Starting phenix.real_space_refine on Fri Feb 16 03:27:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/02_2024/7usx_26742_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/02_2024/7usx_26742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/02_2024/7usx_26742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/02_2024/7usx_26742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/02_2024/7usx_26742_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/02_2024/7usx_26742_updated.pdb" } resolution = 3.09 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= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 S 78 5.16 5 C 9466 2.51 5 N 2282 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 727": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4883 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4883 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.51, per 1000 atoms: 0.67 Number of scatterers: 14220 At special positions: 0 Unit cell: (133.401, 103.197, 106.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 78 16.00 P 4 15.00 O 2382 8.00 N 2282 7.00 C 9466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 816 " distance=2.03 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 Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG A1321 " - " ASN A 209 " " NAG B1321 " - " ASN B 209 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 2 sheets defined 66.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 123 through 149 removed outlier: 3.989A pdb=" N TYR A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 167 through 190 removed outlier: 4.055A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 219 through 225 removed outlier: 4.463A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N HIS A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 225' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 262 through 290 removed outlier: 3.574A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 319 through 342 removed outlier: 3.647A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 380 Processing helix chain 'A' and resid 395 through 417 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 421 through 458 Processing helix chain 'A' and resid 668 through 694 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 725 through 741 Processing helix chain 'A' and resid 749 through 771 removed outlier: 3.827A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 809 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 826 through 833 removed outlier: 4.309A pdb=" N ARG A 831 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 removed outlier: 3.950A pdb=" N HIS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 882 Proline residue: A 856 - end of helix removed outlier: 3.539A pdb=" N SER A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 880 " --> pdb=" O ARG A 876 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 881 " --> pdb=" O GLU A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 100 through 117 Processing helix chain 'B' and resid 123 through 149 removed outlier: 4.006A pdb=" N TYR B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 167 through 190 removed outlier: 4.044A pdb=" N PHE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 212 through 215 No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 219 through 225 removed outlier: 4.468A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N HIS B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 225' Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 262 through 290 removed outlier: 3.576A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 319 through 342 removed outlier: 3.671A pdb=" N LYS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 380 Processing helix chain 'B' and resid 395 through 417 Proline residue: B 407 - end of helix Processing helix chain 'B' and resid 421 through 458 Processing helix chain 'B' and resid 668 through 694 Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 725 through 741 Processing helix chain 'B' and resid 749 through 771 removed outlier: 3.826A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 809 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 833 removed outlier: 4.299A pdb=" N ARG B 831 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 847 removed outlier: 3.950A pdb=" N HIS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 882 Proline residue: B 856 - end of helix removed outlier: 3.537A pdb=" N SER B 870 " --> pdb=" O TYR B 866 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 880 " --> pdb=" O ARG B 876 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 881 " --> pdb=" O GLU B 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 36 through 49 Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 139 through 150 Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 180 through 187 Processing helix chain 'C' and resid 193 through 196 No H-bonds generated for 'chain 'C' and resid 