Starting phenix.real_space_refine (version: dev) on Mon Dec 12 17:44:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/12_2022/7l48_23157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/12_2022/7l48_23157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/12_2022/7l48_23157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/12_2022/7l48_23157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/12_2022/7l48_23157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/12_2022/7l48_23157.pdb" } resolution = 3.9 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B ASP 510": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 11488 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4229 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 504} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4181 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 501} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3074 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 4, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 16, 'rna3p': 127} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3837 SG CYS A 475 13.590 59.792 45.199 1.00144.72 S ATOM 4048 SG CYS A 500 11.483 59.182 41.090 1.00168.30 S ATOM 364 SG CYS A 50 53.063 98.075 78.234 1.00132.99 S ATOM 502 SG CYS A 69 56.898 98.778 78.930 1.00109.77 S ATOM 527 SG CYS A 72 55.165 95.811 80.252 1.00111.13 S ATOM 8022 SG CYS B 475 60.243 58.550 15.167 1.00129.53 S ATOM 8043 SG CYS B 478 59.669 57.064 10.831 1.00129.65 S ATOM 4570 SG CYS B 50 29.666 39.470 31.268 1.00448.64 S Time building chain proxies: 7.02, per 1000 atoms: 0.61 Number of scatterers: 11488 At special positions: 0 Unit cell: (101.85, 119.7, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 37 16.00 P 144 15.00 O 2512 8.00 N 2052 7.00 C 6739 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=0, symmetry=0 Time building additional restraints: 5.64 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 475 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 72 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 50 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 475 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 50 " Number of angles added : 3 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 43.8% alpha, 9.3% beta 47 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.665A pdb=" N ASN A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 4.335A pdb=" N LYS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 94 through 126 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.472A pdb=" N TYR A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.629A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.855A pdb=" N ARG A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.597A pdb=" N GLU A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 Processing helix chain 'A' and resid 382 through 414 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.857A pdb=" N MET A 448 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 508 through 519 removed outlier: 4.673A pdb=" N ILE A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 42 Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.720A pdb=" N ALA B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.242A pdb=" N LYS B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 94 through 126 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.831A pdb=" N VAL B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.807A pdb=" N ALA B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.585A pdb=" N LEU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.998A pdb=" N GLY B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 382 through 415 removed outlier: 3.954A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.572A pdb=" N ARG B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.743A pdb=" N ILE B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 4.215A pdb=" N PHE A 214 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A 251 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 253 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.931A pdb=" N ALA A 49 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 64 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 removed outlier: 7.032A pdb=" N GLY A 323 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.649A pdb=" N TYR B 287 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345 removed outlier: 5.507A pdb=" N THR B 418 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 321 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLN B 420 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B 323 " --> pdb=" O GLN B 420 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 462 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 500 365 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2651 1.34 - 1.46: 3594 1.46 - 1.58: 5439 1.58 - 1.71: 286 1.71 - 1.83: 51 Bond restraints: 12021 Sorted by residual: bond pdb=" CA SER B 51 " pdb=" CB SER B 51 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.59e-02 3.96e+03 2.17e+01 bond pdb=" N LYS A 383 " pdb=" CA LYS A 383 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.36e+01 bond pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.30e+01 bond pdb=" N LEU A 194 " pdb=" CA LEU A 194 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.79e+00 bond pdb=" N LEU A 382 " pdb=" CA LEU A 382 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.94e+00 ... (remaining 12016 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.28: 620 104.28 - 111.71: 5486 111.71 - 119.13: 4565 119.13 - 126.55: 