Starting phenix.real_space_refine on Mon Mar 11 15:21:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/03_2024/7kjw_22900_updated.pdb" } resolution = 2.9 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= 0.079 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: 8 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 15 5.16 5 Cl 1 4.86 5 C 5384 2.51 5 N 1428 2.21 5 O 1685 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 415": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8561 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4317 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 507} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3282 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 29, 'TRANS': 376} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'DNA': 1, 'RNA': 21} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 13} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'EFZ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.26, per 1000 atoms: 0.61 Number of scatterers: 8561 At special positions: 0 Unit cell: (78.72, 106.6, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 1 17.00 S 15 16.00 P 44 15.00 Mg 1 11.99 F 3 9.00 O 1685 8.00 N 1428 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.6 seconds 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 9 sheets defined 34.9% alpha, 12.2% beta 19 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 28 through 43 removed outlier: 3.861A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 154 through 172 removed outlier: 4.683A pdb=" N ALA A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 212 removed outlier: 4.002A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.127A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.997A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.780A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.623A pdb=" N SER A 553 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.546A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 5.486A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.950A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.754A pdb=" N GLN B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 212 removed outlier: 4.085A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 269 removed outlier: 4.119A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.549A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 removed outlier: 3.536A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 395 through 404 removed outlier: 5.506A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing sheet with id= A, first strand: chain 'A' and resid 59 through 63 removed outlier: 3.521A pdb=" N PHE A 61 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 72 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= D, first strand: chain 'A' and resid 414 through 416 removed outlier: 6.484A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 465 through 468 removed outlier: 3.508A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE A 440 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN A 494 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL A 442 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 496 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N GLY A 444 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 60 through 63 Processing sheet with id= G, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= H, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= I, first strand: chain 'B' and resid 414 through 416 removed outlier: 5.803A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 717 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1290 1.30 - 1.43: 2498 1.43 - 1.55: 4975 1.55 - 1.68: 85 1.68 - 1.81: 28 Bond restraints: 8876 Sorted by residual: bond pdb=" C4' G47 D 71 " pdb=" C3' G47 D 71 " ideal model delta sigma weight residual 1.303 1.512 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O3' G D 70 " pdb=" P G47 D 71 " ideal model delta sigma weight residual 1.607 1.745 -0.138 1.50e-02 4.44e+03 8.46e+01 bond pdb=" C4' G47 D 71 " pdb=" O4' G47 D 71 " ideal model delta sigma weight residual 1.623 1.447 0.176 2.00e-02 2.50e+03 7.70e+01 bond pdb=" CA ASP A 76 " pdb=" C ASP A 76 " ideal model delta sigma weight residual 1.524 1.421 0.103 1.23e-02 6.61e+03 7.04e+01 bond pdb=" N3 G47 D 71 " pdb=" C4 G47 D 71 " ideal model delta sigma weight residual 1.492 1.345 0.147 2.00e-02 2.50e+03 5.40e+01 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 