Starting phenix.real_space_refine on Thu Feb 15 06:46:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/02_2024/7l48_23157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/02_2024/7l48_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_23157/02_2024/7l48_23157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/02_2024/7l48_23157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/02_2024/7l48_23157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l48_23157/02_2024/7l48_23157.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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-5238/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: 6.43, per 1000 atoms: 0.56 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: 4.95 Conformation dependent library (CDL) restraints added in 1.6 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: 4.20 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: 4.36 Time building geometry restraints manager: 5.28 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: 6997 35.72 - 71.44: 426 71.44 - 107.16: 48 107.16 - 142.88: 2 142.88 - 178.60: 3 Dihedral angle restraints: 7476 sinusoidal: 4409 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 7473 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 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: 1.180 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: 4.000 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 37.430 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 20.408 178.601 5486 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 % Allowed : 3.56 % Favored : 96.21 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 223 HIS 0.028 0.003 HIS B 210 PHE 0.060 0.003 PHE A 354 TYR 0.032 0.002 TYR B 121 ARG 0.010 0.001 ARG B 363 *********************** 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 : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8106 (t80) cc_final: 0.7831 (t80) REVERT: A 421 MET cc_start: 0.7801 (tmm) cc_final: 0.7521 (tmm) REVERT: A 510 ASP cc_start: 0.8498 (m-30) cc_final: 0.8219 (m-30) REVERT: B 353 HIS cc_start: 0.8389 (t-90) cc_final: 0.8095 (t-170) REVERT: B 358 MET cc_start: 0.8598 (tpt) cc_final: 0.8079 (tpp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2720 time to fit residues: 34.1125 Evaluate side-chains 53 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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: 9.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 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: 0.8143 moved from start: 0.1885 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= 0.190 Angle : 0.569 7.111 16875 Z= 0.302 Chirality : 0.037 0.180 1944 Planarity : 0.004 0.040 1620 Dihedral : 21.242 176.568 3334 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.00 % Allowed : 11.47 % Favored : 87.53 % 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: 460 sheet: -2.07 (0.42), residues: 139 loop : -2.92 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 223 HIS 0.008 0.001 HIS B 210 PHE 0.024 0.001 PHE B 220 TYR 0.010 0.001 TYR A 122 ARG 0.008 0.000 ARG B 163 *********************** 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 77 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LYS cc_start: 0.9101 (pptt) cc_final: 0.8711 (pptt) REVERT: A 510 ASP cc_start: 0.8461 (m-30) cc_final: 0.8208 (m-30) REVERT: A 515 LEU cc_start: 0.9004 (tp) cc_final: 0.8686 (mt) REVERT: B 326 ASP cc_start: 0.8368 (t0) cc_final: 0.8095 (t0) REVERT: B 353 HIS cc_start: 0.8752 (t-90) cc_final: 0.8378 (t-170) REVERT: B 358 MET cc_start: 0.8780 (tpt) cc_final: 0.8561 (tpp) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.2735 time to fit residues: 28.8996 Evaluate side-chains 59 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 232 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 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: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 516 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 12021 Z= 0.475 Angle : 0.783 9.027 16875 Z= 0.412 Chirality : 0.044 0.191 1944 Planarity : 0.006 0.064 1620 Dihedral : 21.824 178.403 3334 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 30.