Starting phenix.real_space_refine on Mon Mar 11 16:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2s_27148/03_2024/8d2s_27148_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1605 atoms to isotropic. 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 3 5.49 5 S 36 5.16 5 Na 1 4.78 5 C 4621 2.51 5 N 1070 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7071 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3523 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 22, 'TRANS': 452} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 475, 3523 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 22, 'TRANS': 452} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 3555 Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1423 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1443 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1432 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 203, 1432 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1460 Chain: "A" Number of atoms: 623 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 43, 588 Unusual residues: {' NA': 1, 'LMT': 17, 'ZGS': 3} Classifications: {'undetermined': 21, 'water': 22} Link IDs: {None: 42} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 60 Conformer: "B" Number of residues, atoms: 43, 588 Unusual residues: {' NA': 1, 'LMT': 17, 'ZGS': 3} Classifications: {'undetermined': 21, 'water': 22} Link IDs: {None: 42} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 60 bond proxies already assigned to first conformer: 531 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AARG A 100 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 100 " occ=0.50 residue: pdb=" N AARG A 108 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 108 " occ=0.50 residue: pdb=" N AHIS A 420 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 420 " occ=0.50 residue: pdb=" N APHE A 427 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 427 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" N AARG C 13 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 13 " occ=0.50 residue: pdb=" C1 ALMT A 616 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 616 " occ=0.50 Time building chain proxies: 6.71, per 1000 atoms: 0.95 Number of scatterers: 7071 At special positions: 0 Unit cell: (73.428, 74.272, 142.636, 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 36 16.00 P 3 15.00 Na 1 11.00 O 1340 8.00 N 1070 7.00 C 4621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 2.3 seconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 11 sheets defined 41.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.659A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix removed outlier: 6.058A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 99 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 110 through 127 Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 137 through 166 Proline residue: A 158 - end of helix removed outlier: 4.093A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 199 removed outlier: 3.555A pdb=" N VAL A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 233 through 261 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 289 through 318 removed outlier: 4.877A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 350 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 363 through 371 removed outlier: 4.304A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 413 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix removed outlier: 3.536A pdb=" N ASP A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 450 removed outlier: 4.047A pdb=" N GLY A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 494 through 506 removed outlier: 4.762A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.640A pdb=" N LYS B 100 " --> pdb=" O LYS B 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 18 through 23 removed outlier: 3.777A pdb=" N ALA B 18 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 83 through 88 removed outlier: 5.884A pdb=" N ASN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU B 45 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= E, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.751A pdb=" N THR B 140 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= G, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.691A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 38 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP C 46 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 89 through 91 Processing sheet with id= I, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.945A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 175 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 149 through 152 removed outlier: 4.743A pdb=" N ALA C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.812A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1024 1.30 - 1.43: 1895 1.43 - 1.56: 4137 1.56 - 1.68: 119 1.68 - 1.81: 51 Bond restraints: 7226 Sorted by residual: bond pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " ideal