59.95 - 83.94: 3 83.94 - 107.93: 760 107.93 - 131.93: 11480 131.93 - 155.92: 44 155.92 - 179.91: 2 Bond angle restraints: 12289 Sorted by residual: angle pdb=" C1' G47 D 71 " pdb=" N9 G47 D 71 " pdb=" C8 G47 D 71 " ideal model delta sigma weight residual 104.99 127.24 -22.25 3.00e+00 1.11e-01 5.50e+01 angle pdb=" C3' G D 70 " pdb=" O3' G D 70 " pdb=" P G47 D 71 " ideal model delta sigma weight residual 120.20 109.89 10.31 1.50e+00 4.44e-01 4.72e+01 angle pdb=" O1P G47 D 71 " pdb=" P G47 D 71 " pdb=" O2P G47 D 71 " ideal model delta sigma weight residual 109.47 120.07 -10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" N ASP A 76 " pdb=" CA ASP A 76 " pdb=" CB ASP A 76 " ideal model delta sigma weight residual 110.42 115.76 -5.34 1.63e+00 3.76e-01 1.07e+01 angle pdb=" C VAL A 75 " pdb=" N ASP A 76 " pdb=" CA ASP A 76 " ideal model delta sigma weight residual 122.77 118.47 4.30 1.33e+00 5.65e-01 1.04e+01 ... (remaining 12284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 5185 35.86 - 71.72: 177 71.72 - 107.58: 24 107.58 - 143.44: 0 143.44 - 179.30: 1 Dihedral angle restraints: 5387 sinusoidal: 2619 harmonic: 2768 Sorted by residual: dihedral pdb=" C10 EFZ A 602 " pdb=" C8 EFZ A 602 " pdb=" C9 EFZ A 602 " pdb=" C7 EFZ A 602 " ideal model delta sinusoidal sigma weight residual -152.64 26.66 -179.30 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA GLN B 151 " pdb=" C GLN B 151 " pdb=" N GLY B 152 " pdb=" CA GLY B 152 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP A 76 " pdb=" CB ASP A 76 " pdb=" CG ASP A 76 " pdb=" OD1 ASP A 76 " ideal model delta sinusoidal sigma weight residual -30.00 -87.54 57.54 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1266 0.071 - 0.142: 122 0.142 - 0.213: 3 0.213 - 0.284: 0 0.284 - 0.354: 1 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA ASP A 76 " pdb=" N ASP A 76 " pdb=" C ASP A 76 " pdb=" CB ASP A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C10 EFZ A 602 " pdb=" C11 EFZ A 602 " pdb=" C12 EFZ A 602 " pdb=" C9 EFZ A 602 " both_signs ideal model delta sigma weight residual True 2.32 -2.52 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2' G D 73 " pdb=" C3' G D 73 " pdb=" O2' G D 73 " pdb=" C1' G D 73 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1389 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G47 D 71 " -0.061 2.00e-02 2.50e+03 1.33e-01 5.71e+02 pdb=" N9 G47 D 71 " -0.010 2.00e-02 2.50e+03 pdb=" C8 G47 D 71 " 0.067 2.00e-02 2.50e+03 pdb=" N7 G47 D 71 " 0.091 2.00e-02 2.50e+03 pdb=" C5 G47 D 71 " 0.023 2.00e-02 2.50e+03 pdb=" C6 G47 D 71 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G47 D 71 " 0.062 2.00e-02 2.50e+03 pdb=" N1 G47 D 71 " -0.066 2.00e-02 2.50e+03 pdb=" C2 G47 D 71 " -0.128 2.00e-02 2.50e+03 pdb=" N2 G47 D 71 " -0.196 2.00e-02 2.50e+03 pdb=" N3 G47 D 71 " -0.116 2.00e-02 2.50e+03 pdb=" C4 G47 D 71 " -0.043 2.00e-02 2.50e+03 pdb=" C6A G47 D 71 " 0.365 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 75 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C VAL A 75 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 75 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP A 76 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 8 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 9 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " 0.028 5.00e-02 4.00e+02 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 733 2.74 - 3.28: 8452 3.28 - 3.82: 14958 3.82 - 4.36: 18870 4.36 - 4.90: 31126 Nonbonded interactions: 74139 Sorted by model distance: nonbonded pdb=" OD2 ASP B 76 " pdb=" NH1 ARG B 78 " model vdw 2.198 2.520 nonbonded pdb=" NH1 ARG B 72 " pdb=" O LYS B 73 " model vdw 2.223 2.520 nonbonded pdb=" O ASN A 348 " pdb=" ND2 ASN A 348 " model vdw 2.236 2.520 nonbonded pdb=" OH TYR B 354 " pdb=" OE1 GLU B 370 " model vdw 2.236 2.440 nonbonded pdb=" NH1 ARG A 277 " pdb=" O ALA A 355 " model vdw 2.243 2.520 ... (remaining 74134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.740 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: 12.620 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.006 0.209 8876 Z= 0.347 Angle : 0.560 22.250 12289 Z= 0.274 Chirality : 0.041 0.354 1392 Planarity : 0.005 0.133 1378 Dihedral : 16.980 179.303 3601 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 0.87 % Allowed : 0.37 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.29), residues: 937 helix: 1.63 (0.31), residues: 319 sheet: -0.77 (0.42), residues: 164 loop : 0.14 