final: 0.8450 (tt) REVERT: M 39 ASP cc_start: 0.7420 (p0) cc_final: 0.6817 (p0) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2469 time to fit residues: 114.8713 Evaluate side-chains 268 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048846 restraints weight = 65334.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.050387 restraints weight = 36533.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051391 restraints weight = 25235.042| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.7761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14595 Z= 0.225 Angle : 0.656 10.985 20918 Z= 0.370 Chirality : 0.036 0.218 2380 Planarity : 0.005 0.090 1650 Dihedral : 29.704 168.068 4276 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.44 (0.27), residues: 958 helix: 0.42 (0.22), residues: 578 sheet: -1.80 (0.62), residues: 50 loop : -1.19 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.020 0.002 PHE G 25 TYR 0.027 0.003 TYR E 54 ARG 0.017 0.001 ARG L1627 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.91 seconds wall clock time: 52 minutes 25.01 seconds (3145.01 seconds total)