Starting phenix.real_space_refine on Tue Jun 25 15:58:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/06_2024/8jew_36201_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/06_2024/8jew_36201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/06_2024/8jew_36201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/06_2024/8jew_36201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/06_2024/8jew_36201_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/06_2024/8jew_36201_updated.pdb" } resolution = 2.49 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 ------------------------------------------------------------------------------- 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= 0.014 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 2 5.49 5 S 58 5.16 5 Na 4 4.78 5 C 5504 2.51 5 N 1246 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8284 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3881 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Unusual residues: {' NA': 2, 'ASC': 1, 'AV0': 2, 'CLR': 2, 'LBN': 1, 'NAG': 1, 'PLM': 1} Classifications: {'undetermined': 10, 'water': 3} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PLM:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3881 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Unusual residues: {' NA': 2, 'ASC': 1, 'AV0': 2, 'CLR': 2, 'LBN': 1, 'NAG': 1, 'PLM': 1} Classifications: {'undetermined': 10, 'water': 3} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PLM:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.04, per 1000 atoms: 0.61 Number of scatterers: 8284 At special positions: 0 Unit cell: (94.62, 108.564, 77.688, 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 58 16.00 P 2 15.00 Na 4 11.00 O 1470 8.00 N 1246 7.00 C 5504 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: 3.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 66.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 41 through 69 removed outlier: 3.720A pdb=" N LEU A 46 " --> pdb=" O TYR A 42 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 76 through 99 Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.644A pdb=" N VAL A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 146 through 172 Proline residue: A 151 - end of helix removed outlier: 3.562A pdb=" N GLU A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.894A pdb=" N LEU A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 181' Processing helix chain 'A' and resid 185 through 207 Proline residue: A 190 - end of helix removed outlier: 4.363A pdb=" N VAL A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 318 through 345 removed outlier: 3.895A pdb=" N SER A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 373 Processing helix chain 'A' and resid 383 through 392 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 425 through 449 removed outlier: 3.540A pdb=" N THR A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 550 through 553 No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 557 through 560 Processing helix chain 'B' and resid 41 through 69 removed outlier: 3.720A pdb=" N LEU B 46 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 112 through 122 removed outlier: 3.644A pdb=" N VAL B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 146 through 172 Proline residue: B 151 - end of helix removed outlier: 3.562A pdb=" N GLU B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.894A pdb=" N LEU B 180 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 181' Processing helix chain 'B' and resid 185 through 207 