Starting phenix.real_space_refine on Sun Mar 10 22:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjs_23883/03_2024/7mjs_23883_updated.pdb" } resolution = 3.03 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= 0.022 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 3618 2.51 5 N 878 2.21 5 O 1013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 68": "OD1" <-> "OD2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X ARG 109": "NH1" <-> "NH2" Residue "X PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 170": "OE1" <-> "OE2" Residue "X PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 237": "OD1" <-> "OD2" Residue "X TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 266": "OE1" <-> "OE2" Residue "X PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 408": "OD1" <-> "OD2" Residue "X ASP 411": "OD1" <-> "OD2" Residue "X ASP 412": "OD1" <-> "OD2" Residue "X PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 421": "NH1" <-> "NH2" Residue "X PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ARG 499": "NH1" <-> "NH2" Residue "X ARG 500": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5536 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1018 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "L" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 863 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "X" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3655 Unusual residues: {'NAG': 2, 'ZGS': 1} Classifications: {'peptide': 458, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 438, None: 3} Not linked: pdbres="ALA X 505 " pdbres="ZGS X 601 " Not linked: pdbres="ZGS X 601 " pdbres="NAG X 602 " Not linked: pdbres="NAG X 602 " pdbres="NAG X 603 " Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.62, per 1000 atoms: 0.65 Number of scatterers: 5536 At special positions: 0 Unit cell: (69.72, 69.72, 131.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 1013 8.00 N 878 7.00 C 3618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS X 207 " - pdb=" SG CYS X 460 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG X 602 " - " ASN X 227 " " NAG X 603 " - " ASN X 218 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 6 sheets defined 50.1% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'X' and resid 38 through 41 No H-bonds generated for 'chain 'X' and resid 38 through 41' Processing helix chain 'X' and resid 43 through 68 removed outlier: 4.022A pdb=" N GLY X 47 " --> pdb=" O CYS X 43 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY X 48 " --> pdb=" O TYR X 44 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) Proline residue: X 50 - end of helix removed outlier: 5.322A pdb=" N GLN X 63 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE X 64 " --> pdb=" O PHE X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 98 removed outlier: 3.630A pdb=" N ASP X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) Proline residue: X 93 - end of helix Processing helix chain 'X' and resid 111 through 126 removed outlier: 3.542A pdb=" N THR X 118 " --> pdb=" O ILE X 114 " (cutoff:3.500A) Proline residue: X 119 - end of helix Processing helix chain 'X' and resid 138 through 167 removed outlier: 3.625A pdb=" N TYR X 142 " --> pdb=" O GLN X 138 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE X 145 " --> pdb=" O TRP X 141 " (cutoff:3.500A) Proline residue: X 159 - end of helix removed outlier: 4.110A pdb=" N THR X 164 " --> pdb=" O TYR X 160 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET X 165 " --> pdb=" O SER X 161 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE X 166 " --> pdb=" O ALA X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 201 removed outlier: 3.599A pdb=" N VAL X 200 " --> pdb=" O GLN X 196 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 222 No H-bonds generated for 'chain 'X' and resid 219 through 222' Processing helix chain 'X' and resid 229 through 263 Processing helix chain 'X' and resid 281 through 290 removed outlier: 3.673A pdb=" N MET X 289 " --> pdb=" O LEU X 285 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN X 290 " --> pdb=" O LYS X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 292 through 321 removed outlier: 4.163A pdb=" N THR X 320 " --> pdb=" O ALA X 316 " (cutoff:3.500A) Processing helix chain 'X' and resid 329 through 353 Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 356 through 376 removed outlier: 3.973A pdb=" N TYR X 361 " --> pdb=" O LYS X 357 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA X 367 " --> pdb=" O GLY X 363 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL X 368 " --> pdb=" O ILE X 364 " (cutoff:3.500A) Proline