Starting phenix.real_space_refine on Tue Feb 13 17:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/02_2024/7d76_30602.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/02_2024/7d76_30602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/02_2024/7d76_30602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/02_2024/7d76_30602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/02_2024/7d76_30602.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/02_2024/7d76_30602.pdb" } resolution = 3.1 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= 0.009 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 S 46 5.16 5 Cl 1 4.86 5 C 4521 2.51 5 N 1174 2.21 5 O 1273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 230": "OD1" <-> "OD2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "R GLU 298": "OE1" <-> "OE2" Residue "R GLU 303": "OE1" <-> "OE2" Residue "R ASP 335": "OD1" <-> "OD2" Residue "R ARG 369": "NH1" <-> "NH2" Residue "R TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 409": "NH1" <-> "NH2" Residue "R ASP 410": "OD1" <-> "OD2" Residue "R GLU 412": "OE1" <-> "OE2" Residue "R GLU 418": "OE1" <-> "OE2" Residue "R ARG 462": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7015 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1707 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 265, 2097 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 4, 'TRANS': 260} Conformer: "B" Number of residues, atoms: 265, 2097 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 4, 'TRANS': 260} bond proxies already assigned to first conformer: 2143 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 155 Unusual residues: {'CLR': 2, 'GXR': 1, 'PLM': 2, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS R 309 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS R 309 " occ=0.50 Time building chain proxies: 5.46, per 1000 atoms: 0.78 Number of scatterers: 7015 At special positions: 0 Unit cell: (79.092, 111.54, 111.54, 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) Cl 1 17.00 S 46 16.00 O 1273 8.00 N 1174 7.00 C 4521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 338 " - pdb=" SG CYS R 420 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 43.2% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.601A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.944A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.720A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 removed outlier: 3.674A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 242 through 256 removed outlier: 4.491A pdb=" N GLU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.262A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.839A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.601A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.500A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.719A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 264 through 297 Processing helix chain 'R' and resid 304 through 329 Processing helix chain 'R' and resid 334 through 368 removed outlier: 3.611A pdb=" N CYS R 338 " --> pdb=" O SER R 334 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 340 " --> pdb=" O ALA R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 400 Proline residue: R 390 - end of helix removed outlier: 3.675A pdb=" N ALA R 400 " --> pdb=" O GLY R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 428 through 435 Processing helix chain 'R' and resid 435 through 464 removed outlier: 4.339A pdb=" N ARG R 462 " --> pdb=" O PHE R 458 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 463 " --> pdb=" O THR R 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 471 through 496 removed outlier: 4.167A pdb=" N LEU R 477 " --> pdb=" O ARG R 473 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU R 485 " --> pdb=" O GLY R 481 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP R 490 " --> pdb=" O VAL R 486 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 525 removed outlier: 3.619A pdb=" N PHE R 506 " --> pdb=" O THR R 502 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE R 517 " --> pdb=" O GLN R 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 6.371A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.559A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.740A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.126A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.032A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.693A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.656A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.612A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 