Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 10:17:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/04_2023/7to3_26028_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/04_2023/7to3_26028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/04_2023/7to3_26028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/04_2023/7to3_26028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/04_2023/7to3_26028_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/04_2023/7to3_26028_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 44 5.16 5 C 9346 2.51 5 N 2572 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14764 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4421 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4421 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2878 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2878 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 7.70, per 1000 atoms: 0.52 Number of scatterers: 14764 At special positions: 0 Unit cell: (147, 126.84, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 12 15.00 Mg 4 11.99 O 2786 8.00 N 2572 7.00 C 9346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.81 Conformation dependent library (CDL) restraints added in 2.3 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 10 sheets defined 34.5% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 129 through 148 Processing helix chain 'A' and resid 179 through 188 Proline residue: A 183 - end of helix removed outlier: 4.243A pdb=" N SER A 187 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 377 No H-bonds generated for 'chain 'A' and resid 374 through 377' Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.575A pdb=" N MET A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.678A pdb=" N GLN A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 557 through 576 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 129 through 148 Processing helix chain 'B' and resid 179 through 188 Proline residue: B 183 - end of helix removed outlier: 4.243A pdb=" N SER B 187 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 272 through 285 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 374 through 377 No H-bonds generated for 'chain 'B' and resid 374 through 377' Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.574A pdb=" N MET B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.676A pdb=" N GLN B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 521 through 530 Processing helix chain 'B' and resid 557 through 576 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 85 through 99 removed outlier: 4.234A pdb=" N PHE C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Proline residue: C 94 - end of helix Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 310 through 332 removed outlier: 3.556A pdb=" N ALA C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 removed outlier: 3.960A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 13 Processing helix chain 'D' and resid 18 through 37 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 85 through 99 removed outlier: 4.234A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Proline residue: D 94 - end of helix Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 207 through 220 Processing helix chain 'D' and resid 225 through 238 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 310 through 332 removed outlier: 3.556A pdb=" N ALA D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 347 removed outlier: 3.961A pdb=" N LEU D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 357 through 360 removed outlier: 6.965A pdb=" N SER A 196 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE A 212 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 194 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A 197 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR A 236 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 294 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER A 241 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 296 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 311 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 593 through 597 removed outlier: 6.861A pdb=" N SER A 448 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ILE A 407 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG A 450 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 39 through 45 Processing sheet with id= E, first strand: chain 'B' and resid 357 through 360 removed outlier: 6.964A pdb=" N SER B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE B 212 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 194 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR B 236 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 294 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SER B 241 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 296 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 311 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 593 through 597 removed outlier: 6.861A pdb=" N SER B 448 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ILE B 407 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG B 450 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 104 through 107 removed outlier: 7.217A pdb=" N ASP C 121 " --> pdb=" O PRO C 68 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL C 70 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 123 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 72 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR C 125 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 74 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP C 71 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 Processing sheet with id= I, first strand: chain 'D' and resid 104 through 107 removed outlier: 7.217A pdb=" N ASP D 121 " --> pdb=" O PRO D 68 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 70 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL D 123 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 72 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR D 125 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 74 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP D 71 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 125 through 127 540 hydrogen bonds defined for protein. 