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 414 HIS 0.003 0.000 HIS A 361 PHE 0.004 0.001 PHE B 346 TYR 0.015 0.001 TYR A 483 ARG 0.005 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.637 Fit side-chains REVERT: A 76 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6611 (t70) REVERT: A 223 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5706 (ptmt) REVERT: A 388 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7507 (tptp) REVERT: B 43 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7676 (mtpt) REVERT: B 173 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7736 (ttmm) REVERT: B 212 TRP cc_start: 0.6863 (m100) cc_final: 0.6106 (t60) REVERT: B 323 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8229 (mtmt) outliers start: 7 outliers final: 1 residues processed: 125 average time/residue: 1.2871 time to fit residues: 171.2244 Evaluate side-chains 74 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 348 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 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 242 GLN A 487 GLN B 91 GLN B 151 GLN B 278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8876 Z= 0.191 Angle : 0.530 7.352 12289 Z= 0.262 Chirality : 0.041 0.158 1392 Planarity : 0.004 0.038 1378 Dihedral : 15.629 90.762 1730 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.74 % Allowed : 8.96 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 937 helix: 1.41 (0.29), residues: 333 sheet: -0.83 (0.42), residues: 157 loop : 0.14 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.002 0.001 HIS A 361 PHE 0.011 0.001 PHE B 416 TYR 0.010 0.001 TYR A 144 ARG 0.005 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.996 Fit side-chains REVERT: A 76 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6398 (t70) REVERT: A 223 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.5784 (ptmt) REVERT: A 388 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7247 (tptm) REVERT: B 43 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7656 (mtpt) REVERT: B 173 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7672 (ttmm) REVERT: B 212 TRP cc_start: 0.6982 (m100) cc_final: 0.6307 (t60) outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 1.2184 time to fit residues: 124.9724 Evaluate side-chains 74 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 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 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8876 Z= 0.288 Angle : 0.547 8.059 12289 Z= 0.271 Chirality : 0.042 0.157 1392 Planarity : 0.004 0.057 1378 Dihedral : 15.599 91.664 1730 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.99 % Allowed : 10.45 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 937 helix: 1.02 (0.28), residues: 342 sheet: -0.92 (0.41), residues: 157 loop : -0.08 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 PHE 0.015 0.002 PHE B 416 TYR 0.011 0.002 TYR B 144 ARG 0.008 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 0.902 Fit side-chains REVERT: A 16 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6446 (mtt) REVERT: A 223 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.5725 (ptmt) REVERT: A 291 GLU cc_start: 0.7230 (tt0) cc_final: 0.6935 (tt0) REVERT: A 388 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7333 (tptp) REVERT: A 511 ASP cc_start: 0.7308 (m-30) cc_final: 0.7050 (t0) REVERT: B 43 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7708 (mtpt) REVERT: B 173 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7779 (ttmm) REVERT: B 212 TRP cc_start: 0.7101 (m100) cc_final: 0.6333 (t60) outliers start: 24 outliers final: 9 residues processed: 85 average time/residue: 1.0034 time to fit residues: 92.4579 Evaluate side-chains 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 78 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8876 Z= 0.288 Angle : 0.547 8.059 12289 Z= 0.271 Chirality : 0.042 0.157 1392 Planarity : 0.004 0.057 1378 Dihedral : 15.552 91.664 1728 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.37 % Allowed : 12.19 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 937 helix: 1.02 (0.28), residues: 342 sheet: -0.92 (0.41), residues: 157 loop : -0.08 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 PHE 0.015 0.002 PHE B 416 TYR 0.011 0.002 TYR B 144 ARG 0.008 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 1.015 Fit side-chains REVERT: A 16 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6444 (mtt) REVERT: A 223 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.5725 (ptmt) REVERT: A 291 GLU cc_start: 0.7220 (tt0) cc_final: 0.6935 (tt0) REVERT: A 388 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7333 (tptp) REVERT: A 511 ASP cc_start: 0.7313 (m-30) cc_final: 0.7049 (t0) REVERT: B 43 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7708 (mtpt) REVERT: B 173 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7779 (ttmm) REVERT: B 212 TRP cc_start: 0.7095 (m100) cc_final: 0.6333 (t60) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.8994 time to fit residues: 70.4854 Evaluate side-chains 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 0.0170 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8876 Z= 0.288 Angle : 0.547 8.059 12289 Z= 0.271 Chirality : 0.042 0.157 1392 Planarity : 0.004 0.057 1378 Dihedral : 15.552 91.664 1728 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.37 % Allowed : 12.19 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 937 helix: 1.02 (0.28), residues: 342 sheet: -0.92 (0.41), residues: 157 loop : -0.08 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 PHE 0.015 0.002 PHE B 416 TYR 0.011 0.002 TYR B 144 ARG 0.008 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.938 Fit side-chains REVERT: A 16 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6444 (mtt) REVERT: A 223 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.5725 (ptmt) REVERT: A 291 GLU cc_start: 0.7220 (tt0) cc_final: 0.6935 (tt0) REVERT: A 388 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7333 (tptp) REVERT: A 511 ASP cc_start: 0.7313 (m-30) cc_final: 0.7049 (t0) REVERT: B 43 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7708 (mtpt) REVERT: B 173 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7779 (ttmm) REVERT: B 212 TRP cc_start: 0.7095 (m100) cc_final: 0.6333 (t60) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.8831 time to fit residues: 69.2233 Evaluate side-chains 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8876 Z= 0.309 Angle : 0.550 7.988 12289 Z= 0.270 Chirality : 0.042 0.160 1392 Planarity : 0.004 0.045 1378 Dihedral : 15.505 91.260 1728 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.11 % Allowed : 10.82 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 937 helix: 0.92 (0.28), residues: 342 sheet: -0.94 (0.41), residues: 157 loop : -0.15 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 402 HIS 0.003 0.001 HIS B 198 PHE 0.014 0.002 PHE B 416 TYR 0.016 0.002 TYR A 483 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 0.938 Fit side-chains REVERT: A 223 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.5638 (ptmt) REVERT: A 291 GLU cc_start: 0.7218 (tt0) cc_final: 0.6934 (tt0) REVERT: A 298 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: A 388 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7342 (tptp) REVERT: A 511 ASP cc_start: 0.7298 (m-30) cc_final: 0.7073 (t0) REVERT: B 43 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7707 (mtpt) REVERT: B 212 TRP cc_start: 0.7210 (m100) cc_final: 0.6414 (t60) outliers start: 25 outliers final: 11 residues processed: 79 average time/residue: 0.9876 time to fit residues: 85.0270 Evaluate side-chains 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8876 Z= 0.309 Angle : 0.550 7.988 12289 Z= 0.270 Chirality : 0.042 0.160 1392 Planarity : 0.004 0.045 1378 Dihedral : 15.503 91.260 1728 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.62 % Allowed : 12.94 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 937 helix: 0.92 (0.28), residues: 342 sheet: -0.94 (0.41), residues: 157 loop : -0.15 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 402 HIS 0.003 0.001 HIS B 198 PHE 0.014 0.002 PHE B 416 TYR 0.016 0.002 TYR A 483 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.988 Fit side-chains REVERT: A 223 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5638 (ptmt) REVERT: A 291 GLU cc_start: 0.7214 (tt0) cc_final: 0.6935 (tt0) REVERT: A 298 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: A 388 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7342 (tptp) REVERT: A 511 ASP cc_start: 0.7301 (m-30) cc_final: 0.7073 (t0) REVERT: B 43 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7706 (mtpt) REVERT: B 212 TRP cc_start: 0.7210 (m100) cc_final: 0.6413 (t60) outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.8629 time to fit residues: 66.7700 Evaluate side-chains 72 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.0170 chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8876 