193 through 196' Processing helix chain 'D' and resid 24 through 44 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 65 No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 77 through 80 No H-bonds generated for 'chain 'E' and resid 77 through 80' Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 139 through 150 Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 180 through 187 Processing helix chain 'E' and resid 193 through 196 No H-bonds generated for 'chain 'E' and resid 193 through 196' Processing helix chain 'F' and resid 24 through 44 Processing helix chain 'F' and resid 54 through 62 Processing sheet with id= A, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'E' and resid 67 through 69 778 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 6.09 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: 2100 1.31 - 1.43: 3916 1.43 - 1.56: 8342 1.56 - 1.68: 8 1.68 - 1.81: 130 Bond restraints: 14496 Sorted by residual: bond pdb=" C21 3PE F 201 " pdb=" O21 3PE F 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C21 3PE D 201 " pdb=" O21 3PE D 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C30 PEE B1303 " pdb=" O3 PEE B1303 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C10 PEE B1303 " pdb=" O2 PEE B1303 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.80: 244 105.80 - 112.85: 7946 112.85 - 119.91: 4732 119.91 - 126.96: 6347 126.96 - 134.01: 159 Bond angle restraints: 19428 Sorted by residual: angle pdb=" O3P PEE B1303 " pdb=" P PEE B1303 " pdb=" O4P PEE B1303 " ideal model delta sigma weight residual 92.91 108.85 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 108.82 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O12 3PE D 201 " pdb=" P 3PE D 201 " pdb=" O14 3PE D 201 " ideal model delta sigma weight residual 123.79 109.41 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE F 201 " pdb=" P 3PE F 201 " pdb=" O14 3PE F 201 " ideal model delta sigma weight residual 123.79 109.46 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C ARG B 334 " pdb=" N GLU B 335 " pdb=" CA GLU B 335 " ideal model delta sigma weight residual 120.72 114.36 6.36 1.67e+00 3.59e-01 1.45e+01 ... (remaining 19423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.07: 8426 31.07 - 62.15: 414 62.15 - 93.22: 32 93.22 - 124.29: 6 124.29 - 155.37: 2 Dihedral angle restraints: 8880 sinusoidal: 3952 harmonic: 4928 Sorted by residual: dihedral pdb=" CB CYS B 667 " pdb=" SG CYS B 667 " pdb=" SG CYS B 816 " pdb=" CB CYS B 816 " ideal model delta sinusoidal sigma weight residual -86.00 -142.54 56.54 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS A 667 " pdb=" SG CYS A 667 " pdb=" SG CYS A 816 " pdb=" CB CYS A 816 " ideal model delta sinusoidal sigma weight residual -86.00 -140.14 54.14 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" C4 PEE A1303 " pdb=" O4P PEE A1303 " pdb=" P PEE A1303 " pdb=" O2P PEE A1303 " ideal model delta sinusoidal sigma weight residual 284.22 128.85 155.37 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1566 0.041 - 0.081: 503 0.081 - 0.122: 79 0.122 - 0.162: 2 0.162 - 0.203: 10 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA GLU B 335 " pdb=" N GLU B 335 " pdb=" C GLU B 335 " pdb=" CB GLU B 335 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA GLU A 335 " pdb=" N GLU A 335 " pdb=" C GLU A 335 " pdb=" CB GLU A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" C2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C3 PEE A1303 " pdb=" O2 PEE A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 2157 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG B1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG B1321 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG A1321 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 209 " 0.155 2.00e-02 2.50e+03 2.83e-01 9.98e+02 pdb=" CG ASN A 209 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 209 " 0.104 2.00e-02 2.50e+03 pdb=" ND2 ASN A 209 " -0.501 2.00e-02 2.50e+03 pdb=" C1 NAG A1321 " 0.326 2.00e-02 2.50e+03 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2314 2.76 - 3.29: 13308 3.29 - 3.83: 23368 3.83 - 4.36: 26182 4.36 - 4.90: 47244 Nonbonded interactions: 112416 Sorted by model distance: nonbonded pdb=" O PRO E 63 " pdb=" OG SER E 101 " model vdw 2.223 2.440 nonbonded pdb=" O TYR E 28 " pdb=" OG1 THR E 32 " model vdw 2.248 2.440 nonbonded pdb=" NH2 ARG A 94 " pdb=" O GLN C 29 " model vdw 2.250 2.520 nonbonded pdb=" OD2 ASP B 683 " pdb=" NZ LYS B 756 " model vdw 2.253 2.520 nonbonded pdb=" NH2 ARG B 94 " pdb=" O GLN E 29 " model vdw 2.253 2.520 ... (remaining 112411 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.640 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 42.620 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.004 0.082 14496 Z= 0.245 Angle : 0.863 15.940 19428 Z= 0.370 Chirality : 0.040 0.203 2160 Planarity : 0.009 0.296 2340 Dihedral : 17.358 155.365 5674 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.14 % Allowed : 19.60 % Favored : 80.26 % 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: 1.65 (0.21), residues: 1654 helix: 2.28 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 25 HIS 0.002 0.001 HIS E 198 PHE 0.031 0.001 PHE A 376 TYR 0.015 0.001 TYR B 245 ARG 0.003 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6651 (tt0) REVERT: A 138 MET cc_start: 0.6652 (ttp) cc_final: 0.5975 (mmt) REVERT: B 138 MET cc_start: 0.6653 (ttp) cc_final: 0.5940 (mmt) REVERT: C 99 ASN cc_start: 0.7248 (m-40) cc_final: 0.7026 (m-40) REVERT: E 99 ASN cc_start: 0.7668 (m-40) cc_final: 0.7360 (m-40) outliers start: 2 outliers final: 2 residues processed: 163 average time/residue: 0.2582 time to fit residues: 63.2201 Evaluate side-chains 162 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.6980 chunk 124 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 144 ASN B 439 ASN B 731 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14496 Z= 0.251 Angle : 0.549 8.706 19428 Z= 0.274 Chirality : 0.040 0.147 2160 Planarity : 0.004 0.067 2340 Dihedral : 11.281 157.266 2471 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.54 % Allowed : 20.29 % Favored : 77.17 % 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 (0.21), residues: 1654 helix: 2.20 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 25 HIS 0.003 0.001 HIS A 731 PHE 0.016 0.002 PHE C 180 TYR 0.018 0.002 TYR A 245 ARG 0.003 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5458 (tm) REVERT: A 138 MET cc_start: 0.6684 (ttp) cc_final: 0.6000 (mmt) REVERT: A 335 GLU cc_start: 0.6311 (mp0) cc_final: 0.5826 (mp0) REVERT: A 720 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 80 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5495 (tm) REVERT: B 138 MET cc_start: 0.6667 (ttp) cc_final: 0.5945 (mmt) REVERT: B 720 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7725 (t80) REVERT: C 99 ASN cc_start: 0.7470 (m-40) cc_final: 0.7195 (m-40) REVERT: C 119 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6039 (pt0) REVERT: E 99 ASN cc_start: 0.7798 (m-40) cc_final: 0.7527 (m-40) REVERT: F 23 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.3604 (tmm160) outliers start: 37 outliers final: 16 residues processed: 183 average time/residue: 0.2696 time to fit residues: 75.5484 Evaluate side-chains 176 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain F residue 23 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 101 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14496 Z= 0.173 Angle : 0.474 6.800 19428 Z= 0.243 Chirality : 0.038 0.121 2160 Planarity : 0.004 0.064 2340 Dihedral : 10.271 151.213 2468 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.16 % Allowed : 21.11 % Favored : 75.72 % 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: 1.78 (0.21), residues: 1654 helix: 2.38 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS C 139 PHE 0.037 0.001 PHE A 208 TYR 0.013 0.001 TYR B 245 ARG 0.005 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5408 (tm) REVERT: A 88 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6613 (tt0) REVERT: A 138 MET cc_start: 0.6671 (ttp) cc_final: 0.5945 (mmt) REVERT: A 335 GLU cc_start: 0.6588 (mp0) cc_final: 0.6211 (mp0) REVERT: A 435 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8124 (tp) REVERT: A 720 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7567 (t80) REVERT: B 80 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5438 (tm) REVERT: B 138 MET cc_start: 0.6707 (ttp) cc_final: 0.5959 (mmt) REVERT: B 254 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6958 (mp) REVERT: B 335 GLU cc_start: 0.6418 (mp0) cc_final: 0.5988 (mp0) REVERT: B 435 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8130 (tp) REVERT: B 720 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7555 (t80) REVERT: C 99 ASN cc_start: 0.7579 (m-40) cc_final: 0.7339 (m-40) REVERT: C 119 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.5951 (pt0) outliers start: 46 outliers final: 20 residues processed: 186 average time/residue: 0.2307 time to fit residues: 66.3643 Evaluate side-chains 183 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14496 Z= 0.221 Angle : 0.498 8.182 19428 Z= 0.255 Chirality : 0.039 0.136 2160 Planarity : 0.004 0.066 2340 Dihedral : 10.078 148.216 2468 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.71 % Allowed : 21.25 % Favored : 75.03 % 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: 1.66 (0.21), residues: 1654 helix: 2.30 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.74 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.003 0.001 HIS A 731 PHE 0.026 0.002 PHE B 208 TYR 0.017 0.001 TYR A 245 ARG 0.004 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 156 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.5408 (tm) REVERT: A 96 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.5713 (mp10) REVERT: A 138 MET cc_start: 0.6678 (ttp) cc_final: 0.5982 (mmt) REVERT: A 335 GLU cc_start: 