1548 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: 4.33 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4847 1.35 - 1.46: 3467 1.46 - 1.58: 6746 1.58 - 1.69: 18 1.69 - 1.81: 72 Bond restraints: 15150 Sorted by residual: bond pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.75e+00 bond pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.68e+00 bond pdb=" C GLU B 69 " pdb=" O GLU B 69 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.24e-02 6.50e+03 9.88e-01 bond pdb=" C4 ADP D 405 " pdb=" C5 ADP D 405 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.57e-01 bond pdb=" C4 AMP D 401 " pdb=" C5 AMP D 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.50e-01 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 98.35 - 106.67: 611 106.67 - 114.98: 9053 114.98 - 123.30: 10172 123.30 - 131.61: 738 131.61 - 139.93: 80 Bond angle restraints: 20654 Sorted by residual: angle pdb=" N ILE B 220 " pdb=" CA ILE B 220 " pdb=" C ILE B 220 " ideal model delta sigma weight residual 113.71 110.28 3.43 9.50e-01 1.11e+00 1.31e+01 angle pdb=" N ILE A 220 " pdb=" CA ILE A 220 " pdb=" C ILE A 220 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.30e+01 angle pdb=" N TRP C 24 " pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 110.16 115.00 -4.84 1.48e+00 4.57e-01 1.07e+01 angle pdb=" N TRP D 24 " pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 110.16 114.93 -4.77 1.48e+00 4.57e-01 1.04e+01 angle pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " pdb=" CG TRP C 24 " ideal model delta sigma weight residual 113.60 119.55 -5.95 1.90e+00 2.77e-01 9.81e+00 ... (remaining 20649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 8864 34.13 - 68.26: 100 68.26 - 102.39: 0 102.39 - 136.51: 2 136.51 - 170.64: 4 Dihedral angle restraints: 8970 sinusoidal: 3608 harmonic: 5362 Sorted by residual: dihedral pdb=" O2A ADP D 405 " pdb=" O3A ADP D 405 " pdb=" PA ADP D 405 " pdb=" PB ADP D 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.36 170.64 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PA ADP C 405 " pdb=" PB ADP C 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.37 170.63 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' AMP C 401 " pdb=" O5' AMP C 401 " pdb=" P AMP C 401 " pdb=" O3P AMP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 148.68 151.32 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 8967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1643 0.033 - 0.067: 426 0.067 - 0.100: 119 0.100 - 0.133: 54 0.133 - 0.167: 8 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2247 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 24 " -0.034 2.00e-02 2.50e+03 3.68e-02 3.38e+01 pdb=" CG TRP D 24 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP D 24 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP D 24 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 24 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 24 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 24 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 24 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 24 " 0.034 2.00e-02 2.50e+03 3.67e-02 3.36e+01 pdb=" CG TRP C 24 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP C 24 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 24 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 24 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 24 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 24 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 24 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 24 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 24 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 49 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 50 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.027 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 34 2.63 - 3.20: 12092 3.20 - 3.76: 22085 3.76 - 4.33: 31875 4.33 - 4.90: 51731 Nonbonded interactions: 117817 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O2B ATP C 404 " model vdw 2.062 2.170 nonbonded pdb="MG MG D 403 " pdb=" O2B ATP D 404 " model vdw 2.062 2.170 nonbonded pdb=" OD2 ASP C 69 " pdb="MG MG C 402 " model vdw 2.079 2.170 nonbonded pdb=" OD2 ASP D 69 " pdb="MG MG D 402 " model vdw 2.080 2.170 nonbonded pdb=" O ALA C 132 " pdb=" ND1 HIS C 136 " model vdw 2.317 2.520 ... (remaining 117812 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 19.180 Check model and map are aligned: 0.260 Set scattering table: 0.120 Process input model: 36.680 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.002 0.023 15150 Z= 0.132 Angle : 0.544 5.950 20654 Z= 0.281 Chirality : 0.037 0.167 2250 Planarity : 0.004 0.049 2648 Dihedral : 11.670 170.644 5478 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1830 helix: 2.69 (0.20), residues: 664 sheet: 0.57 (0.27), residues: 348 loop : -1.32 (0.19), residues: 818 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 1.6838 time to fit residues: 473.3242 Evaluate side-chains 105 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.0670 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN B 94 ASN C 8 ASN C 210 GLN C 254 HIS D 8 ASN D 210 GLN D 254 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 15150 Z= 0.201 Angle : 0.563 6.116 20654 Z= 0.269 Chirality : 0.039 0.176 2250 Planarity : 0.004 0.057 2648 Dihedral : 8.355 141.233 2026 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.87 (0.19), residues: 1830 helix: 2.51 (0.20), residues: 660 sheet: 0.61 (0.27), residues: 334 loop : -1.08 (0.19), residues: 836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 130 average time/residue: 1.4998 time to fit residues: 213.2541 Evaluate side-chains 86 