Z= 0.309 Angle : 0.550 7.988 12289 Z= 0.270 Chirality : 0.042 0.160 1392 Planarity : 0.004 0.045 1378 Dihedral : 15.503 91.260 1728 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.62 % Allowed : 13.06 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 937 helix: 0.92 (0.28), residues: 342 sheet: -0.94 (0.41), residues: 157 loop : -0.15 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 402 HIS 0.003 0.001 HIS B 198 PHE 0.014 0.002 PHE B 416 TYR 0.016 0.002 TYR A 483 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.954 Fit side-chains REVERT: A 223 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5638 (ptmt) REVERT: A 291 GLU cc_start: 0.7215 (tt0) cc_final: 0.6935 (tt0) REVERT: A 298 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: A 388 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7342 (tptp) REVERT: A 511 ASP cc_start: 0.7301 (m-30) cc_final: 0.7073 (t0) REVERT: B 43 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7706 (mtpt) REVERT: B 212 TRP cc_start: 0.7210 (m100) cc_final: 0.6413 (t60) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.8828 time to fit residues: 67.3030 Evaluate side-chains 72 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 83 optimal weight: 0.0770 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8876 Z= 0.172 Angle : 0.498 7.588 12289 Z= 0.246 Chirality : 0.040 0.163 1392 Planarity : 0.004 0.044 1378 Dihedral : 15.447 91.157 1728 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.24 % Allowed : 13.43 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 937 helix: 1.14 (0.29), residues: 340 sheet: -0.98 (0.40), residues: 168 loop : 0.02 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 PHE 0.013 0.001 PHE A 130 TYR 0.027 0.001 TYR A 483 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.946 Fit side-chains REVERT: A 223 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.5560 (ptmt) REVERT: A 291 GLU cc_start: 0.7192 (tt0) cc_final: 0.6936 (tt0) REVERT: A 298 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: A 388 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7359 (tptm) REVERT: A 511 ASP cc_start: 0.7292 (m-30) cc_final: 0.7039 (t0) REVERT: B 43 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7680 (mtpt) REVERT: B 212 TRP cc_start: 0.7146 (m100) cc_final: 0.6397 (t60) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.9447 time to fit residues: 76.0360 Evaluate side-chains 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8876 Z= 0.172 Angle : 0.498 7.588 12289 Z= 0.246 Chirality : 0.040 0.163 1392 Planarity : 0.004 0.044 1378 Dihedral : 15.422 91.157 1726 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.00 % Allowed : 13.56 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 937 helix: 1.14 (0.29), residues: 340 sheet: -0.98 (0.40), residues: 168 loop : 0.02 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 PHE 0.013 0.001 PHE A 130 TYR 0.027 0.001 TYR A 483 ARG 0.003 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.984 Fit side-chains REVERT: A 223 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.5560 (ptmt) REVERT: A 291 GLU cc_start: 0.7187 (tt0) cc_final: 0.6936 (tt0) REVERT: A 298 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: A 388 LYS cc_start: 0.7746 (mtmt) cc_final: 0.7361 (tptm) REVERT: A 511 ASP cc_start: 0.7288 (m-30) cc_final: 0.7039 (t0) REVERT: B 43 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7680 (mtpt) REVERT: B 212 TRP cc_start: 0.7147 (m100) cc_final: 0.6397 (t60) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.8806 time to fit residues: 66.0260 Evaluate side-chains 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 chunk 79 optimal weight: 0.0070 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117885 restraints weight = 9840.963| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.54 r_work: 0.3263 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8876 Z= 0.161 Angle : 0.507 7.548 12289 Z= 0.251 Chirality : 0.040 0.263 1392 Planarity : 0.004 0.044 1378 Dihedral : 15.420 91.105 1726 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.12 % Allowed : 13.68 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 937 helix: 1.20 (0.29), residues: 340 sheet: -0.94 (0.40), residues: 168 loop : 0.06 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 PHE 0.013 0.001 PHE A 130 TYR 0.009 0.001 TYR A 183 ARG 0.003 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.29 seconds wall clock time: 47 minutes 40.20 seconds (2860.20 seconds total)