5692 126.55 - 133.98: 512 Bond angle restraints: 16875 Sorted by residual: angle pdb=" N GLU B 390 " pdb=" CA GLU B 390 " pdb=" CB GLU B 390 " ideal model delta sigma weight residual 110.12 118.78 -8.66 1.47e+00 4.63e-01 3.47e+01 angle pdb=" C PHE A 435 " pdb=" N ASN A 436 " pdb=" CA ASN A 436 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" N GLN B 88 " pdb=" CA GLN B 88 " pdb=" CB GLN B 88 " ideal model delta sigma weight residual 110.13 118.64 -8.51 1.48e+00 4.57e-01 3.31e+01 angle pdb=" C PRO B 219 " pdb=" N PHE B 220 " pdb=" CA PHE B 220 " ideal model delta sigma weight residual 122.20 130.82 -8.62 1.72e+00 3.38e-01 2.51e+01 angle pdb=" CA GLU A 123 " pdb=" CB GLU A 123 " pdb=" CG GLU A 123 " ideal model delta sigma weight residual 114.10 123.94 -9.84 2.00e+00 2.50e-01 2.42e+01 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 6754 35.72 - 71.44: 222 71.44 - 107.16: 19 107.16 - 142.88: 2 142.88 - 178.60: 3 Dihedral angle restraints: 7000 sinusoidal: 3933 harmonic: 3067 Sorted by residual: dihedral pdb=" O4' U E 92 " pdb=" C1' U E 92 " pdb=" N1 U E 92 " pdb=" C2 U E 92 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C E 77 " pdb=" C1' C E 77 " pdb=" N1 C E 77 " pdb=" C2 C E 77 " ideal model delta sinusoidal sigma weight residual 232.00 55.26 176.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U E 110 " pdb=" C1' U E 110 " pdb=" N1 U E 110 " pdb=" C2 U E 110 " ideal model delta sinusoidal sigma weight residual -160.00 -56.82 -103.18 1 1.50e+01 4.44e-03 5.24e+01 ... (remaining 6997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1733 0.089 - 0.179: 181 0.179 - 0.268: 26 0.268 - 0.357: 2 0.357 - 0.446: 2 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CA CYS A 50 " pdb=" N CYS A 50 " pdb=" C CYS A 50 " pdb=" CB CYS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C3' A E 129 " pdb=" C4' A E 129 " pdb=" O3' A E 129 " pdb=" C2' A E 129 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1941 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 52 " 0.025 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C LYS B 52 " -0.090 2.00e-02 2.50e+03 pdb=" O LYS B 52 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS B 53 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 48 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C GLU B 48 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU B 48 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 49 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 84 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS B 84 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 84 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 85 " 0.021 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2561 2.79 - 3.32: 10342 3.32 - 3.85: 21243 3.85 - 4.37: 24108 4.37 - 4.90: 36428 Nonbonded interactions: 94682 Sorted by model distance: nonbonded pdb=" OG SER B 51 " pdb=" CD ARG B 66 " model vdw 2.263 3.440 nonbonded pdb=" O ASN A 133 " pdb=" OG SER A 136 " model vdw 2.273 2.440 nonbonded pdb=" N6 A E 100 " pdb=" O2 C E 123 " model vdw 2.283 2.520 nonbonded pdb=" OG SER A 476 " pdb=" ND2 ASN A 512 " model vdw 2.298 2.520 nonbonded pdb=" C SER B 51 " pdb=" OG SER B 51 " model vdw 2.302 2.616 ... (remaining 94677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 260 or (resid 261 through 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ CB )) or resid 493 through 525 or resid 601 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 144 5.49 5 S 37 5.16 5 C 6739 2.51 5 N 2052 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 4.540 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 39.660 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.005 0.075 12021 Z= 0.293 Angle : 0.965 11.153 16875 Z= 0.547 Chirality : 0.058 0.446 1944 Planarity : 0.006 0.061 1620 Dihedral : 16.897 178.601 5010 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.21), residues: 1037 helix: -1.48 (0.20), residues: 441 sheet: -2.30 (0.40), residues: 132 loop : -3.27 (0.22), residues: 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2844 time to fit residues: 35.7487 Evaluate side-chains 52 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12021 Z= 0.194 Angle : 0.580 11.010 16875 Z= 0.306 Chirality : 0.038 0.179 1944 Planarity : 0.004 0.039 1620 Dihedral : 15.469 176.187 2858 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 1037 helix: 0.11 (0.23), residues: 458 sheet: -2.06 (0.41), residues: 139 loop : -2.91 (0.25), residues: 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.2632 time to fit residues: 27.3287 Evaluate side-chains 56 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1088 time to fit residues: 2.7407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.0870 chunk 88 optimal weight: 0.0470 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 overall best weight: 2.