Proline residue: B 190 - end of helix removed outlier: 4.363A pdb=" N VAL B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 256 through 273 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 318 through 345 removed outlier: 3.895A pdb=" N SER B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 373 Processing helix chain 'B' and resid 383 through 392 Processing helix chain 'B' and resid 397 through 412 Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 425 through 449 removed outlier: 3.540A pdb=" N THR B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 500 through 514 Processing helix chain 'B' and resid 519 through 522 No H-bonds generated for 'chain 'B' and resid 519 through 522' Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 550 through 553 No H-bonds generated for 'chain 'B' and resid 550 through 553' Processing helix chain 'B' and resid 557 through 560 Processing sheet with id= A, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= B, first strand: chain 'B' and resid 108 through 110 422 hydrogen bonds defined for protein. 1260 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: 2.26 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1206 1.31 - 1.44: 2212 1.44 - 1.58: 4978 1.58 - 1.71: 4 1.71 - 1.84: 88 Bond restraints: 8488 Sorted by residual: bond pdb=" C TYR B 474 " pdb=" O TYR B 474 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.15e-02 7.56e+03 2.45e+01 bond pdb=" C TYR A 474 " pdb=" O TYR A 474 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.15e-02 7.56e+03 2.45e+01 bond pdb=" C PRO A 301 " pdb=" O PRO A 301 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.19e-02 7.06e+03 2.06e+01 bond pdb=" C PRO B 301 " pdb=" O PRO B 301 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.19e-02 7.06e+03 2.06e+01 bond pdb=" C GLN B 287 " pdb=" O GLN B 287 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.35e-02 5.49e+03 1.98e+01 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.47: 288 105.47 - 112.76: 4384 112.76 - 120.05: 3896 120.05 - 127.34: 2916 127.34 - 134.63: 104 Bond angle restraints: 11588 Sorted by residual: angle pdb=" N TYR A 42 " pdb=" CA TYR A 42 " pdb=" C TYR A 42 " ideal model delta sigma weight residual 111.71 106.27 5.44 1.15e+00 7.56e-01 2.24e+01 angle pdb=" N TYR B 42 " pdb=" CA TYR B 42 " pdb=" C TYR B 42 " ideal model delta sigma weight residual 111.71 106.27 5.44 1.15e+00 7.56e-01 2.24e+01 angle pdb=" CA ILE A 218 " pdb=" C ILE A 218 " pdb=" O ILE A 218 " ideal model delta sigma weight residual 121.17 116.22 4.95 1.06e+00 8.90e-01 2.18e+01 angle pdb=" CA ILE B 218 " pdb=" C ILE B 218 " pdb=" O ILE B 218 " ideal model delta sigma weight residual 121.17 116.22 4.95 1.06e+00 8.90e-01 2.18e+01 angle pdb=" O ILE A 218 " pdb=" C ILE A 218 " pdb=" N LEU A 219 " ideal model delta sigma weight residual 121.91 126.38 -4.47 9.80e-01 1.04e+00 2.08e+01 ... (remaining 11583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.32: 5262 28.32 - 56.64: 200 56.64 - 84.95: 32 84.95 - 113.27: 0 113.27 - 141.59: 8 Dihedral angle restraints: 5502 sinusoidal: 2602 harmonic: 2900 Sorted by residual: dihedral pdb=" C1 LBN B 605 " pdb=" O1 LBN B 605 " pdb=" P1 LBN B 605 " pdb=" O3 LBN B 605 " ideal model delta sinusoidal sigma weight residual -84.60 56.99 -141.59 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C1 LBN A 605 " pdb=" O1 LBN A 605 " pdb=" P1 LBN A 605 " pdb=" O3 LBN A 605 " ideal model delta sinusoidal sigma weight residual -84.60 56.99 -141.59 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O5 LBN A 605 " pdb=" C2 LBN A 605 " pdb=" C3 LBN A 605 " pdb=" O7 LBN A 605 " ideal model delta sinusoidal sigma weight residual 62.67 -60.77 123.44 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 5499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 630 0.049 - 0.098: 436 0.098 - 0.147: 232 0.147 - 0.196: 100 0.196 - 0.244: 24 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA PRO B 563 " pdb=" N PRO B 563 " pdb=" C PRO B 563 " pdb=" CB PRO B 563 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO A 563 " pdb=" N PRO A 563 " pdb=" C PRO A 563 " pdb=" CB PRO A 563 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA TRP B 149 " pdb=" N TRP B 149 " pdb=" C TRP B 149 " pdb=" CB TRP B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1419 not shown) Planarity restraints: 1352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.056 2.00e-02 2.50e+03 4.63e-02 2.67e+01 pdb=" C7 NAG A 609 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 609 " -0.056 2.00e-02 2.50e+03 4.63e-02 2.67e+01 pdb=" C7 NAG B 609 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG B 609 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG B 609 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 609 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 311 " -0.027 2.00e-02 2.50e+03 2.91e-02 2.11e+01 pdb=" CG TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP A 311 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 311 " 0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 311 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 311 " 0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP A 311 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 311 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 311 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 311 " -0.019 2.00e-02 2.50e+03 ... (remaining 1349 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 34 2.53 - 3.12: 6352 3.12 - 3.71: 13648 3.71 - 4.31: 20092 4.31 - 4.90: 32408 Nonbonded interactions: 72534 Sorted by model distance: nonbonded pdb=" OD2 ASP A 338 " pdb="NA NA A 602 " model vdw 1.932 2.470 nonbonded pdb=" OD2 ASP B 338 " pdb="NA NA B 602 " model vdw 1.932 2.470 nonbonded pdb=" ND2 ASN B 144 " pdb=" C1 NAG B 609 " model vdw 2.059 3.550 nonbonded pdb=" ND2 ASN A 144 " pdb=" C1 NAG A 609 " model vdw 2.059 3.550 nonbonded pdb=" OAI AV0 A 604 " pdb=" OH TYR B 474 " model vdw 2.228 2.440 ... (remaining 72529 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' } 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: 0.140 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: 0.720 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.030 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.015 0.069 8488 Z= 0.978 Angle : 1.791 10.357 11588 Z= 1.295 Chirality : 0.085 0.244 1422 Planarity : 0.014 0.117 1352 Dihedral : 15.566 141.589 3650 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.48 % Allowed : 12.38 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.48 (0.24), residues: 1012 helix: -0.06 (0.18), residues: 664 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.012 TRP A 311 HIS 0.014 0.005 HIS A 210 PHE 0.050 0.010 PHE A 459 TYR 0.043 0.009 TYR B 474 ARG 0.021 0.003 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.736 Fit side-chains REVERT: A 78 MET cc_start: 0.8861 (tmt) cc_final: 0.8390 (tmt) REVERT: A 99 THR cc_start: 0.8314 (t) cc_final: 0.8100 (p) REVERT: A 119 LYS cc_start: 0.7518 (pttp) cc_final: 0.7301 (mtmm) REVERT: A 161 MET cc_start: 0.8740 (mtp) cc_final: 0.8324 (mtm) REVERT: A 172 LEU cc_start: 0.8139 (tp) cc_final: 0.7673 (mt) REVERT: A 201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7092 (mt0) REVERT: A 251 ILE cc_start: 0.7110 (tt) cc_final: 0.6770 (pt) REVERT: A 334 GLU cc_start: 0.8383 (tt0) cc_final: 0.8141 (tt0) REVERT: A 381 SER cc_start: 0.8036 (m) cc_final: 0.7664 (p) REVERT: A 476 GLU cc_start: 0.7849 (tp30) cc_final: 0.7310 (mm-30) REVERT: A 500 GLU cc_start: 0.7758 (mp0) cc_final: 0.7470 (mp0) REVERT: A 550 MET cc_start: 0.3350 (tpt) cc_final: 0.3060 (tpt) REVERT: B 78 MET cc_start: 0.8858 (tmt) cc_final: 0.8387 (tmt) REVERT: B 99 THR cc_start: 0.8316 (t) cc_final: 0.8101 (p) REVERT: B 119 LYS cc_start: 0.7520 (pttp) cc_final: 0.7302 (mtmm) REVERT: B 161 MET cc_start: 0.8740 (mtp) cc_final: 0.8323 (mtm) REVERT: B 172 LEU cc_start: 0.8133 (tp) cc_final: 0.7668 (mt) REVERT: B 201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7093 (mt0) REVERT: B 251 ILE cc_start: 0.7110 (tt) cc_final: 0.6772 (pt) REVERT: B 334 GLU cc_start: 0.8380 (tt0) cc_final: 0.8139 (tt0) REVERT: B 381 SER cc_start: 0.8037 (m) cc_final: 0.7664 (p) REVERT: B 476 GLU cc_start: 0.7850 (tp30) cc_final: 0.7312 (mm-30) REVERT: B 500 GLU cc_start: 0.7762 (mp0) cc_final: 0.7473 (mp0) REVERT: B 550 MET cc_start: 0.3351 (tpt) cc_final: 0.3063 (tpt) outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 1.0859 time to fit residues: 171.7899 Evaluate side-chains 120 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 108 GLN B 147 HIS B 401 GLN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 8488 Z= 0.342 Angle : 1.231 38.575 11588 Z= 0.562 Chirality : 0.065 0.499 1422 Planarity : 0.013 0.195 1352 Dihedral : 12.993 127.904 1940 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.47 % Favored : 96.44 % Rotamer: Outliers : 4.52 % Allowed : 14.76 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.39 (0.26), residues: 1012 helix: 0.07 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP B 265 HIS 0.055 0.006 HIS B 210 PHE 0.104 0.006 PHE B 255 TYR 0.183 0.008 TYR B 402 ARG 0.070 0.005 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 0.804 Fit side-chains REVERT: A 78 MET cc_start: 0.8701 (tmt) cc_final: 0.8462 (ppp) REVERT: A 119 LYS cc_start: 0.7288 (pttp) cc_final: 0.7083 (mtmm) REVERT: A 161 MET cc_start: 0.8555 (mtp) cc_final: 0.8106 (mtm) REVERT: A 172 LEU cc_start: 0.8073 (tp) cc_final: 0.7585 (mt) REVERT: A 251 ILE cc_start: 0.7017 (tt) cc_final: 0.6700 (pt) REVERT: A 381 SER cc_start: 0.7830 (m) cc_final: 0.7504 (p) REVERT: A 476 GLU cc_start: 0.7853 (tp30) cc_final: 0.7350 (pt0) REVERT: A 550 MET cc_start: 0.3354 (tpt) cc_final: 0.3071 (tpt) REVERT: B 78 MET cc_start: 0.8649 (tmt) cc_final: 0.8294 (ppp) REVERT: B 119 LYS cc_start: 0.7384 (pttp) cc_final: 0.7099 (mtmm) REVERT: B 172 LEU cc_start: 0.7920 (tp) cc_final: 0.7428 (OUTLIER) REVERT: B 249 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4268 (mm) REVERT: B 251 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6900 (pt) REVERT: B 282 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7188 (mtpm) REVERT: B 334 GLU cc_start: 0.8077 (tt0) cc_final: 0.7850 (tt0) REVERT: B 476 GLU cc_start: 0.7623 (tp30) cc_final: 0.7085 (mp0) REVERT: B 500 GLU cc_start: 0.7646 (mp0) cc_final: 0.7394 (mp0) REVERT: B 550 MET cc_start: 0.3464 (tpt) cc_final: 0.3157 (tpt) outliers start: 38 outliers final: 9 residues processed: 154 average time/residue: 0.9208 time to fit residues: 153.1408 Evaluate side-chains 120 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8488 Z= 0.210 Angle : 0.639 8.265 11588 Z= 0.307 Chirality : 0.042 0.154 1422 Planarity : 0.005 0.040 