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 3.23 % Allowed : 15.37 % Favored : 81.40 % 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: -2.05 (0.25), residues: 1037 helix: 0.27 (0.23), residues: 455 sheet: -2.08 (0.42), residues: 137 loop : -2.92 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 443 HIS 0.006 0.002 HIS B 139 PHE 0.023 0.002 PHE A 170 TYR 0.023 0.003 TYR A 122 ARG 0.003 0.001 ARG A 490 *********************** 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 81 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 52 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.8634 (tpp) cc_final: 0.8365 (ttp) REVERT: A 379 LYS cc_start: 0.8298 (ttpt) cc_final: 0.8066 (ttpt) REVERT: A 398 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9106 (tptp) REVERT: A 510 ASP cc_start: 0.8784 (m-30) cc_final: 0.8423 (m-30) REVERT: B 326 ASP cc_start: 0.8428 (t0) cc_final: 0.8085 (t0) outliers start: 29 outliers final: 18 residues processed: 76 average time/residue: 0.2223 time to fit residues: 25.4351 Evaluate side-chains 62 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 489 TYR 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: 3.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 HIS B 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12021 Z= 0.327 Angle : 0.662 9.477 16875 Z= 0.346 Chirality : 0.040 0.259 1944 Planarity : 0.005 0.055 1620 Dihedral : 21.762 178.232 3334 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.55 % Favored : 90.36 % Rotamer: Outliers : 3.01 % Allowed : 19.27 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.25), residues: 1037 helix: 0.66 (0.23), residues: 456 sheet: -2.20 (0.41), residues: 143 loop : -2.77 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 223 HIS 0.005 0.001 HIS A 53 PHE 0.014 0.002 PHE B 495 TYR 0.018 0.002 TYR B 445 ARG 0.002 0.000 ARG A 490 *********************** 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 78 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 51 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8821 (tpp) cc_final: 0.8535 (ttp) REVERT: A 346 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6590 (mp) REVERT: A 358 MET cc_start: 0.8103 (mtm) cc_final: 0.7691 (mtt) REVERT: A 398 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9078 (tptp) REVERT: A 510 ASP cc_start: 0.8701 (m-30) cc_final: 0.8421 (m-30) REVERT: B 326 ASP cc_start: 0.8433 (t0) cc_final: 0.8074 (t0) REVERT: B 353 HIS cc_start: 0.8850 (t-90) cc_final: 0.8649 (t-170) outliers start: 27 outliers final: 16 residues processed: 74 average time/residue: 0.2366 time to fit residues: 26.4104 Evaluate side-chains 62 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.0030 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12021 Z= 0.149 Angle : 0.562 9.549 16875 Z= 0.285 Chirality : 0.036 0.174 1944 Planarity : 0.004 0.038 1620 Dihedral : 21.296 171.432 3334 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.12 % Allowed : 19.71 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1037 helix: 1.10 (0.24), residues: 466 sheet: -1.76 (0.44), residues: 138 loop : -2.57 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.003 0.001 HIS A 139 PHE 0.014 0.001 PHE A 341 TYR 0.013 0.001 TYR A 287 ARG 0.002 0.000 ARG B 363 *********************** 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 83 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8603 (t80) cc_final: 0.8094 (t80) REVERT: A 178 MET cc_start: 0.8760 (tpp) cc_final: 0.8205 (ttp) REVERT: A 303 MET cc_start: 0.8658 (mmm) cc_final: 0.8416 (mmm) REVERT: A 309 ASP cc_start: 0.8393 (m-30) cc_final: 0.8193 (m-30) REVERT: A 317 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7748 (p) REVERT: A 515 LEU cc_start: 0.8950 (tp) cc_final: 0.8575 (mt) REVERT: B 187 SER cc_start: 0.7795 (OUTLIER) cc_final: 0.7355 (m) REVERT: B 326 ASP cc_start: 0.8486 (t0) cc_final: 0.8081 (t0) outliers start: 19 outliers final: 11 residues processed: 79 average time/residue: 0.2058 time to fit residues: 25.2069 Evaluate side-chains 63 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 271 THR 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: 9.