model delta sigma weight residual 1.393 1.516 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C1BBLMT A 616 " pdb=" O5BBLMT A 616 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1B LMT A 612 " pdb=" O5B LMT A 612 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C1BALMT A 616 " pdb=" O5BALMT A 616 " ideal model delta sigma weight residual 1.393 1.512 -0.119 2.00e-02 2.50e+03 3.54e+01 ... (remaining 7221 not shown) Histogram of bond angle deviations from ideal: 82.22 - 97.37: 1 97.37 - 112.52: 4121 112.52 - 127.67: 5604 127.67 - 142.82: 75 142.82 - 157.97: 9 Bond angle restraints: 9810 Sorted by residual: angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 109.50 137.41 -27.91 3.00e+00 1.11e-01 8.66e+01 angle pdb=" O26 ZGS A 601 " pdb=" P25 ZGS A 601 " pdb=" O28 ZGS A 601 " ideal model delta sigma weight residual 109.46 82.22 27.24 3.00e+00 1.11e-01 8.25e+01 angle pdb=" C04 ZGS A 602 " pdb=" C05 ZGS A 602 " pdb=" C06 ZGS A 602 " ideal model delta sigma weight residual 109.50 132.91 -23.41 3.00e+00 1.11e-01 6.09e+01 angle pdb=" C04 ZGS A 603 " pdb=" C05 ZGS A 603 " pdb=" C06 ZGS A 603 " ideal model delta sigma weight residual 109.50 132.03 -22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" N ASP A 87 " pdb=" CA ASP A 87 " pdb=" C ASP A 87 " ideal model delta sigma weight residual 111.07 106.81 4.26 1.07e+00 8.73e-01 1.58e+01 ... (remaining 9805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 4308 34.37 - 68.73: 228 68.73 - 103.10: 71 103.10 - 137.46: 52 137.46 - 171.83: 2 Dihedral angle restraints: 4661 sinusoidal: 2141 harmonic: 2520 Sorted by residual: dihedral pdb=" C06 ZGS A 602 " pdb=" C07 ZGS A 602 " pdb=" C08 ZGS A 602 " pdb=" C09 ZGS A 602 " ideal model delta sinusoidal sigma weight residual 77.11 -111.06 -171.83 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C23 ZGS A 603 " pdb=" O24 ZGS A 603 " pdb=" P25 ZGS A 603 " pdb=" O26 ZGS A 603 " ideal model delta sinusoidal sigma weight residual 290.13 130.44 159.69 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C23 ZGS A 602 " pdb=" C21 ZGS A 602 " pdb=" C22 ZGS A 602 " pdb=" O20 ZGS A 602 " ideal model delta sinusoidal sigma weight residual 200.65 75.22 125.43 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 4658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 902 0.054 - 0.109: 195 0.109 - 0.163: 43 0.163 - 0.217: 8 0.217 - 0.271: 1 Chirality restraints: 1149 Sorted by residual: chirality pdb=" C1B LMT A 608 " pdb=" C2B LMT A 608 " pdb=" O1B LMT A 608 " pdb=" O5B LMT A 608 " both_signs ideal model delta sigma weight residual False -2.20 -2.47 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C4' LMT A 608 " pdb=" C3' LMT A 608 " pdb=" C5' LMT A 608 " pdb=" O1B LMT A 608 " both_signs ideal model delta sigma weight residual False -2.55 -2.34 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1B LMT A 613 " pdb=" C2B LMT A 613 " pdb=" O1B LMT A 613 " pdb=" O5B LMT A 613 " both_signs ideal model delta sigma weight residual False -2.20 -2.41 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1146 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO C 47 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 431 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C PHE A 431 " -0.043 2.00e-02 2.50e+03 pdb=" O PHE A 431 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 432 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 85 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ALA A 85 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA A 85 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP A 86 " 0.011 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2009 2.82 - 3.34: 6372 3.34 - 3.86: 12139 3.86 - 4.38: 13892 4.38 - 4.90: 24275 Nonbonded interactions: 58687 Sorted by model distance: nonbonded pdb=" OG1 THR A 209 " pdb=" O HOH A 701 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR A 53 " pdb=" NE2 GLN A 152 " model vdw 2.303 2.520 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.341 2.440 nonbonded pdb=" NZ LYS A 353 " pdb=" OD2 ASP A 405 " model vdw 2.347 2.520 nonbonded pdb=" O TYR A 452 " pdb=" ND2 ASN C 99 " model vdw 2.353 2.520 ... (remaining 58682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 11.280 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.011 0.123 7226 Z= 0.693 Angle : 1.352 27.915 9810 Z= 0.521 Chirality : 0.050 0.271 1149 Planarity : 0.006 0.070 1173 Dihedral : 26.512 171.826 3045 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.80 % Allowed : 5.91 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 891 helix: 0.58 (0.25), residues: 385 sheet: -0.50 (0.38), residues: 189 loop : -2.46 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 140 HIS 0.005 0.001 HIS A 156 PHE 0.016 0.002 PHE B 89 TYR 0.013 0.001 TYR A 251 ARG 0.002 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 0.712 Fit side-chains REVERT: A 106 PHE cc_start: 0.8869 (m-80) cc_final: 0.8656 (m-80) REVERT: A 132 SER cc_start: 0.8705 (p) cc_final: 0.8156 (m) REVERT: A 134 ASP cc_start: 0.6688 (p0) cc_final: 