406 through 408 removed outlier: 3.662A pdb=" N LEU R 417 " --> pdb=" O ILE R 408 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 1000 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: 2.15 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1249 1.33 - 1.46: 2695 1.46 - 1.60: 3152 1.60 - 1.73: 5 1.73 - 1.87: 65 Bond restraints: 7166 Sorted by residual: bond pdb=" CAS Y01 R 601 " pdb=" CAU Y01 R 601 " ideal model delta sigma weight residual 1.530 1.304 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 1.550 1.374 0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C ASN A 347 " pdb=" N LEU A 348 " ideal model delta sigma weight residual 1.335 1.453 -0.118 1.35e-02 5.49e+03 7.63e+01 bond pdb=" CAS Y01 R 601 " pdb=" CBF Y01 R 601 " ideal model delta sigma weight residual 1.533 1.365 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" CBF Y01 R 601 " pdb=" CBH Y01 R 601 " ideal model delta sigma weight residual 1.550 1.691 -0.141 2.00e-02 2.50e+03 4.96e+01 ... (remaining 7161 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.13: 122 106.13 - 113.11: 3993 113.11 - 120.10: 2566 120.10 - 127.09: 2956 127.09 - 134.07: 76 Bond angle restraints: 9713 Sorted by residual: angle pdb=" C ALA R 337 " pdb=" N CYS R 338 " pdb=" CA CYS R 338 " ideal model delta sigma weight residual 121.94 112.94 9.00 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA CYS R 420 " pdb=" CB CYS R 420 " pdb=" SG CYS R 420 " ideal model delta sigma weight residual 114.40 122.00 -7.60 2.30e+00 1.89e-01 1.09e+01 angle pdb=" C CYS R 420 " pdb=" N TRP R 421 " pdb=" CA TRP R 421 " ideal model delta sigma weight residual 121.74 126.82 -5.08 1.58e+00 4.01e-01 1.04e+01 angle pdb=" CBD Y01 R 601 " pdb=" CBG Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 115.11 105.76 9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" CBB Y01 R 601 " pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 119.27 110.22 9.05 3.00e+00 1.11e-01 9.09e+00 ... (remaining 9708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.02: 4065 20.02 - 40.04: 311 40.04 - 60.05: 49 60.05 - 80.07: 7 80.07 - 100.09: 5 Dihedral angle restraints: 4437 sinusoidal: 1911 harmonic: 2526 Sorted by residual: dihedral pdb=" CB CYS R 338 " pdb=" SG CYS R 338 " pdb=" SG CYS R 420 " pdb=" CB CYS R 420 " ideal model delta sinusoidal sigma weight residual 93.00 165.80 -72.80 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CA CYS R 338 " pdb=" C CYS R 338 " pdb=" N TRP R 339 " pdb=" CA TRP R 339 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" O1 GXR R 604 " pdb=" C15 GXR R 604 " pdb=" C5 GXR R 604 " pdb=" O3 GXR R 604 " ideal model delta sinusoidal sigma weight residual 167.26 67.17 100.09 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 4434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1065 0.107 - 0.215: 35 0.215 - 0.322: 7 0.322 - 0.429: 2 0.429 - 0.537: 1 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CBG Y01 R 601 " pdb=" CAQ Y01 R 601 " pdb=" CBD Y01 R 601 " pdb=" CBI Y01 R 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1107 not shown) Planarity restraints: 1201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 GXR R 604 " -0.008 2.00e-02 2.50e+03 1.64e-01 3.35e+02 pdb=" C13 GXR R 604 " -0.183 2.00e-02 2.50e+03 pdb=" C14 GXR R 604 " 0.194 2.00e-02 2.50e+03 pdb=" C19 GXR R 604 " 0.175 2.00e-02 2.50e+03 pdb=" C22 GXR R 604 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 347 " 0.017 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ASN A 347 " -0.056 2.00e-02 2.50e+03 pdb=" O ASN A 347 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A 348 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.014 2.00e-02 2.50e+03 1.42e-02 4.05e+00 pdb=" CG TYR B 105 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 ... (remaining 1198 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 298 2.71 - 3.26: 7066 3.26 - 3.81: 10800 3.81 - 4.35: 13812 4.35 - 4.90: 23764 Nonbonded interactions: 55740 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.167 2.440 nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.198 2.440 nonbonded pdb=" O ALA R 430 " pdb=" OG1 THR R 434 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP A 341 " pdb=" ND2 ASN R 472 " model vdw 2.226 2.520 nonbonded pdb=" OE2 GLU A 187 " pdb=" NH1 ARG A 198 " model vdw 2.256 2.520 ... (remaining 55735 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=0.50 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: 0.420 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: 0.000 Extract box with map and model: 1.