Starting phenix.real_space_refine on Fri Dec 8 13:30:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/12_2023/8qsk_18634.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/12_2023/8qsk_18634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/12_2023/8qsk_18634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/12_2023/8qsk_18634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/12_2023/8qsk_18634.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsk_18634/12_2023/8qsk_18634.pdb" } resolution = 3.3 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= 0.001 sd= 0.016 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 2 5.49 5 S 48 5.16 5 C 5702 2.51 5 N 1310 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.23, per 1000 atoms: 0.61 Number of scatterers: 8506 At special positions: 0 Unit cell: (126.445, 76.285, 87.78, 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 48 16.00 P 2 15.00 O 1444 8.00 N 1310 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 153 " 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 A 603 " - " ASN A 140 " " NAG C 604 " - " ASN C 140 " Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 81.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.541A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.639A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.943A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.846A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 183 removed outlier: 4.480A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.660A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 3.531A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.686A pdb=" N ALA A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 4.155A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.681A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.236A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 348 Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.874A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 367 through 395 removed outlier: 4.525A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 4.612A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix removed outlier: 4.114A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.912A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 3.512A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.516A pdb=" N TYR A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 560 removed outlier: 4.009A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.670A pdb=" N ALA C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 57 removed outlier: 3.649A pdb=" N CYS C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 70 through 98 removed outlier: 3.930A pdb=" N SER C 89 " --> pdb=" O THR C 85 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 118 through 125 removed outlier: 3.869A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 153 through 183 removed outlier: 4.510A pdb=" N THR C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix removed outlier: 3.701A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 220 removed outlier: 3.517A pdb=" N THR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 248 removed outlier: 3.697A pdb=" N ALA C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) Proline residue: C 229 - end of helix removed outlier: 4.153A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 273 removed outlier: 3.892A pdb=" N MET C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 303 Processing helix chain 'C' and resid 308 through 348 Proline residue: C 323 - end of helix Proline residue: C 330 - end of helix removed outlier: 3.848A pdb=" N VAL C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 367 through 395 removed outlier: 4.512A pdb=" N ASP C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Proline residue: C 382 - end of helix removed outlier: 4.615A pdb=" N ASP C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 390 - end of helix removed outlier: 4.112A pdb=" N HIS C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 430 removed outlier: 3.947A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 removed outlier: 3.518A pdb=" N TRP C 453 " --> pdb=" O SER C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 454 through 479 removed outlier: 3.503A pdb=" N TYR C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 511 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 532 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA2, first strand: chain 'C' and resid 435 through 436 592 hydrogen bonds defined for protein. 1746 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: 2.36 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1253 1.32 - 1.44: 2341 1.44 - 1.56: 5074 1.56 - 1.69: 4 1.69 - 1.81: 70 Bond restraints: 8742 Sorted by residual: bond pdb=" N HIS C 303 " pdb=" CA HIS C 303 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.51e+00 bond pdb=" N THR C 308 " pdb=" CA THR C 308 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.88e+00 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.75e+00 bond pdb=" N ILE C 421 " pdb=" CA ILE C 421 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.75e+00 ... (remaining 8737 not shown) Histogram of bond angle deviations from ideal: 92.92 - 101.13: 33 101.13 - 109.35: 619 109.35 - 117.56: 6101 117.56 - 125.77: 5040 125.77 - 133.99: 139 Bond angle restraints: 11932 Sorted by residual: angle pdb=" N LEU C 429 " pdb=" CA LEU C 429 " pdb=" C LEU C 429 " ideal model delta sigma weight residual 113.18 108.36 4.82 1.21e+00 6.83e-01 1.59e+01 angle pdb=" N LEU A 429 " pdb=" CA LEU A 429 " pdb=" C LEU A 429 " ideal model delta sigma weight residual 113.18 108.42 4.76 1.21e+00 6.83e-01 1.55e+01 angle pdb=" N ASN A 428 " pdb=" CA ASN A 428 " pdb=" C ASN A 428 " ideal model delta sigma weight residual 113.88 109.04 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" N ASN C 428 " pdb=" CA ASN C 428 " pdb=" C ASN C 428 " ideal model delta sigma weight residual 113.88 109.07 4.81 1.23e+00 6.61e-01 1.53e+01 angle pdb=" CA GLY A 305 " pdb=" C GLY A 305 " pdb=" O GLY A 305 " ideal model delta sigma weight residual 122.46 118.70 3.76 9.70e-01 1.06e+00 1.50e+01 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 5593 31.88 - 63.76: 136 63.76 - 95.65: 3 95.65 - 127.53: 0 127.53 - 159.41: 2 Dihedral angle restraints: 5734 sinusoidal: 2742 harmonic: 2992 Sorted by residual: dihedral pdb=" C3 PGT A 607 " pdb=" C1 PGT A 607 " pdb=" C2 PGT A 607 " pdb=" O3P PGT A 