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 516 ASN B 32 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN B 189 ASN B 339 ASN B 349 ASN B 516 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 12021 Z= 0.292 Angle : 0.637 10.833 16875 Z= 0.333 Chirality : 0.039 0.209 1944 Planarity : 0.005 0.057 1620 Dihedral : 15.622 179.997 2858 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1037 helix: 0.67 (0.24), residues: 454 sheet: -1.91 (0.42), residues: 136 loop : -2.75 (0.27), residues: 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 72 average time/residue: 0.2230 time to fit residues: 24.1438 Evaluate side-chains 53 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1224 time to fit residues: 3.6502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 0.0980 chunk 30 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 12021 Z= 0.316 Angle : 0.650 9.176 16875 Z= 0.338 Chirality : 0.039 0.162 1944 Planarity : 0.005 0.047 1620 Dihedral : 15.885 178.794 2858 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.26), residues: 1037 helix: 0.93 (0.24), residues: 451 sheet: -1.99 (0.42), residues: 142 loop : -2.68 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 70 average time/residue: 0.2314 time to fit residues: 24.4654 Evaluate side-chains 56 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1671 time to fit residues: 3.6470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 210 HIS A 349 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12021 Z= 0.165 Angle : 0.568 8.952 16875 Z= 0.292 Chirality : 0.037 0.158 1944 Planarity : 0.004 0.039 1620 Dihedral : 15.505 175.264 2858 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.20 % Favored : 91.71 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.26), residues: 1037 helix: 1.22 (0.24), residues: 460 sheet: -1.58 (0.45), residues: 135 loop : -2.59 (0.27), residues: 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 68 average time/residue: 0.2109 time to fit residues: 22.3283 Evaluate side-chains 56 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1062 time to fit residues: 2.5249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 12021 Z= 0.369 Angle : 0.692 9.095 16875 Z= 0.360 Chirality : 0.040 0.179 1944 Planarity : 0.005 0.048 1620 Dihedral : 15.937 178.727 2858 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 1037 helix: 0.97 (0.24), residues: 459 sheet: -1.93 (0.43), residues: 142 loop : -2.64 (0.28), residues: 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 64 average time/residue: 0.2203 time to fit residues: 21.9011 Evaluate side-chains 53 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1291 time to fit residues: 3.5828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 210 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 12021 Z= 0.240 Angle : 0.626 13.068 16875 Z= 0.321 Chirality : 0.039 0.264 1944 Planarity : 0.005 0.133 1620 Dihedral : 15.681 175.926 2858 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.26), residues: 1037 helix: 1.11 (0.24), residues: 461 sheet: -1.81 (0.44), residues: 142 loop : -2.54 (0.28), residues: 434 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 65 average time/residue: 0.2036 time to fit residues: 21.2149 Evaluate side-chains 54 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1617 time to fit residues: 3.1235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 0.0370 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 210 HIS ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 12021 Z= 0.153 Angle : 0.599 16.715 16875 Z= 0.298 Chirality : 0.037 0.221 1944 Planarity : 0.004 0.091 1620 Dihedral : 15.178 171.462 2858 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.27), residues: 1037 helix: 1.25 (0.25), residues: 463 sheet: -1.61 (0.45), residues: 139 loop : -2.51 (0.28), residues: 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.2205 time to fit residues: 22.7185 Evaluate side-chains 55 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1107 time to fit residues: 2.8415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.0000 chunk 32 optimal weight: 0.0370 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 overall best weight: 1.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 210 HIS ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12021 Z= 0.176 Angle : 0.606 13.891 16875 Z= 0.304 Chirality : 0.037 0.266 1944 Planarity : 0.004 0.088 1620 Dihedral : 15.052 171.779 2858 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 1037 helix: 1.28 (0.24), residues: 464 sheet: -1.64 (0.45), residues: 139 loop : -2.43 (0.29), residues: 434 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.2244 time to fit residues: 18.3888 Evaluate side-chains 47 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0975 time to fit residues: 1.6141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 12021 Z= 0.332 Angle : 0.693 13.471 16875 Z= 0.354 Chirality : 0.040 0.288 1944 Planarity : 0.005 0.092 1620 Dihedral : 15.372 174.850 2858 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.26), residues: 1037 helix: 1.10 (0.24), residues: 461 sheet: -1.84 (0.43), residues: 144 loop : -2.52 (0.28), residues: 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 1.094 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.2185 time to fit residues: 17.8106 Evaluate side-chains 47 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1206 time to fit residues: 1.9634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0370 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.070658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051389 restraints weight = 63973.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.052815 restraints weight = 32339.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.053613 restraints weight = 21706.656| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12021 Z= 0.169 Angle : 0.611 13.174 16875 Z= 0.309 Chirality : 0.037 0.283 1944 Planarity : 0.004 0.078 1620 Dihedral : 15.038 174.637 2858 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.27), residues: 1037 helix: 1.21 (0.24), residues: 463 sheet: -1.64 (0.44), residues: 139 loop : -2.44 (0.29), residues: 435 =============================================================================== Job complete usr+sys time: 1762.32 seconds wall clock time: 33 minutes 43.57 seconds (2023.57 seconds total)