Starting phenix.real_space_refine on Mon Nov 18 02:20:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/11_2024/8evg_28628.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/11_2024/8evg_28628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/11_2024/8evg_28628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/11_2024/8evg_28628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/11_2024/8evg_28628.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/11_2024/8evg_28628.cif" } resolution = 2.75 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= 0.078 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 294 5.49 5 S 32 5.16 5 C 8886 2.51 5 N 2827 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15577 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 8.53, per 1000 atoms: 0.55 Number of scatterers: 15577 At special positions: 0 Unit cell: (138.336, 125.664, 124.608, 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 32 16.00 P 294 15.00 O 3538 8.00 N 2827 7.00 C 8886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 23 sheets defined 46.1% alpha, 18.2% beta 116 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.525A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.776A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.590A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.587A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.848A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.845A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.597A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.577A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.177A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.317A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR M 54 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR M 74 " --> pdb=" O TYR M 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'M' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.683A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 211 through 212 removed outlier: 6.531A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.676A pdb=" N GLY N 71 " --> pdb=" O TRP N 58 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.191A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 163 through 164 removed outlier: 3.624A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.531A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.439A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1968 1.31 - 1.43: 6054 1.43 - 1.56: 7989 1.56 - 1.69: 408 1.69 - 1.82: 55 Bond restraints: 16474 Sorted by residual: bond pdb=" O3' DG I 117 " pdb=" P DG I 118 " ideal model delta sigma weight residual 1.607 1.339 0.268 1.50e-02 4.44e+03 3.19e+02 bond pdb=" O3' DG J 80 " pdb=" P DG J 81 " ideal model delta sigma weight residual 1.607 1.359 0.248 1.50e-02 4.44e+03 2.73e+02 bond pdb=" O3' DG I 85 " pdb=" P DA I 86 " ideal model delta sigma weight residual 1.607 1.364 0.243 1.50e-02 4.44e+03 2.62e+02 bond pdb=" O3' DC I 107 " pdb=" P DA I 108 " ideal model delta sigma weight residual 1.607 1.370 0.237 1.50e-02 4.44e+03 2.49e+02 bond pdb=" O3' DT I 35 " pdb=" P DG I 36 " ideal model delta sigma weight residual 1.607 1.376 0.231 1.50e-02 4.44e+03 2.38e+02 ... (remaining 16469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.87: 22934 5.87 - 11.74: 464 11.74 - 17.62: 101 17.62 - 23.49: 17 23.49 - 29.36: 5 Bond angle restraints: 23521 Sorted by residual: angle pdb=" O3' DC I 96 " pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 111.50 90.34 21.16 1.50e+00 4.44e-01 1.99e+02 angle pdb=" O3' DA J 82 " pdb=" C3' DA J 82 " pdb=" C2' DA J 82 " ideal model delta sigma weight residual 111.50 90.71 20.79 1.50e+00 4.44e-01 1.92e+02 angle pdb=" O3' DA J 97 " pdb=" C3' DA J 97 " pdb=" C2' DA J 97 " ideal model delta sigma weight residual 111.50 130.96 -19.46 1.50e+00 4.44e-01 1.68e+02 angle pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " ideal model delta sigma weight residual 110.00 129.08 -19.08 1.50e+00 4.44e-01 1.62e+02 angle pdb=" O3' DC J 19 " pdb=" C3' DC J 19 " pdb=" C2' DC J 19 " ideal model delta sigma weight residual 111.50 130.56 -19.06 1.50e+00 4.44e-01 1.62e+02 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 7209 32.94 - 65.88: 1834 65.88 - 98.82: 116 98.82 - 131.76: 2 131.76 - 164.70: 4 Dihedral angle restraints: 9165 sinusoidal: 5645 harmonic: 3520 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 24.70 -164.70 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " pdb=" P DT I 132 " ideal model delta sinusoidal sigma weight residual -140.00 24.49 -164.49 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 92 " pdb=" C3' DC I 92 " pdb=" O3' DC I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual 220.00 62.35 157.65 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 2394 0.209 - 0.418: 211 0.418 - 0.627: 34 0.627 - 0.836: 11 0.836 - 1.045: 2 Chirality restraints: 2652 Sorted by residual: chirality pdb=" C3' DG I 53 " pdb=" C4' DG I 53 " pdb=" O3' DG I 53 " pdb=" C2' DG I 53 " both_signs ideal model delta sigma weight residual False -2.66 -1.61 -1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" C3' DC I 92 " pdb=" C4' DC I 92 " pdb=" O3' DC I 92 " pdb=" C2' DC I 92 " both_signs ideal model delta sigma weight residual False -2.66 -1.68 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" P DT I 87 " pdb=" OP1 DT I 87 " pdb=" OP2 DT I 87 " pdb=" O5' DT I 87 " both_signs ideal model delta sigma weight residual True 2.35 -1.55 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 2649 not shown) Planarity restraints: 1948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 68 " -0.119 2.00e-02 2.50e+03 6.09e-02 9.28e+01 pdb=" N1 DT J 68 " 0.098 2.00e-02 2.50e+03 pdb=" C2 DT J 68 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DT J 68 " 0.064 2.00e-02 2.50e+03 pdb=" N3 DT J 68 " -0.079 2.00e-02 2.50e+03 pdb=" C4 DT J 68 " -0.015 2.00e-02 2.50e+03 pdb=" O4 DT J 68 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DT J 68 " 0.045 2.00e-02 2.50e+03 pdb=" C7 DT J 68 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT J 68 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 98 " 0.117 2.00e-02 2.50e+03 5.78e-02 9.19e+01 pdb=" N9 DA I 98 " -0.123 2.00e-02 2.50e+03 pdb=" C8 DA I 98 " 0.029 2.00e-02 2.50e+03 pdb=" N7 DA I 98 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 98 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DA I 98 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 98 " 0.024 2.00e-02 2.50e+03 pdb=" N1 DA I 98 " 0.061 2.00e-02 2.50e+03 pdb=" C2 DA I 98 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA I 98 " -0.040 2.00e-02 2.50e+03 pdb=" C4 DA I 98 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 122 " 0.098 2.00e-02 2.50e+03 5.04e-02 7.61e+01 pdb=" N9 DG J 122 " -0.063 2.00e-02 2.50e+03 pdb=" C8 DG J 122 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DG J 122 " 0.034 2.00e-02 2.50e+03 pdb=" C6 DG J 122 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J 122 " 0.050 2.00e-02 2.50e+03 pdb=" C2 DG J 122 " 0.012 2.00e-02 2.50e+03 pdb=" N2 DG J 122 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG J 122 " -0.104 2.00e-02 2.50e+03 pdb=" C4 DG J 122 " -0.026 2.00e-02 2.50e+03 ... (remaining 1945 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 27 2.42 - 3.04: 8939 3.04 - 3.66: 23614 3.66 - 4.28: 41684 4.28 - 4.90: 62662 Nonbonded interactions: 136926 Sorted by model distance: nonbonded pdb=" N2 DG I 109 " pdb=" O2 DC J 54 " model vdw 1.794 3.120 nonbonded pdb=" N2 DG I 25 " pdb=" O2 DC J 138 " model vdw 1.815 2.496 nonbonded pdb=" O2 DC I 134 " pdb=" N2 DG J 29 " model vdw 2.066 2.496 nonbonded pdb=" OD2 ASP M 95 " pdb=" OG SER M 98 " model vdw 2.219 3.040 nonbonded pdb=" N2 DG I 53 " pdb=" O2 DT J 111 " model vdw 2.227 3.120 ... (remaining 136921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.990 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.020 0.268 16474 Z= 0.985 Angle : 2.030 29.362 23521 Z= 1.164 Chirality : 0.131 1.045 2652 Planarity : 0.010 0.086 1948 Dihedral : 28.950 164.699 6897 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.29 % Allowed : 20.41 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1188 helix: 2.19 (0.22), residues: 543 sheet: -0.04 (0.35), residues: 226 loop : -0.74 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 69 HIS 0.004 0.001 HIS M 249 PHE 0.013 0.001 PHE D 67 TYR 0.024 0.001 TYR H 37 ARG 0.008 0.000 ARG N 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.7907 (mtt) cc_final: 0.7703 (mtt) outliers start: 3 outliers final: 1 residues processed: 289 average time/residue: 1.7941 time to fit residues: 555.9517 Evaluate side-chains 191 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN D 46 HIS E 39 HIS E 108 ASN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 81 ASN N 25 GLN N 196 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16474 Z= 0.239 Angle : 0.678 8.721 23521 Z= 0.391 Chirality : 0.041 0.212 2652 Planarity : 0.005 0.048 1948 Dihedral : 30.372 177.755 4574 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.01 % Allowed : 22.93 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1188 helix: 2.55 (0.22), residues: 544 sheet: 0.26 (0.35), residues: 226 loop : -0.74 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 132 HIS 0.008 