0.6504 (mp0) cc_final: 0.6243 (mp0) REVERT: A 435 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 720 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 80 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5430 (tm) REVERT: B 96 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.5696 (mp10) REVERT: B 138 MET cc_start: 0.6694 (ttp) cc_final: 0.6009 (mmt) REVERT: B 254 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6989 (mp) REVERT: B 331 ILE cc_start: 0.8031 (mt) cc_final: 0.6808 (mp) REVERT: B 335 GLU cc_start: 0.6481 (mp0) cc_final: 0.6019 (mp0) REVERT: B 435 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8225 (tp) REVERT: B 720 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7667 (t80) REVERT: C 99 ASN cc_start: 0.7618 (m-40) cc_final: 0.7372 (m-40) REVERT: C 119 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6045 (pt0) outliers start: 54 outliers final: 24 residues processed: 192 average time/residue: 0.2338 time to fit residues: 68.2696 Evaluate side-chains 187 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 0.5980 chunk 142 optimal weight: 0.0030 chunk 40 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 731 HIS B 144 ASN B 394 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14496 Z= 0.173 Angle : 0.465 7.123 19428 Z= 0.239 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.715 142.099 2468 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 21.05 % Favored : 75.38 % 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: 1.79 (0.21), residues: 1654 helix: 2.41 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS C 139 PHE 0.020 0.001 PHE A 208 TYR 0.014 0.001 TYR B 245 ARG 0.004 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 158 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5365 (tm) REVERT: A 138 MET cc_start: 0.6654 (ttp) cc_final: 0.5961 (mmt) REVERT: A 324 ASN cc_start: 0.7787 (t0) cc_final: 0.7515 (t0) REVERT: A 331 ILE cc_start: 0.7960 (mm) cc_final: 0.6965 (mt) REVERT: A 335 GLU cc_start: 0.6426 (mp0) cc_final: 0.6218 (mp0) REVERT: A 435 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 720 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7654 (t80) REVERT: B 80 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.5421 (tm) REVERT: B 96 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.5652 (mp10) REVERT: B 138 MET cc_start: 0.6670 (ttp) cc_final: 0.5998 (mmt) REVERT: B 254 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6934 (mp) REVERT: B 324 ASN cc_start: 0.7857 (t0) cc_final: 0.7592 (t0) REVERT: B 331 ILE cc_start: 0.8022 (mt) cc_final: 0.6828 (mp) REVERT: B 335 GLU cc_start: 0.6501 (mp0) cc_final: 0.6123 (mp0) REVERT: B 435 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8123 (tp) REVERT: B 720 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7632 (t80) REVERT: B 810 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8200 (mtt) REVERT: C 99 ASN cc_start: 0.7598 (m-40) cc_final: 0.7354 (m-40) REVERT: C 119 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6003 (pt0) REVERT: E 119 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6103 (pt0) outliers start: 52 outliers final: 27 residues processed: 196 average time/residue: 0.2347 time to fit residues: 70.5403 Evaluate side-chains 190 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 0.0000 chunk 31 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 731 HIS B 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14496 Z= 0.142 Angle : 0.451 6.685 19428 Z= 0.232 Chirality : 0.037 0.133 2160 Planarity : 0.004 0.063 2340 Dihedral : 9.386 133.118 2468 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.37 % Allowed : 21.05 % Favored : 75.58 % 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: 1.96 (0.21), residues: 1654 helix: 2.53 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.002 0.000 HIS C 139 PHE 0.021 0.001 PHE B 208 TYR 0.011 0.001 TYR B 245 ARG 0.007 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 160 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5399 (tm) REVERT: A 138 MET cc_start: 0.6639 (ttp) cc_final: 0.5957 (mmt) REVERT: A 189 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8307 (tp) REVERT: A 291 MET cc_start: 0.6803 (ttp) cc_final: 0.6434 (mmm) REVERT: A 324 ASN cc_start: 0.7710 (t0) cc_final: 0.7445 (t0) REVERT: A 331 ILE cc_start: 0.7906 (mm) cc_final: 0.6892 (mt) REVERT: A 435 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8103 (tp) REVERT: A 720 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 80 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5430 (tm) REVERT: B 96 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6469 (mp10) REVERT: B 138 MET cc_start: 0.6666 (ttp) cc_final: 0.5987 (mmt) REVERT: B 189 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8309 (tp) REVERT: B 324 ASN cc_start: 0.7705 (t0) cc_final: 0.7329 (t0) REVERT: B 331 ILE cc_start: 0.8052 (mt) cc_final: 0.6789 (mp) REVERT: B 335 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: B 435 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8104 (tp) REVERT: B 720 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7553 (t80) REVERT: B 810 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8087 (mtt) REVERT: C 119 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.5955 (pt0) outliers start: 49 outliers final: 26 residues processed: 193 average time/residue: 0.2323 time to fit residues: 69.0808 Evaluate side-chains 190 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 98 optimal weight: 0.0020 chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14496 Z= 0.166 Angle : 0.466 6.760 19428 Z= 0.239 Chirality : 0.038 0.195 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.313 124.350 2468 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.30 % Allowed : 20.91 % Favored : 75.79 % 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: 1.92 (0.21), residues: 1654 helix: 2.49 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 25 HIS 0.002 0.001 HIS A 731 PHE 0.014 0.001 PHE A 376 TYR 0.014 0.001 TYR B 245 ARG 0.005 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5386 (tm) REVERT: A 138 MET cc_start: 0.6643 (ttp) cc_final: 0.5961 (mmt) REVERT: A 189 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8392 (tp) REVERT: A 291 MET cc_start: 0.6812 (ttp) cc_final: 0.6429 (mmm) REVERT: A 324 ASN cc_start: 0.7729 (t0) cc_final: 0.7467 (t0) REVERT: A 335 GLU cc_start: 0.6595 (mp0) cc_final: 0.6244 (mp0) REVERT: A 435 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 720 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7611 (t80) REVERT: B 80 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5444 (tm) REVERT: B 96 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.5623 (mp10) REVERT: B 138 MET cc_start: 0.6672 (ttp) cc_final: 0.5991 (mmt) REVERT: B 189 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8384 (tp) REVERT: B 324 ASN cc_start: 0.7767 (t0) cc_final: 0.7402 (t0) REVERT: B 331 ILE cc_start: 0.8045 (mt) cc_final: 0.6889 (mp) REVERT: B 335 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: B 435 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8193 (tp) REVERT: B 720 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7658 (t80) REVERT: B 810 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8155 (mtt) REVERT: C 119 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.5969 (pt0) REVERT: E 119 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6110 (pt0) outliers start: 48 outliers final: 29 residues processed: 190 average time/residue: 0.2370 time to fit residues: 69.6150 Evaluate side-chains 196 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 124 optimal weight: 7.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14496 Z= 0.163 Angle : 0.464 6.930 19428 Z= 0.238 Chirality : 0.038 0.156 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.284 114.221 2468 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.51 % Allowed : 20.84 % Favored : 75.65 % 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: 1.92 (0.21), residues: 1654 helix: 2.48 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 25 HIS 0.002 0.001 HIS C 139 PHE 0.014 0.001 PHE B 208 TYR 0.014 0.001 TYR A 245 ARG 0.005 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 154 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5384 (tm) REVERT: A 138 MET cc_start: 0.6642 (ttp) cc_final: 0.5957 (mmt) REVERT: A 291 MET cc_start: 0.6729 (ttp) cc_final: 0.6357 (mmm) REVERT: A 324 ASN cc_start: 0.7711 (t0) cc_final: 0.7451 (t0) REVERT: A 335 GLU cc_start: 0.6406 (mp0) cc_final: 0.6047 (mp0) REVERT: A 435 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 720 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7625 (t80) REVERT: B 80 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5448 (tm) REVERT: B 96 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.5615 (mp10) REVERT: B 138 MET cc_start: 0.6670 (ttp) cc_final: 0.5988 (mmt) REVERT: B 324 ASN cc_start: 0.7736 (t0) cc_final: 0.7393 (t0) REVERT: B 331 ILE cc_start: 0.8034 (mt) cc_final: 0.6879 (mp) REVERT: B 335 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: B 435 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8193 (tp) REVERT: B 720 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7598 (t80) REVERT: C 119 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5993 (pt0) REVERT: E 119 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.6112 (pt0) REVERT: F 23 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.3738 (tmm160) outliers start: 51 outliers final: 35 residues processed: 188 average time/residue: 0.2379 time to fit residues: 68.4738 Evaluate side-chains 200 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 154 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.0370 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14496 Z= 0.179 Angle : 0.474 7.081 19428 Z= 0.243 Chirality : 0.038 0.160 