Starting phenix.real_space_refine on Sun Dec 10 07:23:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/12_2023/5kgf_8246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/12_2023/5kgf_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_8246/12_2023/5kgf_8246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/12_2023/5kgf_8246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/12_2023/5kgf_8246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kgf_8246/12_2023/5kgf_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.23, per 1000 atoms: 0.52 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: 7.06 Conformation dependent library (CDL) restraints added in 1.5 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: 7.49 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: 4.85 Time building geometry restraints manager: 7.49 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: 0.100 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: 1.370 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 43.390 Find NCS groups from input model: 0.520 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.550 ------------------------------------------------------------------------------- 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 : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.3318 time to fit residues: 187.9429 Evaluate side-chains 276 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6207 time to fit residues: 2.0452 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14595 Z= 0.329 Angle : 0.866 12.832 20918 Z= 0.484 Chirality : 0.046 0.237 2380 Planarity : 0.008 0.141 1650 Dihedral : 32.128 159.187 4276 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.91 % Favored : 94.68 % Rotamer: Outliers : 0.24 % Allowed : 4.58 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -2.09 (0.23), residues: 958 helix: -1.11 (0.18), residues: 561 sheet: -2.38 (0.52), residues: 50 loop : -1.43 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 31 PHE 0.014 0.002 PHE G 25 TYR 0.027 0.003 TYR G 39 ARG 0.020 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 392 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 1.118 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 outliers start: 2 outliers final: 0 residues processed: 390 average time/residue: 0.2796 time to fit residues: 151.9148 Evaluate side-chains 270 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3231 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 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 G 104 GLN ** 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: 0.7743 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14595 Z= 0.227 Angle : 0.730 9.569 20918 Z= 0.413 Chirality : 0.041 0.209 2380 Planarity : 0.006 0.127 1650 Dihedral : 31.347 160.688 4276 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.22 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -0.58 (0.26), residues: 958 helix: 0.27 (0.21), residues: 568 sheet: -2.22 (0.58), residues: 52 loop : -1.04 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 82 PHE 0.010 0.002 PHE O 4 TYR 0.019 0.002 TYR G 57 ARG 0.005 0.001 ARG H 96 *********************** 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 383 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.203 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 outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2883 time to fit residues: 154.3840 Evaluate side-chains 275 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3829 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.0970 chunk 12 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 0.0020 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 93 GLN ** 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 94 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14595 Z= 0.203 Angle : 0.697 13.581 20918 Z= 0.392 Chirality : 0.039 0.252 2380 Planarity : 0.005 0.080 1650 Dihedral : 30.833 159.676 4276 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.49 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -0.11 (0.27), residues: 958 helix: 0.78 (0.22), residues: 569 sheet: -2.00 (0.59), residues: 50 loop : -1.13 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS D 106 PHE 0.012 0.002 PHE M 45 TYR 0.026 0.002 TYR G 39 ARG 0.006 0.000 ARG B 45 *********************** 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 367 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.203 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 outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2815 time to fit residues: 144.6278 Evaluate side-chains 275 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4020 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 68 GLN E 85 GLN ** E 93 GLN ** 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** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14595 Z= 0.302 Angle : 0.708 9.736 20918 Z= 0.401 Chirality : 0.039 0.268 2380 Planarity : 0.006 0.138 1650 Dihedral : 30.358 162.667 4276 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.43 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: -0.41 (0.26), residues: 958 helix: 0.40 (0.21), residues: 575 sheet: -1.93 (0.58), residues: 50 loop : -1.04 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 82 PHE 0.028 0.002 PHE A 104 TYR 0.029 0.003 TYR F 88 ARG 0.011 0.001 ARG L1627 *********************** 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 326 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.218 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 outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2819 time to fit residues: 128.9483 Evaluate side-chains 256 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4088 ------------------------------------------------------------------------------- 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: 3.