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 305 ASN B 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 12021 Z= 0.375 Angle : 0.703 12.769 16875 Z= 0.362 Chirality : 0.041 0.192 1944 Planarity : 0.005 0.052 1620 Dihedral : 21.565 176.928 3334 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 3.34 % Allowed : 21.38 % Favored : 75.28 % 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: -1.31 (0.26), residues: 1037 helix: 0.99 (0.24), residues: 464 sheet: -2.00 (0.42), residues: 142 loop : -2.63 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 443 HIS 0.006 0.002 HIS B 139 PHE 0.016 0.002 PHE B 495 TYR 0.014 0.002 TYR A 18 ARG 0.006 0.001 ARG B 163 *********************** 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 77 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 47 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8766 (t80) cc_final: 0.8183 (t80) REVERT: A 178 MET cc_start: 0.8771 (tpp) cc_final: 0.8567 (ttp) REVERT: A 346 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6718 (mp) REVERT: A 358 MET cc_start: 0.8236 (mtm) cc_final: 0.7823 (mtm) REVERT: A 485 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7051 (t80) REVERT: B 78 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7872 (t70) REVERT: B 326 ASP cc_start: 0.8459 (t0) cc_final: 0.8053 (t0) outliers start: 30 outliers final: 20 residues processed: 73 average time/residue: 0.2102 time to fit residues: 23.9548 Evaluate side-chains 67 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 510 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4388 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= 0.200 Angle : 0.587 11.298 16875 Z= 0.299 Chirality : 0.037 0.171 1944 Planarity : 0.004 0.036 1620 Dihedral : 21.358 172.932 3334 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.56 % Allowed : 22.27 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 1037 helix: 1.24 (0.24), residues: 464 sheet: -1.92 (0.43), residues: 142 loop : -2.60 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.012 0.001 HIS B 353 PHE 0.009 0.001 PHE A 341 TYR 0.012 0.001 TYR A 82 ARG 0.002 0.000 ARG B 440 *********************** 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 77 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8714 (t80) cc_final: 0.8177 (t80) REVERT: A 178 MET cc_start: 0.8651 (tpp) cc_final: 0.8451 (mtp) REVERT: A 485 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7187 (t80) REVERT: A 510 ASP cc_start: 0.8805 (m-30) cc_final: 0.8249 (t0) REVERT: B 78 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7943 (t70) REVERT: B 118 ILE cc_start: 0.9303 (mm) cc_final: 0.9068 (mm) REVERT: B 326 ASP cc_start: 0.8472 (t0) cc_final: 0.8050 (t0) outliers start: 23 outliers final: 17 residues processed: 73 average time/residue: 0.2004 time to fit residues: 22.8919 Evaluate side-chains 69 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12021 Z= 0.400 Angle : 0.732 14.558 16875 Z= 0.374 Chirality : 0.042 0.243 1944 Planarity : 0.005 0.052 1620 Dihedral : 21.504 176.341 3334 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 28.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 3.12 % Allowed : 22.72 % Favored : 74.16 % 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: -1.37 (0.26), residues: 1037 helix: 0.91 (0.24), residues: 464 sheet: -2.00 (0.43), residues: 142 loop : -2.63 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 223 HIS 0.011 0.002 HIS B 353 PHE 0.015 0.002 PHE B 495 TYR 0.016 0.002 TYR A 18 ARG 0.003 0.001 ARG B 34 *********************** 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 77 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 49 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8730 (t80) cc_final: 0.8156 (t80) REVERT: A 303 MET cc_start: 0.8881 (mmm) cc_final: 0.8425 (mmm) REVERT: A 358 MET cc_start: 0.8292 (mtm) cc_final: 0.7928 (mtm) REVERT: A 485 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7062 (t80) REVERT: B 78 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7878 (t70) REVERT: B 118 ILE cc_start: 0.9312 (mm) cc_final: 0.9063 (mm) REVERT: B 326 ASP cc_start: 0.8415 (t0) cc_final: 0.7969 (t0) REVERT: B 358 MET cc_start: 0.8570 (tpp) cc_final: 0.8365 (tpp) REVERT: B 427 MET cc_start: 0.8551 (ttp) cc_final: 0.8236 (tmm) outliers start: 28 outliers final: 22 