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.290 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.008 0.226 7166 Z= 0.517 Angle : 0.787 9.350 9713 Z= 0.404 Chirality : 0.054 0.537 1110 Planarity : 0.006 0.164 1201 Dihedral : 14.402 100.088 2806 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % 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: -2.55 (0.26), residues: 867 helix: 0.07 (0.26), residues: 351 sheet: -3.13 (0.32), residues: 183 loop : -2.68 (0.28), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.001 PHE R 345 TYR 0.035 0.002 TYR B 105 ARG 0.005 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8608 (tpp) cc_final: 0.8118 (tpp) REVERT: G 36 ASP cc_start: 0.8444 (m-30) cc_final: 0.8128 (m-30) REVERT: R 280 MET cc_start: 0.7017 (mtm) cc_final: 0.6708 (mtp) REVERT: R 299 ARG cc_start: 0.7108 (ttp-170) cc_final: 0.6620 (tmm-80) REVERT: R 401 ASN cc_start: 0.7979 (m-40) cc_final: 0.7741 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2533 time to fit residues: 42.4072 Evaluate side-chains 100 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 214 HIS A 295 ASN A 307 GLN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 311 HIS R 266 HIS R 346 HIS R 362 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7166 Z= 0.212 Angle : 0.568 8.206 9713 Z= 0.288 Chirality : 0.042 0.194 1110 Planarity : 0.003 0.034 1201 Dihedral : 7.987 56.717 1269 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.63 % Allowed : 11.43 % Favored : 86.94 % 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: -0.94 (0.28), residues: 867 helix: 1.65 (0.27), residues: 352 sheet: -2.38 (0.36), residues: 171 loop : -2.12 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 339 HIS 0.003 0.001 HIS B 142 PHE 0.018 0.001 PHE R 292 TYR 0.019 0.001 TYR B 105 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8492 (tpp) cc_final: 0.8074 (tpp) REVERT: B 219 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7358 (mtt-85) REVERT: B 241 PHE cc_start: 0.9025 (p90) cc_final: 0.8729 (p90) outliers start: 12 outliers final: 6 residues processed: 121 average time/residue: 0.2062 time to fit residues: 32.9365 Evaluate side-chains 110 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 312 ASN B 16 ASN R 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7166 Z= 0.170 Angle : 0.524 8.646 9713 Z= 0.267 Chirality : 0.041 0.155 1110 Planarity : 0.003 0.036 1201 Dihedral : 6.565 56.485 1269 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.31 % Allowed : 13.06 % 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: -0.33 (0.29), residues: 867 helix: 2.30 (0.28), residues: 354 sheet: -2.10 (0.38), residues: 169 loop : -1.97 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 339 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR B 105 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.772 Fit side-chains REVERT: A 244 MET cc_start: 0.8491 (tpp) cc_final: 0.8036 (tpp) REVERT: B 219 ARG cc_start: 0.7875 (mtt-85) cc_final: 0.7378 (mtt-85) REVERT: B 234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: B 241 PHE cc_start: 0.8963 (p90) cc_final: 0.8726 (p90) REVERT: R 326 ASN cc_start: 0.8805 (m-40) cc_final: 0.8547 (m-40) REVERT: R 414 ARG cc_start: 0.5551 (tpt170) cc_final: 0.4987 (mmm-85) outliers start: 17 outliers final: 8 residues processed: 130 average time/residue: 0.1866 time to fit residues: 32.5623 Evaluate side-chains 123 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 423 ARG Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN R 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7166 Z= 0.188 Angle : 0.521 8.250 9713 Z= 0.268 Chirality : 0.041 0.158 1110 Planarity : 0.003 0.036 1201 Dihedral : 6.182 55.454 1269 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.72 % Allowed : 14.56 % Favored : 82.72 % 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: 0.01 (0.30), residues: 867 helix: 2.51 (0.28), residues: 357 sheet: -1.88 (0.38), residues: 174 loop : -1.76 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR B 105 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.801 Fit side-chains REVERT: A 244 MET cc_start: 0.8480 (tpp) cc_final: 0.8004 (tpp) REVERT: A 277 GLU cc_start: 0.8200 (tp30) cc_final: 0.7915 (tp30) REVERT: A 316 ASN cc_start: 0.7548 (t0) cc_final: 0.7348 (t0) REVERT: B 219 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7577 (mtt-85) REVERT: B 234 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: B 241 PHE cc_start: 0.8909 (p90) cc_final: 