residue: X 369 - end of helix removed outlier: 4.098A pdb=" N VAL X 375 " --> pdb=" O LEU X 371 " (cutoff:3.500A) Processing helix chain 'X' and resid 381 through 416 removed outlier: 3.620A pdb=" N TYR X 385 " --> pdb=" O LEU X 381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE X 386 " --> pdb=" O VAL X 382 " (cutoff:3.500A) Proline residue: X 402 - end of helix Proline residue: X 407 - end of helix Processing helix chain 'X' and resid 426 through 452 removed outlier: 3.628A pdb=" N THR X 438 " --> pdb=" O PHE X 434 " (cutoff:3.500A) Processing helix chain 'X' and resid 464 through 472 Processing helix chain 'X' and resid 476 through 491 removed outlier: 3.865A pdb=" N LYS X 490 " --> pdb=" O LEU X 486 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU X 491 " --> pdb=" O LEU X 487 " (cutoff:3.500A) Processing helix chain 'X' and resid 498 through 504 Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'H' and resid 13 through 15 removed outlier: 5.786A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA H 43 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU H 48 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 100 through 109 removed outlier: 3.809A pdb=" N TYR H 121 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU H 103 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU H 119 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR H 105 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N THR H 117 " --> pdb=" O TYR H 105 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR H 107 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N TRP H 115 " --> pdb=" O TYR H 107 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER H 109 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= E, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.974A pdb=" N LYS L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'L' and resid 86 through 92 removed outlier: 6.559A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 836 1.31 - 1.44: 1687 1.44 - 1.56: 3112 1.56 - 1.69: 3 1.69 - 1.82: 39 Bond restraints: 5677 Sorted by residual: bond pdb=" N VAL X 226 " pdb=" CA VAL X 226 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" N ASN X 227 " pdb=" CA ASN X 227 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.72e+00 bond pdb=" N THR X 217 " pdb=" CA THR X 217 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.32e-02 5.74e+03 7.24e+00 bond pdb=" N ASN X 218 " pdb=" CA ASN X 218 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.22e-02 6.72e+03 5.78e+00 bond pdb=" C MET X 228 " pdb=" O MET X 228 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.29e-02 6.01e+03 5.37e+00 ... (remaining 5672 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.30: 127 106.30 - 113.24: 3084 113.24 - 120.18: 2082 120.18 - 127.12: 2369 127.12 - 134.06: 58 Bond angle restraints: 7720 Sorted by residual: angle pdb=" C09 ZGS X 601 " pdb=" C10 ZGS X 601 " pdb=" C11 ZGS X 601 " ideal model delta sigma weight residual 152.65 121.04 31.61 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C06 ZGS X 601 " pdb=" C07 ZGS X 601 " pdb=" C08 ZGS X 601 " ideal model delta sigma weight residual 152.65 121.52 31.13 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C03 ZGS X 601 " pdb=" C04 ZGS X 601 " pdb=" C05 ZGS X 601 " ideal model delta sigma weight residual 152.66 122.51 30.15 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N CYS X 460 " pdb=" CA CYS X 460 " pdb=" C CYS X 460 " ideal model delta sigma weight residual 114.31 108.51 5.80 1.29e+00 6.01e-01 2.02e+01 angle pdb=" N PHE X 219 " pdb=" CA PHE X 219 " pdb=" C PHE X 219 " ideal model delta sigma weight residual 113.23 108.29 4.94 1.24e+00 6.50e-01 1.59e+01 ... (remaining 7715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.38: 3017 18.38 - 36.75: 243 36.75 - 55.13: 39 55.13 - 73.51: 10 73.51 - 91.89: 4 Dihedral angle restraints: 3313 sinusoidal: 1275 harmonic: 2038 Sorted by residual: dihedral pdb=" CB CYS X 207 " pdb=" SG CYS X 207 " pdb=" SG CYS X 460 " pdb=" CB CYS X 460 " ideal model delta sinusoidal sigma weight residual -86.00 -31.66 -54.34 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CA ASN L 96 " pdb=" C ASN L 96 " pdb=" N GLN L 97 " pdb=" CA GLN L 97 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C THR X 217 " pdb=" N THR X 217 " pdb=" CA THR X 217 " pdb=" CB THR X 217 " ideal model delta harmonic sigma weight residual -122.00 -131.98 9.98 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 3310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 881 0.198 - 0.396: 3 0.396 - 0.595: 0 0.595 - 0.793: 0 0.793 - 0.991: 1 Chirality restraints: 885 Sorted by residual: chirality pdb=" C1 