residues processed: 73 average time/residue: 0.2055 time to fit residues: 23.6395 Evaluate side-chains 71 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 47 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.0470 chunk 104 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12021 Z= 0.171 Angle : 0.607 13.345 16875 Z= 0.301 Chirality : 0.038 0.250 1944 Planarity : 0.004 0.036 1620 Dihedral : 21.160 170.686 3334 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.34 % Allowed : 24.28 % Favored : 73.39 % 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: -1.03 (0.26), residues: 1037 helix: 1.24 (0.24), residues: 465 sheet: -1.76 (0.44), residues: 139 loop : -2.55 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.014 0.001 HIS B 353 PHE 0.011 0.001 PHE A 240 TYR 0.012 0.001 TYR A 82 ARG 0.004 0.000 ARG B 34 *********************** 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 79 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8650 (t80) cc_final: 0.8137 (t80) REVERT: A 303 MET cc_start: 0.8694 (mmm) cc_final: 0.8270 (mmm) REVERT: A 358 MET cc_start: 0.8042 (mtm) cc_final: 0.7716 (mtm) REVERT: A 388 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9269 (mm) REVERT: A 485 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 510 ASP cc_start: 0.8752 (m-30) cc_final: 0.8165 (t0) REVERT: B 118 ILE cc_start: 0.9284 (mm) cc_final: 0.9035 (mm) REVERT: B 326 ASP cc_start: 0.8433 (t0) cc_final: 0.7999 (t0) REVERT: B 427 MET cc_start: 0.8368 (ttp) cc_final: 0.8126 (tmm) outliers start: 21 outliers final: 18 residues processed: 75 average time/residue: 0.2071 time to fit residues: 24.2937 Evaluate side-chains 74 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 510 ASP 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: 0.5980 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12021 Z= 0.296 Angle : 0.666 12.661 16875 Z= 0.335 Chirality : 0.039 0.223 1944 Planarity : 0.004 0.043 1620 Dihedral : 21.236 173.392 3334 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 3.12 % Allowed : 23.61 % Favored : 73.27 % 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: -1.17 (0.26), residues: 1037 helix: 1.07 (0.24), residues: 470 sheet: -1.93 (0.43), residues: 143 loop : -2.55 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 223 HIS 0.014 0.002 HIS B 353 PHE 0.016 0.002 PHE A 214 TYR 0.015 0.002 TYR A 18 ARG 0.003 0.000 ARG B 163 ********************** 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 77 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 49 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8731 (t80) cc_final: 0.8142 (t80) REVERT: A 303 MET cc_start: 0.8863 (mmm) cc_final: 0.8439 (mmm) REVERT: A 358 MET cc_start: 0.8203 (mtm) cc_final: 0.7940 (mtm) REVERT: A 388 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 485 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7087 (t80) REVERT: A 510 ASP cc_start: 0.8906 (m-30) cc_final: 0.8376 (t0) REVERT: B 78 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7804 (t70) REVERT: B 326 ASP cc_start: 0.8395 (t0) cc_final: 0.7946 (t0) outliers start: 28 outliers final: 22 residues processed: 73 average time/residue: 0.2054 time to fit residues: 23.3560 Evaluate side-chains 74 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.070362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051578 restraints weight = 61990.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052980 restraints weight = 32316.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.053782 restraints weight = 21726.973| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12021 Z= 0.163 Angle : 0.611 12.822 16875 Z= 0.302 Chirality : 0.037 0.230 1944 Planarity : 0.004 0.039 1620 Dihedral : 21.050 169.603 3334 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.45 % Allowed : 24.61 % Favored : 72.94 % 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: 1.36 (0.24), residues: 465 sheet: -1.78 (0.44), residues: 139 loop : -2.48 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.015 0.001 HIS B 353 PHE 0.010 0.001 PHE A 214 TYR 0.012 0.001 TYR A 82 ARG 0.004 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.21 seconds wall clock time: 35 minutes 11.39 seconds (2111.39 seconds total)