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR N 117 ARG 0.006 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7748 (t80) cc_final: 0.7463 (t80) outliers start: 31 outliers final: 6 residues processed: 232 average time/residue: 1.6677 time to fit residues: 417.5444 Evaluate side-chains 188 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain M residue 239 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 141 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 ASN D 64 ASN E 39 HIS E 55 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN M 83 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16474 Z= 0.258 Angle : 0.622 8.930 23521 Z= 0.360 Chirality : 0.039 0.182 2652 Planarity : 0.004 0.038 1948 Dihedral : 30.283 179.592 4573 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.21 % Allowed : 23.03 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1188 helix: 2.60 (0.22), residues: 543 sheet: 0.47 (0.36), residues: 226 loop : -0.86 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 58 HIS 0.005 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.008 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7790 (t80) cc_final: 0.7412 (t80) REVERT: H 56 MET cc_start: 0.8080 (tpp) cc_final: 0.7650 (tpt) outliers start: 33 outliers final: 9 residues processed: 225 average time/residue: 1.6101 time to fit residues: 392.6765 Evaluate side-chains 189 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16474 Z= 0.262 Angle : 0.608 9.122 23521 Z= 0.350 Chirality : 0.037 0.166 2652 Planarity : 0.004 0.037 1948 Dihedral : 30.022 178.906 4573 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.33 % Allowed : 23.71 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1188 helix: 2.67 (0.22), residues: 541 sheet: 0.48 (0.36), residues: 226 loop : -0.97 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 132 HIS 0.005 0.001 HIS M 249 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.009 0.001 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7818 (t80) cc_final: 0.7390 (t80) outliers start: 24 outliers final: 15 residues processed: 206 average time/residue: 1.6578 time to fit residues: 369.2011 Evaluate side-chains 189 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16474 Z= 0.310 Angle : 0.618 8.630 23521 Z= 0.354 Chirality : 0.038 0.151 2652 Planarity : 0.004 0.036 1948 Dihedral : 30.070 179.474 4573 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.94 % Allowed : 25.17 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1188 helix: 2.59 (0.22), residues: 543 sheet: 0.39 (0.35), residues: 226 loop : -0.95 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 132 HIS 0.006 0.001 HIS E 39 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR H 37 ARG 0.007 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8330 (mp) cc_final: 0.8113 (mt) REVERT: D 39 TYR cc_start: 0.7864 (t80) cc_final: 0.7425 (t80) outliers start: 20 outliers final: 13 residues processed: 198 average time/residue: 1.6904 time to fit residues: 361.3123 Evaluate side-chains 180 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.0670 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 0.0030 overall best weight: 0.3928 ------------------------------------------------------------------------------- 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** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16474 Z= 0.173 Angle : 0.579 8.303 23521 Z= 0.333 Chirality : 0.035 0.135 2652 Planarity : 0.004 0.037 1948 Dihedral : 29.556 178.736 4573 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.75 % Allowed : 25.46 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1188 helix: 2.79 (0.22), residues: 543 sheet: 0.46 (0.36), residues: 224 loop : -0.75 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 199 HIS 0.004 0.001 HIS A 39 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR N 72 ARG 0.011 0.000 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7758 (t80) cc_final: 0.7324 (t80) REVERT: E 97 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6376 (mp0) REVERT: H 56 MET cc_start: 0.7940 (tpp) cc_final: 0.7659 (tpt) REVERT: N 23 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6076 (tp30) outliers start: 18 outliers final: 10 residues processed: 203 average time/residue: 1.7417 time to fit residues: 385.0767 Evaluate side-chains 185 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0030 chunk 79 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 39 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16474 Z= 0.365 Angle : 0.638 9.088 23521 Z= 0.363 Chirality : 0.039 0.151 2652 Planarity : 0.004 0.040 1948 Dihedral : 30.037 178.308 