Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 19:57:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_22900_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_22900.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_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_22900/07_2023/7kjw_22900_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_22900_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_22900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_22900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_22900_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjw_22900/07_2023/7kjw_22900_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 4.67, per 1000 atoms: 0.55 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: 3.70 Conformation dependent library (CDL) restraints added in 1.2 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: 3.13 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: 2.68 Time building geometry restraints manager: 3.97 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 - 18.84: 4730 18.84 - 37.68: 375 37.68 - 56.52: 59 56.52 - 75.37: 22 75.37 - 94.21: 5 Dihedral angle restraints: 5191 sinusoidal: 2423 harmonic: 2768 Sorted by residual: 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 dihedral pdb=" CA ASN A 348 " pdb=" CB ASN A 348 " pdb=" CG ASN A 348 " pdb=" OD1 ASN A 348 " ideal model delta sinusoidal sigma weight residual 120.00 -173.31 -66.69 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 5188 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: 3.020 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: 13.560 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.070 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.370 ------------------------------------------------------------------------------- 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 : 13.763 94.206 3405 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 % 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 *********************** 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 : 1.030 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 125 average time/residue: 1.3348 time to fit residues: 177.3242 Evaluate side-chains 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2325 time to fit residues: 1.5117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 348 ASN A 487 GLN B 91 GLN B 151 GLN B 278 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8876 Z= 0.185 Angle : 0.515 7.225 12289 Z= 0.256 Chirality : 0.040 0.154 1392 Planarity : 0.004 0.038 1378 Dihedral : 6.972 91.205 1526 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.37 % 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: 0.56 (0.28), residues: 937 helix: 1.47 (0.30), residues: 333 sheet: -0.87 (0.42), residues: 158 loop : 0.13 (0.30), residues: 446 *********************** 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 94 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.996 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 91 average time/residue: 1.2136 time to fit residues: 118.2749 Evaluate side-chains 69 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.1499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 8876 Z= 0.396 Angle : 0.599 8.835 12289 Z= 0.294 Chirality : 0.043 0.165 1392 Planarity : 0.004 0.043 1378 Dihedral : 7.362 91.822 1526 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 3.11 % 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: -0.03 (0.27), residues: 937 helix: 0.85 (0.28), residues: 341 sheet: -1.07 (0.40), residues: 157 loop : -0.16 (0.29), residues: 439 *********************** 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 87 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 0.889 Fit side-chains outliers start: 25 outliers final: 7 residues processed: 81 average time/residue: 1.0020 time to fit residues: 88.8209 Evaluate side-chains 62 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.2862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 78 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8876 Z= 0.178 Angle : 0.509 7.608 12289 Z= 0.250 Chirality : 0.040 0.161 1392 Planarity : 0.004 0.044 1378 Dihedral : 7.286 91.541 1526 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 2.36 % 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: 0.14 (0.27), residues: 937 helix: 1.02 (0.28), residues: 342 sheet: -1.01 (0.40), residues: 168 loop : -0.06 (0.29), residues: 427 *********************** 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 82 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.896 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 77 average time/residue: 0.9669 time to fit residues: 81.5848 Evaluate side-chains 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1338 time to fit residues: 1.5203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 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 B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8876 Z= 0.178 Angle : 0.509 7.608 12289 Z= 0.250 Chirality : 0.040 0.161 1392 Planarity : 0.004 0.044 1378 Dihedral : 7.286 91.541 1526 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.37 % 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: 0.14 (0.27), residues: 937 helix: 1.02 (0.28), residues: 342 sheet: -1.01 (0.40), residues: 168 loop : -0.06 (0.29), residues: 427 *********************** 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 69 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.929 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.9542 time to fit residues: 72.1958 Evaluate side-chains 66 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.2825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8876 Z= 0.263 Angle : 0.539 11.823 12289 Z= 0.261 Chirality : 0.041 0.162 1392 Planarity : 0.004 0.044 1378 Dihedral : 7.374 91.036 1526 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.86 % 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: 0.07 (0.27), residues: 937 helix: 0.95 (0.28), residues: 340 sheet: -1.08 (0.40), residues: 168 loop : -0.06 (0.29), residues: 429 *********************** 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 79 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.894 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 75 average time/residue: 1.0285 time to fit residues: 84.1256 Evaluate side-chains 66 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1359 time to fit residues: 2.0316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 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 85 GLN A 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8876 Z= 0.175 Angle : 0.502 11.468 12289 Z= 0.242 Chirality : 0.039 0.161 1392 Planarity : 0.004 0.044 1378 Dihedral : 7.318 90.258 1526 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 2.24 % 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: 0.24 (0.28), residues: 937 helix: 1.11 (0.29), residues: 341 sheet: -0.98 (0.40), residues: 168 loop : 0.01 (0.30), residues: 428 *********************** 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 81 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.970 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 1.0119 time to fit residues: 86.1204 Evaluate side-chains 67 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.2651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.0070 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8876 Z= 0.167 Angle : 0.501 10.667 12289 Z= 0.242 Chirality : 0.039 0.159 1392 Planarity : 0.004 0.045 1378 Dihedral : 7.296 90.031 1526 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 2.11 % 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: 0.32 (0.28), residues: 937 helix: 1.15 (0.29), residues: 341 sheet: -0.91 (0.40), residues: 168 loop : 0.07 (0.30), residues: 428 *********************** 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 77 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.945 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.9918 time to fit residues: 82.1851 Evaluate side-chains 69 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.3647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 90 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8876 Z= 0.266 Angle : 0.535 7.878 12289 Z= 0.261 Chirality : 0.040 0.161 1392 Planarity : 0.004 0.045 1378 Dihedral : 7.404 89.862 1526 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.99 % 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: 0.23 (0.27), residues: 937 helix: 1.01 (0.29), residues: 339 sheet: -0.98 (0.40), residues: 168 loop : 0.09 (0.29), residues: 430 *********************** 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 73 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 1.436 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 1.0350 time to fit residues: 82.7022 Evaluate side-chains 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.2607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0470 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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: 0.7959 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8876 Z= 0.155 Angle : 0.501 11.392 12289 Z= 0.241 Chirality : 0.039 0.160 1392 Planarity : 0.004 0.045 1378 Dihedral : 7.330 89.463 1526 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.74 % 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: 0.42 (0.28), residues: 937 helix: 1.21 (0.29), residues: 339 sheet: -0.80 (0.40), residues: 167 loop : 0.13 (0.30), residues: 431 ********************** 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 76 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 74 average time/residue: 0.9734 time to fit residues: 78.9745 Evaluate side-chains 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.2841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 79 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118477 restraints weight = 9651.621| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.67 r_work: 0.3269 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2572 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= 0.160 Angle : 0.504 10.742 12289 Z= 0.243 Chirality : 0.039 0.159 1392 Planarity : 0.004 0.059 1378 Dihedral : 7.314 89.253 1526 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.62 % 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: 0.43 (0.28), residues: 937 helix: 1.19 (0.29), residues: 341 sheet: -0.72 (0.40), residues: 167 loop : 0.13 (0.30), residues: 429 =============================================================================== Job complete usr+sys time: 2628.18 seconds wall clock time: 47 minutes 59.76 seconds (2879.76 seconds total)