607 " ideal model delta sinusoidal sigma weight residual -66.13 93.28 -159.41 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C3 PGT C 608 " pdb=" C1 PGT C 608 " pdb=" C2 PGT C 608 " pdb=" O3P PGT C 608 " ideal model delta sinusoidal sigma weight residual -66.13 92.55 -158.68 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA LEU C 397 " pdb=" C LEU C 397 " pdb=" N LEU C 398 " pdb=" CA LEU C 398 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1042 0.037 - 0.073: 245 0.073 - 0.109: 86 0.109 - 0.146: 13 0.146 - 0.182: 12 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB VAL A 430 " pdb=" CA VAL A 430 " pdb=" CG1 VAL A 430 " pdb=" CG2 VAL A 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA ILE C 421 " pdb=" N ILE C 421 " pdb=" C ILE C 421 " pdb=" CB ILE C 421 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB VAL C 430 " pdb=" CA VAL C 430 " pdb=" CG1 VAL C 430 " pdb=" CG2 VAL C 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 1395 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 426 " -0.401 9.50e-02 1.11e+02 1.80e-01 1.99e+01 pdb=" NE ARG C 426 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 426 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 426 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 426 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 426 " 0.344 9.50e-02 1.11e+02 1.54e-01 1.47e+01 pdb=" NE ARG A 426 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 426 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 426 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 426 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 462 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C GLY C 462 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY C 462 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 463 " 0.009 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1490 2.77 - 3.30: 9050 3.30 - 3.83: 14177 3.83 - 4.37: 16095 4.37 - 4.90: 27384 Nonbonded interactions: 68196 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.235 2.440 nonbonded pdb=" O LEU A 122 " pdb=" OG1 THR A 128 " model vdw 2.254 2.440 nonbonded pdb=" O LEU C 122 " pdb=" OG1 THR C 128 " model vdw 2.257 2.440 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.261 2.440 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.265 2.440 ... (remaining 68191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 560 or resid 601 through 602 or resid 605 throu \ gh 606)) selection = (chain 'C' and (resid 16 through 560 or resid 601 through 602 or resid 605 throu \ gh 606)) } 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: 1.010 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: 3.220 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.300 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.003 0.035 8742 Z= 0.210 Angle : 0.630 6.757 11932 Z= 0.367 Chirality : 0.040 0.182 1398 Planarity : 0.008 0.180 1410 Dihedral : 12.956 159.410 3806 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 1.59 % Allowed : 8.90 % Favored : 89.51 % 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: 1.79 (0.28), residues: 1038 helix: 2.22 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -2.00 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 197 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE A 67 TYR 0.008 0.001 TYR A 458 ARG 0.005 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 229 average time/residue: 0.1798 time to fit residues: 58.3737 Evaluate side-chains 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.931 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.0857 time to fit residues: 1.9910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.3980 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8742 Z= 0.222 Angle : 0.663 11.567 11932 Z= 0.317 Chirality : 0.041 0.184 1398 Planarity : 0.004 0.035 1410 Dihedral : 10.855 154.205 2106 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.88 % Allowed : 14.27 % Favored : 80.85 % 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: 2.01 (0.28), residues: 1038 helix: 2.41 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -2.16 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.002 0.001 HIS A 521 PHE 0.021 0.001 PHE C 198 TYR 0.009 0.001 TYR A 534 ARG 0.003 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 101 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 126 average time/residue: 0.1688 time to fit residues: 31.8364 Evaluate side-chains 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.924 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.0782 time to fit residues: 4.0833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 50.0000 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8742 Z= 0.333 Angle : 0.745 6.824 11932 Z= 0.369 Chirality : 0.045 0.234 1398 Planarity : 0.006 0.087 1410 Dihedral : 10.819 151.394 2106 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.29 % Allowed : 18.05 % Favored : 78.66 % 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: 1.29 (0.27), residues: 1038 helix: 1.67 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -1.73 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 368 HIS 0.005 0.001 HIS C 445 PHE 0.020 0.002 PHE A 67 TYR 0.044 0.003 TYR C 266 ARG 0.006 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 108 average time/residue: 0.1493 time to fit residues: 25.1223 Evaluate side-chains 81 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.848 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.0896 time to fit residues: 3.