NAG X 603 " pdb=" ND2 ASN X 218 " pdb=" C2 NAG X 603 " pdb=" O5 NAG X 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG X 602 " pdb=" ND2 ASN X 227 " pdb=" C2 NAG X 602 " pdb=" O5 NAG X 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA THR X 217 " pdb=" N THR X 217 " pdb=" C THR X 217 " pdb=" CB THR X 217 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 882 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 602 " -0.114 2.00e-02 2.50e+03 9.38e-02 1.10e+02 pdb=" C7 NAG X 602 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG X 602 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG X 602 " 0.150 2.00e-02 2.50e+03 pdb=" O7 NAG X 602 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 603 " 0.091 2.00e-02 2.50e+03 7.74e-02 7.48e+01 pdb=" C7 NAG X 603 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG X 603 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG X 603 " -0.125 2.00e-02 2.50e+03 pdb=" O7 NAG X 603 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 44 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO L 45 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.022 5.00e-02 4.00e+02 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1003 2.76 - 3.30: 5494 3.30 - 3.83: 9200 3.83 - 4.37: 11282 4.37 - 4.90: 19601 Nonbonded interactions: 46580 Sorted by model distance: nonbonded pdb=" O SER H 66 " pdb=" NH1 ARG H 70 " model vdw 2.228 2.520 nonbonded pdb=" OG SER H 58 " pdb=" O PHE X 213 " model vdw 2.247 2.440 nonbonded pdb=" O GLY X 363 " pdb=" OG SER X 366 " model vdw 2.287 2.440 nonbonded pdb=" NH1 ARG H 41 " pdb=" OD1 ASP H 93 " model vdw 2.304 2.520 nonbonded pdb=" OH TYR H 105 " pdb=" OG SER L 92 " model vdw 2.333 2.440 ... (remaining 46575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 9.700 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.870 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 0.048 5677 Z= 0.305 Angle : 0.944 31.614 7720 Z= 0.464 Chirality : 0.057 0.991 885 Planarity : 0.006 0.094 951 Dihedral : 13.970 91.887 2004 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.15 % 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: -3.02 (0.26), residues: 695 helix: -1.42 (0.23), residues: 341 sheet: -2.47 (0.41), residues: 114 loop : -2.35 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 349 HIS 0.003 0.001 HIS X 291 PHE 0.015 0.002 PHE X 318 TYR 0.014 0.001 TYR X 146 ARG 0.002 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.576 Fit side-chains REVERT: H 46 LYS cc_start: 0.8527 (mttp) cc_final: 0.8312 (mttp) REVERT: H 49 GLU cc_start: 0.7553 (tt0) cc_final: 0.7207 (tt0) REVERT: L 46 LYS cc_start: 0.8591 (mttt) cc_final: 0.8258 (mttp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1717 time to fit residues: 25.2127 Evaluate side-chains 93 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.0370 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 112 GLN L 38 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 GLN X 240 ASN X 290 ASN ** X 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5677 Z= 0.181 Angle : 0.535 7.884 7720 Z= 0.279 Chirality : 0.042 0.293 885 Planarity : 0.004 0.039 951 Dihedral : 7.017 80.086 825 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.35 % Allowed : 11.49 % Favored : 87.16 % 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: -1.40 (0.30), residues: 695 helix: 0.04 (0.27), residues: 345 sheet: -2.01 (0.42), residues: 113 loop : -1.62 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 349 HIS 0.005 0.001 HIS X 291 PHE 0.014 0.001 PHE X 318 TYR 0.015 0.001 TYR X 492 ARG 0.001 0.000 ARG X 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.623 Fit side-chains REVERT: H 49 GLU cc_start: 0.7522 (tt0) cc_final: 0.7177 (tt0) REVERT: L 46 LYS cc_start: 0.8563 (mttt) cc_final: 0.8236 (mttp) REVERT: X 109 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7151 (ttt-90) REVERT: X 123 ILE cc_start: 0.8545 (mt) cc_final: 0.8205 (tt) REVERT: X 240 ASN cc_start: 0.8496 (m-40) cc_final: 0.8117 (m-40) outliers start: 8 outliers final: 7 residues processed: 111 average time/residue: 0.1459 time to fit residues: 22.1365 Evaluate side-chains 102 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 429 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5677 Z= 0.209 Angle : 0.533 7.090 7720 Z= 0.279 Chirality : 0.042 0.265 885 Planarity : 0.004 0.042 951 Dihedral : 6.631 75.242 825 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.21 % Allowed : 12.16 % Favored : 84.63 % 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: -0.85 (0.31), residues: 695 helix: 0.52 (0.28), residues: 347 sheet: -1.73 (0.43), residues: 113 loop : -1.45 