0.8635 (p90) REVERT: R 326 ASN cc_start: 0.8802 (m-40) cc_final: 0.8565 (m-40) outliers start: 20 outliers final: 12 residues processed: 129 average time/residue: 0.1858 time to fit residues: 32.5534 Evaluate side-chains 124 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 423 ARG Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.0010 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7166 Z= 0.160 Angle : 0.507 10.221 9713 Z= 0.259 Chirality : 0.040 0.145 1110 Planarity : 0.003 0.036 1201 Dihedral : 5.903 55.924 1269 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.31 % Allowed : 15.92 % Favored : 81.77 % 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: 0.27 (0.30), residues: 867 helix: 2.75 (0.28), residues: 355 sheet: -1.75 (0.38), residues: 174 loop : -1.62 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.007 0.001 HIS R 266 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR R 290 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.773 Fit side-chains REVERT: A 244 MET cc_start: 0.8499 (tpp) cc_final: 0.8063 (tpp) REVERT: A 280 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7659 (ptpp) REVERT: A 281 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8500 (mmmt) REVERT: A 316 ASN cc_start: 0.7648 (t0) cc_final: 0.7386 (t0) REVERT: B 219 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7601 (mtt-85) REVERT: B 234 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: R 326 ASN cc_start: 0.8731 (m-40) cc_final: 0.8472 (m-40) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.1817 time to fit residues: 31.9368 Evaluate side-chains 123 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 423 ARG Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.0020 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN R 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7166 Z= 0.193 Angle : 0.514 10.727 9713 Z= 0.262 Chirality : 0.041 0.146 1110 Planarity : 0.003 0.036 1201 Dihedral : 5.922 54.480 1269 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.99 % Allowed : 16.19 % Favored : 80.82 % 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: 0.37 (0.30), residues: 867 helix: 2.77 (0.28), residues: 356 sheet: -1.66 (0.38), residues: 180 loop : -1.50 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 421 HIS 0.007 0.001 HIS R 266 PHE 0.011 0.001 PHE B 234 TYR 0.009 0.001 TYR R 504 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.977 Fit side-chains REVERT: A 244 MET cc_start: 0.8485 (tpp) cc_final: 0.8031 (tpp) REVERT: A 316 ASN cc_start: 0.7750 (t0) cc_final: 0.7440 (t0) REVERT: B 219 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7481 (mtt-85) REVERT: B 234 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: R 326 ASN cc_start: 0.8799 (m-40) cc_final: 0.8554 (m-40) outliers start: 22 outliers final: 17 residues processed: 127 average time/residue: 0.1734 time to fit residues: 30.0128 Evaluate side-chains 131 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 423 ARG Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN R 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7166 Z= 0.160 Angle : 0.518 10.037 9713 Z= 0.264 Chirality : 0.040 0.134 1110 Planarity : 0.003 0.036 1201 Dihedral : 5.803 55.282 1269 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.59 % Allowed : 17.01 % Favored : 80.41 % 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: 0.47 (0.31), residues: 867 helix: 2.84 (0.28), residues: 356 sheet: -1.61 (0.38), residues: 180 loop : -1.44 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.012 0.001 HIS R 266 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR R 504 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.712 Fit side-chains REVERT: A 43 ASN cc_start: 0.8129 (m-40) cc_final: 0.7652 (t0) REVERT: A 244 MET cc_start: 0.8491 (tpp) cc_final: 0.8032 (tpp) REVERT: A 316 ASN cc_start: 0.7722 (t0) cc_final: 0.7435 (t0) REVERT: B 219 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7449 (mtt-85) REVERT: B 234 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: R 326 ASN cc_start: 0.8723 (m-40) cc_final: 0.8456 (m-40) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 0.1825 time to fit residues: 31.8376 Evaluate side-chains 122 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 0.0000 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 overall best weight: 2.