1352 Dihedral : 12.617 131.105 1940 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.02 % Allowed : 17.50 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.15 (0.26), residues: 1012 helix: 1.13 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.23 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.001 HIS B 51 PHE 0.021 0.002 PHE B 502 TYR 0.015 0.002 TYR B 339 ARG 0.006 0.001 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.823 Fit side-chains REVERT: A 78 MET cc_start: 0.8722 (tmt) cc_final: 0.8397 (ppp) REVERT: A 119 LYS cc_start: 0.7435 (pttp) cc_final: 0.7200 (mtmm) REVERT: A 161 MET cc_start: 0.8563 (mtp) cc_final: 0.8118 (mtm) REVERT: A 172 LEU cc_start: 0.8081 (tp) cc_final: 0.7645 (mt) REVERT: A 251 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6710 (pt) REVERT: A 381 SER cc_start: 0.7932 (m) cc_final: 0.7521 (p) REVERT: A 476 GLU cc_start: 0.7783 (tp30) cc_final: 0.7300 (pt0) REVERT: A 550 MET cc_start: 0.3601 (tpt) cc_final: 0.3278 (tpt) REVERT: B 119 LYS cc_start: 0.7449 (pttp) cc_final: 0.7186 (mtmm) REVERT: B 172 LEU cc_start: 0.7978 (tp) cc_final: 0.7496 (OUTLIER) REVERT: B 251 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6959 (pt) REVERT: B 282 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7197 (mtpm) REVERT: B 381 SER cc_start: 0.7929 (m) cc_final: 0.7557 (p) REVERT: B 476 GLU cc_start: 0.7864 (tp30) cc_final: 0.7248 (mp0) REVERT: B 550 MET cc_start: 0.3518 (tpt) cc_final: 0.3199 (tpt) outliers start: 17 outliers final: 8 residues processed: 125 average time/residue: 1.0571 time to fit residues: 141.7214 Evaluate side-chains 124 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 76 GLN B 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8488 Z= 0.207 Angle : 0.606 7.543 11588 Z= 0.291 Chirality : 0.042 0.143 1422 Planarity : 0.005 0.048 1352 Dihedral : 12.495 133.592 1940 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.67 % Allowed : 17.98 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 1012 helix: 1.46 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.92 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.001 HIS B 210 PHE 0.018 0.002 PHE B 502 TYR 0.010 0.001 TYR B 474 ARG 0.005 0.001 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.877 Fit side-chains REVERT: A 78 MET cc_start: 0.8675 (tmt) cc_final: 0.8322 (ppp) REVERT: A 119 LYS cc_start: 0.7379 (pttp) cc_final: 0.7171 (mtmm) REVERT: A 161 MET cc_start: 0.8562 (mtp) cc_final: 0.8122 (mtm) REVERT: A 172 LEU cc_start: 0.8030 (tp) cc_final: 0.7626 (mt) REVERT: A 251 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6656 (pt) REVERT: A 393 LYS cc_start: 0.6272 (mmmt) cc_final: 0.6050 (mmmt) REVERT: A 476 GLU cc_start: 0.7868 (tp30) cc_final: 0.7370 (pt0) REVERT: A 550 MET cc_start: 0.3580 (tpt) cc_final: 0.3310 (tpt) REVERT: B 119 LYS cc_start: 0.7355 (pttp) cc_final: 0.7120 (mtmm) REVERT: B 172 LEU cc_start: 0.8033 (tp) cc_final: 0.7543 (OUTLIER) REVERT: B 251 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6854 (pt) REVERT: B 282 LYS cc_start: 0.7592 (mtmm) cc_final: 0.7137 (mtpm) REVERT: B 381 SER cc_start: 0.7943 (m) cc_final: 0.7498 (p) REVERT: B 476 GLU cc_start: 0.7921 (tp30) cc_final: 0.7376 (pt0) REVERT: B 550 MET cc_start: 0.3647 (tpt) cc_final: 0.3331 (tpt) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 1.0297 time to fit residues: 134.9967 Evaluate side-chains 126 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 144 ASN A 483 ASN B 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8488 Z= 0.442 Angle : 0.786 8.070 11588 Z= 0.380 