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.004 0.001 HIS X 291 PHE 0.015 0.001 PHE X 318 TYR 0.018 0.001 TYR H 33 ARG 0.001 0.000 ARG X 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.633 Fit side-chains REVERT: H 49 GLU cc_start: 0.7530 (tt0) cc_final: 0.7206 (tt0) REVERT: L 46 LYS cc_start: 0.8573 (mttt) cc_final: 0.8286 (mttp) REVERT: X 123 ILE cc_start: 0.8578 (mt) cc_final: 0.8254 (tt) outliers start: 19 outliers final: 14 residues processed: 112 average time/residue: 0.1453 time to fit residues: 22.2724 Evaluate side-chains 112 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5677 Z= 0.183 Angle : 0.524 7.449 7720 Z= 0.270 Chirality : 0.042 0.243 885 Planarity : 0.004 0.043 951 Dihedral : 6.375 67.738 825 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.70 % Allowed : 13.85 % Favored : 83.45 % 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: -0.49 (0.32), residues: 695 helix: 0.79 (0.28), residues: 347 sheet: -1.52 (0.43), residues: 113 loop : -1.27 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.017 0.001 TYR X 492 ARG 0.001 0.000 ARG L 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.664 Fit side-chains REVERT: H 49 GLU cc_start: 0.7512 (tt0) cc_final: 0.7144 (tt0) REVERT: H 124 GLN cc_start: 0.7969 (tp40) cc_final: 0.7737 (tp40) REVERT: L 46 LYS cc_start: 0.8591 (mttt) cc_final: 0.8227 (mttp) REVERT: X 123 ILE cc_start: 0.8527 (mt) cc_final: 0.8227 (tt) REVERT: X 314 ASN cc_start: 0.7307 (m110) cc_final: 0.6861 (m-40) outliers start: 16 outliers final: 15 residues processed: 108 average time/residue: 0.1570 time to fit residues: 23.2512 Evaluate side-chains 114 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5677 Z= 0.204 Angle : 0.528 7.050 7720 Z= 0.274 Chirality : 0.042 0.243 885 Planarity : 0.004 0.042 951 Dihedral : 6.330 63.584 825 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.89 % Allowed : 14.19 % Favored : 81.93 % 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: -0.34 (0.32), residues: 695 helix: 0.91 (0.28), residues: 347 sheet: -1.39 (0.44), residues: 113 loop : -1.22 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.028 0.001 TYR X 492 ARG 0.001 0.000 ARG L 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.699 Fit side-chains REVERT: H 49 GLU cc_start: 0.7524 (tt0) cc_final: 0.7155 (tt0) REVERT: L 46 LYS cc_start: 0.8589 (mttt) cc_final: 0.8222 (mttp) REVERT: X 123 ILE cc_start: 0.8548 (mt) cc_final: 0.8242 (tt) REVERT: X 297 LEU cc_start: 0.8552 (tt) cc_final: 0.8330 (tp) REVERT: X 314 ASN cc_start: 0.7388 (m110) cc_final: 0.6964 (m-40) outliers start: 23 outliers final: 19 residues processed: 113 average time/residue: 0.1476 time to fit residues: 22.8925 Evaluate side-chains 116 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5677 Z= 0.182 Angle : 0.519 7.422 7720 Z= 0.269 Chirality : 0.041 0.236 885 Planarity : 0.004 0.050 951 Dihedral : 6.103 58.483 825 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.38 % Allowed : 15.03 % Favored : 81.59 % 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: -0.13 (0.32), residues: 695 helix: 1.08 (0.28), residues: 345 sheet: -1.26 (0.44), residues: 113 loop : -1.11 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.023 0.001 TYR X 492 ARG 0.001 0.000 ARG L 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.560 Fit side-chains REVERT: H 49 GLU cc_start: 0.7518 (tt0) cc_final: 0.7155 (tt0) REVERT: L 46 LYS cc_start: 0.8530 (mttt) cc_final: 0.8169 (mttp) REVERT: X 123 ILE cc_start: 0.8532 (mt) cc_final: 0.8234 (tt) REVERT: X 297 LEU cc_start: 0.8517 (tt) cc_final: 0.8286 (tp) REVERT: X 314 ASN cc_start: 0.7264 (m110) cc_final: 0.6865 (m-40) outliers start: 20 outliers final: 17 residues processed: 105 average time/residue: 0.1389 time to fit residues: 20.3148 Evaluate side-chains 113 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 423 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5677 Z= 0.191 Angle : 0.523 7.146 7720 Z= 0.271 Chirality : 0.042 0.234 885 Planarity : 0.004 0.041 951 Dihedral : 5.785 52.144 825 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.21 % Allowed : 16.05 % Favored : 80.74 % 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: -0.02 (0.32), residues: 695 helix: 1.14 (0.28), residues: 346 sheet: -1.17 (0.45), residues: 113 loop : -1.05 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.023 0.001 TYR X 492 ARG 0.001 0.000 ARG L 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.595 Fit side-chains REVERT: H 49 GLU cc_start: 0.7522 (tt0) cc_final: 0.7161 (tt0) REVERT: L 46 LYS cc_start: 0.8528 (mttt) cc_final: 0.8160 (mttp) REVERT: X 123 ILE cc_start: 0.8536 (mt) cc_final: 0.8233 (tt) REVERT: X 314 ASN cc_start: 0.7267 (m110) cc_final: 0.6886 (m-40) outliers start: 19 outliers final: 17 residues processed: 106 average time/residue: 0.1385 time to fit residues: 20.4815 Evaluate side-chains 115 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.0060 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5677 Z= 0.160 Angle : 0.509 7.479 7720 Z= 0.262 Chirality : 0.041 0.226 885 Planarity : 0.004 0.041 951 Dihedral : 5.392 49.994 825 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 16.05 % Favored : 80.91 % 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: 0.21 (0.32), residues: 695 helix: 1.29 (0.28), residues: 348 sheet: -1.01 (0.46), residues: 113 loop : -0.91 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 349 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.039 0.001 TYR X 492 ARG 0.001 0.000 ARG X 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.630 Fit side-chains REVERT: H 49 GLU cc_start: 0.7518 (tt0) cc_final: 0.7158 (tt0) REVERT: L 46 LYS cc_start: 0.8523 (mttt) cc_final: 0.8156 (mttp) REVERT: X 123 ILE cc_start: 0.8494 (mt) cc_final: 0.8195 (tt) outliers start: 18 outliers final: 16 residues processed: 113 average time/residue: 0.1468 time to fit residues: 22.8148 Evaluate side-chains 116 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 435 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 423 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5677 Z= 0.233 Angle : 0.546 7.631 7720 Z= 0.281 Chirality : 0.043 0.231 885 Planarity : 0.004 0.041 951 Dihedral : 5.449 51.307 825 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.38 % Allowed : 16.55 % Favored : 80.07 % 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: 0.10 (0.32), residues: 695 helix: 1.14 (0.28), residues: 348 sheet: -1.02 (0.45), residues: 113 loop : -0.89 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 141 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.047 0.002 TYR X 492 ARG 0.001 0.000 ARG X 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.627 Fit side-chains REVERT: H 49 GLU cc_start: 0.7531 (tt0) cc_final: 0.7174 (tt0) REVERT: L 46 LYS cc_start: 0.8532 (mttt) cc_final: 0.8161 (mttp) REVERT: X 123 ILE cc_start: 0.8534 (mt) cc_final: 0.8202 (tt) REVERT: X 240 ASN cc_start: 0.8486 (m-40) cc_final: 0.8095 (m-40) outliers start: 20 outliers final: 19 residues processed: 107 average time/residue: 0.1434 time to fit residues: 21.1482 Evaluate side-chains 116 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 423 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 331 ASN X 423 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5677 Z= 0.210 Angle : 0.540 7.876 7720 Z= 0.279 Chirality : 0.043 0.261 885 Planarity : 0.004 0.041 951 Dihedral : 5.403 51.790 825 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.21 % Allowed : 16.72 % Favored : 80.07 % 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: 0.20 (0.32), residues: 695 helix: 1.23 (0.28), residues: 348 sheet: -0.96 (0.46), residues: 113 loop : -0.85 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.004 0.001 HIS X 423 PHE 0.015 0.001 PHE X 318 TYR 0.030 0.001 TYR X 492 ARG 0.002 0.000 ARG X 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.649 Fit side-chains REVERT: H 49 GLU cc_start: 0.7528 (tt0) cc_final: 0.7167 (tt0) REVERT: L 46 LYS cc_start: 0.8530 (mttt) cc_final: 0.8162 (mttp) REVERT: X 123 ILE cc_start: 0.8515 (mt) cc_final: 0.8194 (tt) REVERT: X 169 ARG cc_start: 0.7617 (mmt-90) cc_final: 0.7246 (mmt180) REVERT: X 240 ASN cc_start: 0.8483 (m-40) cc_final: 0.8094 (m-40) outliers start: 19 outliers final: 19 residues processed: 110 average time/residue: 0.1489 time to fit residues: 22.5074 Evaluate side-chains 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 423 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.0770 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126675 restraints weight = 6928.058| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.94 r_work: 0.3431 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5677 Z= 0.185 Angle : 0.527 7.747 7720 Z= 0.273 Chirality : 0.042 0.224 885 Planarity : 0.004 0.041 951 Dihedral : 5.331 52.061 825 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.21 % Allowed : 16.72 % Favored : 80.07 % 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: 0.30 (0.32), residues: 695 helix: 1.30 (0.28), residues: 348 sheet: -0.92 (0.46), residues: 113 loop : -0.80 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.003 0.001 HIS X 423 PHE 0.015 0.001 PHE X 318 TYR 0.030 0.001 TYR X 492 ARG 0.001 0.000 ARG L 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1626.02 seconds wall clock time: 30 minutes 12.46 seconds (1812.46 seconds total)