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 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 2 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14595 Z= 0.256 Angle : 0.676 11.389 20918 Z= 0.384 Chirality : 0.038 0.241 2380 Planarity : 0.005 0.065 1650 Dihedral : 30.199 163.651 4276 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.53 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -0.49 (0.26), residues: 958 helix: 0.37 (0.21), residues: 571 sheet: -2.17 (0.58), residues: 50 loop : -1.07 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 68 PHE 0.015 0.002 PHE E 104 TYR 0.027 0.003 TYR F 88 ARG 0.008 0.001 ARG M 54 *********************** 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 317 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.108 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 outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2711 time to fit residues: 121.9277 Evaluate side-chains 244 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4951 ------------------------------------------------------------------------------- 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: 2.9990 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 118 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.0980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** 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 94 ASN ** H 106 HIS ** 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 ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14595 Z= 0.197 Angle : 0.654 8.498 20918 Z= 0.370 Chirality : 0.036 0.228 2380 Planarity : 0.005 0.091 1650 Dihedral : 30.001 166.615 4276 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.53 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -0.48 (0.27), residues: 958 helix: 0.38 (0.22), residues: 570 sheet: -2.40 (0.57), residues: 52 loop : -1.02 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.021 0.002 TYR G 57 ARG 0.007 0.000 ARG M 54 *********************** 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 342 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.143 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 outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2665 time to fit residues: 130.0868 Evaluate side-chains 258 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4150 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 0.0570 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 113 optimal weight: 0.5980 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 31 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 25 ASN ** 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 94 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14595 Z= 0.214 Angle : 0.666 8.757 20918 Z= 0.375 Chirality : 0.037 0.237 2380 Planarity : 0.005 0.074 1650 Dihedral : 29.827 167.498 4276 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.05 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.60 (0.27), residues: 958 helix: 0.27 (0.21), residues: 568 sheet: -2.28 (0.58), residues: 52 loop : -1.07 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS F 75 PHE 0.017 0.002 PHE A 67 TYR 0.021 0.002 TYR F 88 ARG 0.006 0.001 ARG C 35 *********************** 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 336 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.088 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 outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.2617 time to fit residues: 125.9528 Evaluate side-chains 264 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3960 ------------------------------------------------------------------------------- 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: 0.0670 chunk 113 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 104 GLN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.7454 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= 0.223 Angle : 0.680 8.592 20918 Z= 0.378 Chirality : 0.037 0.218 2380 Planarity : 0.005 0.062 1650 Dihedral : 29.758 168.333 4276 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.26 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.68 (0.27), residues: 958 helix: 0.26 (0.22), residues: 566 sheet: -2.19 (0.60), residues: 52 loop : -1.22 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS F 75 PHE 0.033 0.002 PHE A 67 TYR 0.018 0.002 TYR A 54 ARG 0.008 0.001 ARG H 89 *********************** 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 323 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.179 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 outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2540 time to fit residues: 119.4105 Evaluate side-chains 259 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2929 ------------------------------------------------------------------------------- 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: 0.7980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** 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** H 106 HIS ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14595 Z= 0.227 Angle : 0.665 8.883 20918 Z= 0.373 Chirality : 0.037 0.211 2380 Planarity : 0.005 0.039 1650 Dihedral : 29.673 169.546 4276 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.65 (0.27), residues: 958 helix: 0.26 (0.22), residues: 566 sheet: -2.19 (0.62), residues: 52 loop : -1.18 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.002 HIS F 75 PHE 0.018 0.002 PHE A 67 TYR 0.020 0.002 TYR E 54 ARG 0.007 0.001 ARG M 42 ********************** 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 319 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.114 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 outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2550 time to fit residues: 118.1306 Evaluate side-chains 247 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4431 ------------------------------------------------------------------------------- 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: 0.5980 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 0.0570 chunk 27 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 5.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 94 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** 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** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047150 restraints weight = 66645.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.048589 restraints weight = 39569.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.049537 restraints weight = 28159.910| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.7891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14595 Z= 0.322 Angle : 0.719 12.506 20918 Z= 0.403 Chirality : 0.039 0.213 2380 Planarity : 0.006 0.049 1650 Dihedral : 29.666 172.399 4276 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.26 % Favored : 93.42 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % 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: -0.74 (0.27), residues: 958 helix: 0.11 (0.21), residues: 567 sheet: -2.10 (0.61), residues: 52 loop : -1.07 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.002 HIS F 75 PHE 0.024 0.003 PHE A 104 TYR 0.034 0.003 TYR A 54 ARG 0.007 0.001 ARG H 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.31 seconds wall clock time: 53 minutes 19.14 seconds (3199.14 seconds total)