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN R 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7166 Z= 0.308 Angle : 0.585 10.476 9713 Z= 0.300 Chirality : 0.043 0.159 1110 Planarity : 0.003 0.036 1201 Dihedral : 6.297 52.594 1269 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.45 % Allowed : 17.69 % Favored : 79.86 % 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: 0.25 (0.30), residues: 867 helix: 2.60 (0.27), residues: 358 sheet: -1.63 (0.38), residues: 180 loop : -1.55 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 421 HIS 0.006 0.001 HIS R 266 PHE 0.018 0.002 PHE R 292 TYR 0.013 0.001 TYR R 504 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.821 Fit side-chains REVERT: A 43 ASN cc_start: 0.8167 (m-40) cc_final: 0.7695 (t0) REVERT: A 244 MET cc_start: 0.8492 (tpp) cc_final: 0.8017 (tpp) REVERT: A 316 ASN cc_start: 0.7731 (t0) cc_final: 0.7389 (t0) outliers start: 18 outliers final: 16 residues processed: 117 average time/residue: 0.1803 time to fit residues: 28.7262 Evaluate side-chains 116 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 266 HIS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN R 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7166 Z= 0.171 Angle : 0.536 10.496 9713 Z= 0.273 Chirality : 0.041 0.144 1110 Planarity : 0.003 0.041 1201 Dihedral : 5.958 55.221 1269 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.18 % Allowed : 18.10 % Favored : 79.73 % 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: 0.47 (0.30), residues: 867 helix: 2.79 (0.28), residues: 356 sheet: -1.46 (0.39), residues: 172 loop : -1.48 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 421 HIS 0.011 0.001 HIS R 266 PHE 0.022 0.001 PHE B 292 TYR 0.009 0.001 TYR R 504 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.790 Fit side-chains REVERT: A 43 ASN cc_start: 0.7991 (m-40) cc_final: 0.7573 (t0) REVERT: A 244 MET cc_start: 0.8497 (tpp) cc_final: 0.8034 (tpp) REVERT: A 315 PRO cc_start: 0.8023 (Cg_exo) cc_final: 0.7766 (Cg_endo) REVERT: A 316 ASN cc_start: 0.7669 (t0) cc_final: 0.7401 (t0) REVERT: B 219 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7292 (mtt-85) REVERT: B 234 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: B 292 PHE cc_start: 0.8409 (m-10) cc_final: 0.8052 (m-10) REVERT: R 279 SER cc_start: 0.8398 (t) cc_final: 0.8151 (t) REVERT: R 326 ASN cc_start: 0.8791 (m-40) cc_final: 0.8545 (m-40) REVERT: R 414 ARG cc_start: 0.5343 (tpt170) cc_final: 0.4756 (mmm-85) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.1907 time to fit residues: 30.7990 Evaluate side-chains 121 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7166 Z= 0.190 Angle : 0.542 10.422 9713 Z= 0.274 Chirality : 0.041 0.142 1110 Planarity : 0.003 0.044 1201 Dihedral : 5.920 53.791 1269 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.04 % Allowed : 18.50 % Favored : 79.46 % 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: 0.50 (0.30), residues: 867 helix: 2.79 (0.27), residues: 358 sheet: -1.40 (0.39), residues: 172 loop : -1.48 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 421 HIS 0.010 0.001 HIS R 266 PHE 0.021 0.001 PHE B 292 TYR 0.009 0.001 TYR R 504 ARG 0.009 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.778 Fit side-chains REVERT: A 43 ASN cc_start: 0.7958 (m-40) cc_final: 0.7568 (t0) REVERT: A 244 MET cc_start: 0.8475 (tpp) cc_final: 0.7996 (tpp) REVERT: A 315 PRO cc_start: 0.7903 (Cg_exo) cc_final: 0.7702 (Cg_endo) REVERT: A 316 ASN cc_start: 0.7634 (t0) cc_final: 0.7400 (t0) REVERT: B 219 ARG cc_start: 0.7898 (mtt-85) cc_final: 0.7330 (mtt-85) REVERT: B 234 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: B 292 PHE cc_start: 0.8469 (m-10) cc_final: 0.8157 (m-10) REVERT: R 326 ASN cc_start: 0.8797 (m-40) cc_final: 0.8558 (m-40) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.1941 time to fit residues: 31.6227 Evaluate side-chains 123 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129071 restraints weight = 20054.631| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 5.47 r_work: 0.3221 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7166 Z= 0.160 Angle : 0.524 10.451 9713 Z= 0.264 Chirality : 0.040 0.136 1110 Planarity : 0.003 0.044 1201 Dihedral : 5.721 53.699 1269 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.04 % Allowed : 18.23 % Favored : 79.73 % 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: 0.60 (0.30), residues: 867 helix: 2.87 (0.28), residues: 358 sheet: -1.35 (0.39), residues: 172 loop : -1.43 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.009 0.001 HIS R 266 PHE 0.020 0.001 PHE R 292 TYR 0.009 0.001 TYR R 504 ARG 0.010 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.18 seconds wall clock time: 32 minutes 27.26 seconds (1947.26 seconds total)