Chirality : 0.050 0.202 1422 Planarity : 0.006 0.052 1352 Dihedral : 13.708 134.150 1940 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.74 % Allowed : 17.74 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.25 (0.26), residues: 1012 helix: 1.02 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.71 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 149 HIS 0.004 0.001 HIS B 150 PHE 0.027 0.003 PHE A 200 TYR 0.017 0.002 TYR A 42 ARG 0.010 0.001 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.896 Fit side-chains REVERT: A 78 MET cc_start: 0.8706 (tmt) cc_final: 0.8274 (tmt) REVERT: A 119 LYS cc_start: 0.7445 (pttp) cc_final: 0.7137 (mtmm) REVERT: A 161 MET cc_start: 0.8575 (mtp) cc_final: 0.8178 (mtm) REVERT: A 172 LEU cc_start: 0.8051 (tp) cc_final: 0.7590 (mt) REVERT: A 229 ARG cc_start: 0.7019 (ttp80) cc_final: 0.6374 (ptt-90) REVERT: A 476 GLU cc_start: 0.7820 (tp30) cc_final: 0.7277 (pt0) REVERT: A 550 MET cc_start: 0.3410 (tpt) cc_final: 0.3157 (tpt) REVERT: B 119 LYS cc_start: 0.7482 (pttp) cc_final: 0.7147 (mtmm) REVERT: B 172 LEU cc_start: 0.8103 (tp) cc_final: 0.7565 (mt) REVERT: B 229 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6425 (ptt180) REVERT: B 251 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6785 (pt) REVERT: B 282 LYS cc_start: 0.7366 (mtmm) cc_final: 0.6947 (mtpm) REVERT: B 476 GLU cc_start: 0.7908 (tp30) cc_final: 0.7377 (pt0) REVERT: B 550 MET cc_start: 0.3529 (tpt) cc_final: 0.3210 (tpt) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 1.0891 time to fit residues: 144.7545 Evaluate side-chains 126 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.4816 > 50: distance: 24 - 46: 18.197 distance: 34 - 57: 20.959 distance: 43 - 46: 20.765 distance: 46 - 47: 13.564 distance: 47 - 48: 16.578 distance: 47 - 50: 16.603 distance: 48 - 49: 22.747 distance: 48 - 57: 20.583 distance: 50 - 51: 10.915 distance: 51 - 52: 11.913 distance: 52 - 53: 5.242 distance: 53 - 54: 4.106 distance: 57 - 58: 8.345 distance: 58 - 59: 5.553 distance: 58 - 61: 15.167 distance: 59 - 60: 11.241 distance: 59 - 65: 13.592 distance: 61 - 62: 13.366 distance: 62 - 63: 9.069 distance: 62 - 64: 7.828 distance: 65 - 66: 9.551 distance: 66 - 67: 10.403 distance: 66 - 69: 24.465 distance: 67 - 68: 31.688 distance: 67 - 70: 28.801 distance: 70 - 71: 13.444 distance: 71 - 72: 27.360 distance: 72 - 73: 22.820 distance: 72 - 74: 30.678 distance: 74 - 75: 31.620 distance: 75 - 76: 8.875 distance: 75 - 78: 32.108 distance: 76 - 77: 21.835 distance: 76 - 79: 28.027 distance: 79 - 80: 16.590 distance: 79 - 85: 13.868 distance: 80 - 81: 18.383 distance: 80 - 83: 5.429 distance: 81 - 82: 32.679 distance: 81 - 86: 19.414 distance: 83 - 84: 18.759 distance: 84 - 85: 14.522 distance: 86 - 87: 18.757 distance: 86 - 92: 47.341 distance: 87 - 88: 12.225 distance: 87 - 90: 31.419 distance: 88 - 89: 13.727 distance: 88 - 93: 28.204 distance: 90 - 91: 39.659 distance: 91 - 92: 36.586 distance: 93 - 94: 24.420 distance: 93 - 99: 23.257 distance: 94 - 97: 27.782 distance: 95 - 96: 12.554 distance: 95 - 100: 20.599 distance: 97 - 98: 19.553 distance: 98 - 99: 18.703 distance: 100 - 101: 19.753 distance: 100 - 106: 13.309 distance: 101 - 102: 16.493 distance: 101 - 104: 26.036 distance: 102 - 103: 26.089 distance: 102 - 107: 23.782 distance: 104 - 105: 21.692 distance: 105 - 106: 36.164 distance: 107 - 108: 14.888 distance: 108 - 109: 5.343 distance: 108 - 111: 9.634 distance: 109 - 110: 15.728 distance: 109 - 114: 11.355 distance: 110 - 136: 20.063 distance: 111 - 112: 11.047 distance: 111 - 113: 14.960