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8742 Z= 0.240 Angle : 0.636 8.812 11932 Z= 0.307 Chirality : 0.040 0.190 1398 Planarity : 0.004 0.042 1410 Dihedral : 10.628 151.385 2106 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.68 % Allowed : 20.37 % Favored : 76.95 % 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: 1.79 (0.28), residues: 1038 helix: 2.06 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.002 0.000 HIS A 395 PHE 0.014 0.001 PHE C 198 TYR 0.010 0.001 TYR C 444 ARG 0.006 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.919 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 95 average time/residue: 0.1477 time to fit residues: 22.4543 Evaluate side-chains 77 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0829 time to fit residues: 2.5663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8742 Z= 0.250 Angle : 0.633 7.632 11932 Z= 0.304 Chirality : 0.039 0.187 1398 Planarity : 0.004 0.044 1410 Dihedral : 10.451 150.405 2106 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.32 % Allowed : 20.85 % Favored : 76.83 % 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: 1.81 (0.28), residues: 1038 helix: 2.04 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -1.55 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 368 HIS 0.003 0.001 HIS A 395 PHE 0.013 0.001 PHE C 198 TYR 0.053 0.002 TYR A 266 ARG 0.005 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.031 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 92 average time/residue: 0.1545 time to fit residues: 22.4138 Evaluate side-chains 80 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0855 time to fit residues: 2.4471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 97 optimal weight: 0.6980 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 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8742 Z= 0.183 Angle : 0.605 10.208 11932 Z= 0.288 Chirality : 0.038 0.176 1398 Planarity : 0.004 0.052 1410 Dihedral : 10.291 149.562 2106 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.83 % Allowed : 20.12 % Favored : 78.05 % 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: 1.87 (0.28), residues: 1038 helix: 2.07 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -1.58 (0.46), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 395 PHE 0.018 0.001 PHE C 493 TYR 0.008 0.001 TYR A 52 ARG 0.004 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.976 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 91 average time/residue: 0.1454 time to fit residues: 21.1118 Evaluate side-chains 79 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0853 time to fit residues: 2.0068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 0.0020 chunk 59 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8742 Z= 0.159 Angle : 0.600 11.898 11932 Z= 0.284 Chirality : 0.038 0.169 1398 Planarity : 0.004 0.046 1410 Dihedral : 10.106 148.390 2106 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.10 % Allowed : 21.46 % Favored : 77.44 % 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: 1.97 (0.28), residues: 1038 helix: 2.12 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -1.50 (0.47), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 395 PHE 0.015 0.001 PHE C 493 TYR 0.048 0.001 TYR A 266 ARG 0.003 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.916 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 86 average time/residue: 0.1591 time to fit residues: 21.3145 Evaluate side-chains 78 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1008 time to fit residues: 1.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 91 optimal weight: 0.0770 chunk 96 optimal weight: 0.0570 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8742 Z= 0.161 Angle : 0.617 11.723 11932 Z= 0.290 Chirality : 0.038 0.180 1398 Planarity : 0.004 0.048 1410 Dihedral : 9.955 147.413 2106 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.61 % Allowed : 22.32 % Favored : 77.07 % 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: 1.98 (0.28), residues: 1038 helix: 2.25 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.73 (0.45), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.004 0.000 HIS C 348 PHE 0.019 0.001 PHE C 493 TYR 0.009 0.001 TYR C 113 ARG 0.004 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.842 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 0.1527 time to fit residues: 20.0727 Evaluate side-chains 80 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0813 time to fit residues: 1.4517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.0020 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.0050 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8742 Z= 0.160 Angle : 0.630 12.805 11932 Z= 0.291 Chirality : 0.038 0.241 1398 Planarity : 0.004 0.040 1410 Dihedral : 9.833 146.677 2106 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 0.61 % Allowed : 22.44 % Favored : 76.95 % 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: 2.02 (0.28), residues: 1038 helix: 2.28 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.71 (0.45), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 452 HIS 0.004 0.000 HIS C 348 PHE 0.012 0.001 PHE C 198 TYR 0.045 0.001 TYR A 266 ARG 0.003 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.949 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 81 average time/residue: 0.1586 time to fit residues: 20.1411 Evaluate side-chains 79 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0957 time to fit residues: 1.7198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8742 Z= 0.186 Angle : 0.635 12.993 11932 Z= 0.297 Chirality : 0.039 0.239 1398 Planarity : 0.004 0.044 1410 Dihedral : 9.731 146.459 2106 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 0.37 % Allowed : 22.68 % Favored : 76.95 % 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: 2.01 (0.28), residues: 1038 helix: 2.27 (0.19), residues: 778 sheet: -0.00 (1.18), residues: 20 loop : -1.85 (0.47), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.003 0.000 HIS C 348 PHE 0.012 0.001 PHE C 198 TYR 0.008 0.001 TYR A 52 ARG 0.003 0.000 ARG A 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.909 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.1580 time to fit residues: 19.4159 Evaluate side-chains 76 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0916 time to fit residues: 1.5317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 0.0040 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 0.0010 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.116383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092681 restraints weight = 18252.219| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.00 r_work: 0.3315 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8742 Z= 0.140 Angle : 0.627 13.062 11932 Z= 0.289 Chirality : 0.038 0.218 1398 Planarity : 0.004 0.037 1410 Dihedral : 9.626 145.519 2106 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.24 % Allowed : 22.93 % Favored : 76.83 % 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: 2.13 (0.28), residues: 1038 helix: 2.38 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -1.75 (0.44), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 94 HIS 0.003 0.000 HIS C 348 PHE 0.015 0.001 PHE A 67 TYR 0.039 0.001 TYR A 266 ARG 0.003 0.000 ARG A 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.15 seconds wall clock time: 32 minutes 6.97 seconds (1926.97 seconds total)