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.264 140.075 2468 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.30 % Allowed : 21.11 % Favored : 75.58 % 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: 1.88 (0.21), residues: 1654 helix: 2.45 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 25 HIS 0.002 0.001 HIS A 731 PHE 0.012 0.001 PHE A 376 TYR 0.015 0.001 TYR B 245 ARG 0.005 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5424 (tm) REVERT: A 138 MET cc_start: 0.6648 (ttp) cc_final: 0.5960 (mmt) REVERT: A 291 MET cc_start: 0.6776 (ttp) cc_final: 0.6403 (mmm) REVERT: A 324 ASN cc_start: 0.7737 (t0) cc_final: 0.7479 (t0) REVERT: A 335 GLU cc_start: 0.6377 (mp0) cc_final: 0.5984 (mp0) REVERT: A 435 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 720 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 80 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.5452 (tm) REVERT: B 96 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.5642 (mp10) REVERT: B 138 MET cc_start: 0.6656 (ttp) cc_final: 0.5987 (mmt) REVERT: B 324 ASN cc_start: 0.7759 (t0) cc_final: 0.7423 (t0) REVERT: B 331 ILE cc_start: 0.7994 (mt) cc_final: 0.6813 (mp) REVERT: B 335 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6299 (mp0) REVERT: B 435 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8241 (tt) REVERT: B 720 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7697 (t80) REVERT: C 119 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6034 (pt0) REVERT: E 119 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6122 (pt0) REVERT: F 23 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.3809 (tmm160) outliers start: 48 outliers final: 31 residues processed: 190 average time/residue: 0.2398 time to fit residues: 69.5764 Evaluate side-chains 197 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 155 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 150 optimal weight: 0.0370 chunk 130 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14496 Z= 0.171 Angle : 0.469 7.018 19428 Z= 0.241 Chirality : 0.038 0.148 2160 Planarity : 0.004 0.063 2340 Dihedral : 9.259 154.737 2468 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.16 % Allowed : 21.18 % Favored : 75.65 % 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: 1.88 (0.21), residues: 1654 helix: 2.44 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 25 HIS 0.002 0.001 HIS C 139 PHE 0.014 0.001 PHE A 376 TYR 0.014 0.001 TYR A 245 ARG 0.005 0.000 ARG D 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 154 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.5673 (OUTLIER) cc_final: 0.5428 (tm) REVERT: A 138 MET cc_start: 0.6642 (ttp) cc_final: 0.5965 (mmt) REVERT: A 291 MET cc_start: 0.6774 (ttp) cc_final: 0.6398 (mmm) REVERT: A 324 ASN cc_start: 0.7698 (t0) cc_final: 0.7444 (t0) REVERT: A 331 ILE cc_start: 0.7877 (mm) cc_final: 0.6912 (mm) REVERT: A 335 GLU cc_start: 0.6383 (mp0) cc_final: 0.5956 (mp0) REVERT: A 419 TYR cc_start: 0.6632 (m-10) cc_final: 0.6274 (m-10) REVERT: A 435 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8192 (tp) REVERT: A 720 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7701 (t80) REVERT: B 80 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.5449 (tm) REVERT: B 96 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.5624 (mp10) REVERT: B 138 MET cc_start: 0.6640 (ttp) cc_final: 0.5972 (mmt) REVERT: B 324 ASN cc_start: 0.7734 (t0) cc_final: 0.7390 (t0) REVERT: B 331 ILE cc_start: 0.7997 (mt) cc_final: 0.6807 (mp) REVERT: B 335 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: B 435 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 720 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7650 (t80) REVERT: C 119 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6003 (pt0) REVERT: E 119 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6114 (pt0) outliers start: 46 outliers final: 34 residues processed: 186 average time/residue: 0.2351 time to fit residues: 67.4535 Evaluate side-chains 196 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS B 144 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.203097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145542 restraints weight = 14515.636| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.02 r_work: 0.3442 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14496 Z= 0.213 Angle : 0.503 9.815 19428 Z= 0.256 Chirality : 0.039 0.144 2160 Planarity : 0.004 0.065 2340 Dihedral : 9.573 165.826 2468 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.09 % Allowed : 21.46 % Favored : 75.45 % 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: 1.76 (0.21), residues: 1654 helix: 2.34 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.69 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 PHE 0.015 0.001 PHE A 376 TYR 0.018 0.001 TYR A 245 ARG 0.004 0.000 ARG D 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.47 seconds wall clock time: 57 minutes 59.40 seconds (3479.40 seconds total)