4573 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.33 % Allowed : 25.66 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1188 helix: 2.58 (0.22), residues: 541 sheet: 0.31 (0.35), residues: 220 loop : -0.92 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 132 HIS 0.005 0.001 HIS C 82 PHE 0.009 0.002 PHE E 67 TYR 0.013 0.002 TYR H 37 ARG 0.009 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7888 (t80) cc_final: 0.7455 (t80) REVERT: E 97 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6735 (mp0) outliers start: 24 outliers final: 16 residues processed: 192 average time/residue: 1.8014 time to fit residues: 371.4102 Evaluate side-chains 184 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 162 MET Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16474 Z= 0.196 Angle : 0.596 9.388 23521 Z= 0.340 Chirality : 0.036 0.168 2652 Planarity : 0.004 0.038 1948 Dihedral : 29.637 178.230 4573 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.85 % Allowed : 26.82 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1188 helix: 2.68 (0.22), residues: 543 sheet: 0.42 (0.36), residues: 218 loop : -0.77 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 132 HIS 0.004 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR E 54 ARG 0.009 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7761 (t80) cc_final: 0.7260 (t80) REVERT: E 97 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: H 56 MET cc_start: 0.8002 (tpp) cc_final: 0.7749 (tpt) outliers start: 19 outliers final: 12 residues processed: 194 average time/residue: 1.7659 time to fit residues: 368.5759 Evaluate side-chains 180 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 165 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** E 39 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16474 Z= 0.249 Angle : 0.615 9.803 23521 Z= 0.348 Chirality : 0.037 0.205 2652 Planarity : 0.004 0.052 1948 Dihedral : 29.662 178.208 4573 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.33 % Allowed : 27.02 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1188 helix: 2.64 (0.22), residues: 543 sheet: 0.39 (0.35), residues: 218 loop : -0.70 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 132 HIS 0.005 0.001 HIS M 249 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR H 37 ARG 0.016 0.001 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8182 (tppp) cc_final: 0.7970 (tptp) REVERT: D 39 TYR cc_start: 0.7782 (t80) cc_final: 0.7287 (t80) REVERT: E 97 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: H 56 MET cc_start: 0.7992 (tpp) cc_final: 0.7625 (tpt) outliers start: 24 outliers final: 14 residues processed: 193 average time/residue: 1.7000 time to fit residues: 353.8611 Evaluate side-chains 182 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** E 39 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16474 Z= 0.266 Angle : 0.623 10.823 23521 Z= 0.352 Chirality : 0.037 0.200 2652 Planarity : 0.004 0.047 1948 Dihedral : 29.677 178.032 4573 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.85 % Allowed : 27.31 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1188 helix: 2.58 (0.22), residues: 543 sheet: 0.41 (0.36), residues: 218 loop : -0.71 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 132 HIS 0.005 0.001 HIS M 249 PHE 0.008 0.001 PHE A 67 TYR 0.016 0.001 TYR E 54 ARG 0.016 0.001 ARG M 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7801 (t80) cc_final: 0.7315 (t80) REVERT: E 97 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: H 56 MET cc_start: 0.8007 (tpp) cc_final: 0.7630 (tpt) outliers start: 19 outliers final: 15 residues processed: 187 average time/residue: 1.7485 time to fit residues: 352.7764 Evaluate side-chains 184 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** E 39 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068074 restraints weight = 30357.775| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.02 r_work: 0.2894 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16474 Z= 0.195 Angle : 0.616 10.624 23521 Z= 0.348 Chirality : 0.036 0.196 2652 Planarity : 0.005 0.059 1948 Dihedral : 29.670 178.108 4573 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.55 % Allowed : 27.89 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1188 helix: 2.62 (0.22), residues: 543 sheet: 0.40 (0.36), residues: 218 loop : -0.67 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 132 HIS 0.004 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.017 0.001 TYR E 54 ARG 0.016 0.001 ARG M 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6139.95 seconds wall clock time: 110 minutes 36.40 seconds (6636.40 seconds total)