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.2686 time to fit residues: 2.6739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS D 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15150 Z= 0.217 Angle : 0.559 7.021 20654 Z= 0.266 Chirality : 0.040 0.172 2250 Planarity : 0.004 0.045 2648 Dihedral : 7.280 125.342 2026 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.81 (0.20), residues: 1830 helix: 2.39 (0.21), residues: 666 sheet: 0.73 (0.27), residues: 354 loop : -1.20 (0.20), residues: 810 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 109 average time/residue: 1.3597 time to fit residues: 163.9814 Evaluate side-chains 87 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1989 time to fit residues: 2.6084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 15150 Z= 0.284 Angle : 0.592 7.523 20654 Z= 0.283 Chirality : 0.041 0.177 2250 Planarity : 0.004 0.042 2648 Dihedral : 6.551 98.794 2026 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.66 (0.19), residues: 1830 helix: 2.17 (0.21), residues: 670 sheet: 0.80 (0.27), residues: 348 loop : -1.29 (0.19), residues: 812 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 82 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 115 average time/residue: 1.3616 time to fit residues: 173.4395 Evaluate side-chains 87 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.6986 time to fit residues: 4.0421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.0370 chunk 150 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 HIS ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15150 Z= 0.183 Angle : 0.539 7.373 20654 Z= 0.255 Chirality : 0.039 0.168 2250 Planarity : 0.004 0.038 2648 Dihedral : 6.163 80.127 2026 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.72 (0.20), residues: 1830 helix: 2.15 (0.21), residues: 672 sheet: 0.89 (0.27), residues: 344 loop : -1.20 (0.20), residues: 814 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 95 average time/residue: 1.3868 time to fit residues: 146.2290 Evaluate side-chains 85 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.1715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 15150 Z= 0.380 Angle : 0.628 8.810 20654 Z= 0.303 Chirality : 0.043 0.189 2250 Planarity : 0.005 0.038 2648 Dihedral : 6.296 82.766 2026 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.43 (0.20), residues: 1830 helix: 1.85 (0.21), residues: 682 sheet: 0.71 (0.27), residues: 344 loop : -1.34 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 93 average time/residue: 1.3478 time to fit residues: 139.5280 Evaluate side-chains 83 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 2.6093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15150 Z= 0.173 Angle : 0.535 7.445 20654 Z= 0.254 Chirality : 0.039 0.167 2250 Planarity : 0.004 0.036 2648 Dihedral : 6.073 89.044 2026 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.69 (0.20), residues: 1830 helix: 2.08 (0.21), residues: 672 sheet: 0.89 (0.28), residues: 344 loop : -1.19 (0.20), residues: 814 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 1.3559 time to fit residues: 138.0788 Evaluate side-chains 83 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 2.3385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15150 Z= 0.245 Angle : 0.567 8.941 20654 Z= 0.268 Chirality : 0.040 0.169 2250 Planarity : 0.004 0.035 2648 Dihedral : 5.992 88.760 2026 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.62 (0.20), residues: 1830 helix: 2.00 (0.21), residues: 672 sheet: 0.85 (0.28), residues: 344 loop : -1.21 (0.20), residues: 814 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 94 average time/residue: 1.3153 time to fit residues: 137.1302 Evaluate side-chains 84 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.1808 time to fit residues: 2.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 128 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 162 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 15150 Z= 0.143 Angle : 0.527 9.569 20654 Z= 0.248 Chirality : 0.038 0.165 2250 Planarity : 0.004 0.033 2648 Dihedral : 5.657 80.374 2026 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.79 (0.20), residues: 1830 helix: 2.17 (0.21), residues: 674 sheet: 0.91 (0.28), residues: 340 loop : -1.13 (0.20), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 98 average time/residue: 1.4117 time to fit residues: 152.6476 Evaluate side-chains 85 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 2.4159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 0.0470 chunk 120 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 144 optimal weight: 0.0870 chunk 14 optimal weight: 0.3980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 15150 Z= 0.151 Angle : 0.547 9.355 20654 Z= 0.257 Chirality : 0.038 0.167 2250 Planarity : 0.004 0.058 2648 Dihedral : 5.427 73.404 2026 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.83 (0.20), residues: 1830 helix: 2.18 (0.21), residues: 676 sheet: 0.96 (0.28), residues: 340 loop : -1.10 (0.20), residues: 814 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 17 residues processed: 94 average time/residue: 1.4617 time to fit residues: 151.3190 Evaluate side-chains 89 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 1 average time/residue: 0.2629 time to fit residues: 2.6993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065149 restraints weight = 30167.983| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.07 r_work: 0.2879 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 15150 Z= 0.178 Angle : 0.559 10.603 20654 Z= 0.264 Chirality : 0.039 0.168 2250 Planarity : 0.004 0.034 2648 Dihedral : 5.372 70.019 2026 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.83 (0.20), residues: 1830 helix: 2.16 (0.21), residues: 672 sheet: 0.96 (0.28), residues: 340 loop : -1.06 (0.20), residues: 818 =============================================================================== Job complete usr+sys time: 4186.59 seconds wall clock time: 75 minutes 50.08 seconds (4550.08 seconds total)