0.6453 (p0) REVERT: A 180 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7670 (ttp-170) REVERT: A 345 GLN cc_start: 0.8644 (mt0) cc_final: 0.8371 (mt0) REVERT: B 91 LYS cc_start: 0.7936 (mttt) cc_final: 0.7563 (mmtm) REVERT: B 168 MET cc_start: 0.8467 (ttt) cc_final: 0.8262 (ttp) REVERT: C 37 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7449 (mt) outliers start: 5 outliers final: 1 residues processed: 143 average time/residue: 0.9282 time to fit residues: 142.0492 Evaluate side-chains 106 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 197 GLN A 420 HIS B B 187 ASN C 19 GLN C 171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7226 Z= 0.325 Angle : 0.838 9.953 9810 Z= 0.377 Chirality : 0.047 0.261 1149 Planarity : 0.005 0.069 1173 Dihedral : 17.695 164.774 1785 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.88 % Allowed : 12.62 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.27), residues: 891 helix: 1.16 (0.26), residues: 382 sheet: -0.22 (0.41), residues: 162 loop : -2.46 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 140 HIS 0.004 0.001 HIS A 156 PHE 0.026 0.003 PHE C 35 TYR 0.014 0.002 TYR A 141 ARG 0.007 0.001 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.659 Fit side-chains REVERT: A 106 PHE cc_start: 0.8949 (m-80) cc_final: 0.8717 (m-80) REVERT: A 132 SER cc_start: 0.8731 (p) cc_final: 0.8182 (m) REVERT: A 264 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: A 345 GLN cc_start: 0.8645 (mt0) cc_final: 0.8334 (mt0) REVERT: B 91 LYS cc_start: 0.8028 (mttt) cc_final: 0.7691 (mmtm) REVERT: C 19 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8752 (tp40) REVERT: C 37 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7614 (mt) REVERT: C 188 VAL cc_start: 0.8012 (m) cc_final: 0.7788 (t) outliers start: 18 outliers final: 7 residues processed: 121 average time/residue: 0.9621 time to fit residues: 124.5410 Evaluate side-chains 117 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 0.0870 chunk 21 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN B 153 ASN C 19 GLN C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7226 Z= 0.192 Angle : 0.641 8.433 9810 Z= 0.300 Chirality : 0.041 0.165 1149 Planarity : 0.005 0.065 1173 Dihedral : 14.109 175.792 1785 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.04 % Allowed : 13.58 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 891 helix: 1.57 (0.26), residues: 383 sheet: -0.39 (0.39), residues: 179 loop : -2.39 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 95 HIS 0.003 0.001 HIS A 230 PHE 0.015 0.002 PHE C 35 TYR 0.013 0.001 TYR A 179 ARG 0.002 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.701 Fit side-chains REVERT: A 106 PHE cc_start: 0.8912 (m-80) cc_final: 0.8679 (m-80) REVERT: A 132 SER cc_start: 0.8662 (p) cc_final: 0.8130 (m) REVERT: B 91 LYS cc_start: 0.7770 (mttt) cc_final: 0.7563 (mmtm) REVERT: C 37 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7512 (mt) outliers start: 19 outliers final: 6 residues processed: 111 average time/residue: 0.9264 time to fit residues: 110.2789 Evaluate side-chains 105 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.0370 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 142 GLN C 19 GLN C 74 GLN C 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7226 Z= 0.218 Angle : 0.631 8.445 9810 Z= 0.301 Chirality : 0.041 0.151 1149 Planarity : 0.005 0.067 1173 Dihedral : 13.136 175.290 1785 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.19 % Allowed : 13.74 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 891 helix: 1.70 (0.26), residues: 384 sheet: -0.33 (0.40), residues: 174 loop : -2.37 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 95 HIS 0.002 0.001 HIS A 156 PHE 0.024 0.002 PHE A 431 TYR 0.011 0.001 TYR A 251 ARG 0.008 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.754 Fit side-chains REVERT: A 106 PHE cc_start: 0.8929 (m-80) cc_final: 0.8693 (m-80) REVERT: A 132 SER cc_start: 0.8682 (p) cc_final: 0.8144 (m) REVERT: A 264 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: B 27 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6961 (tm130) REVERT: B 154 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7391 (mtp) REVERT: B 168 MET cc_start: 0.8350 (ttp) cc_final: 0.8128 (ttt) REVERT: C 37 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7449 (mp) outliers start: 20 outliers final: 7 residues processed: 112 average time/residue: 1.0764 time to fit residues: 128.7615 Evaluate side-chains 108 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN C 19 GLN C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7226 Z= 0.255 Angle : 0.644 8.205 9810 Z= 0.310 Chirality : 0.041 0.144 1149 Planarity : 0.005 0.068 1173 Dihedral : 12.733 161.431 1785 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.35 % Allowed : 14.70 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 891 helix: 1.73 (0.26), residues: 384 sheet: -0.33 (0.40), residues: 174 loop : -2.33 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 PHE 0.026 0.002 PHE A 431 TYR 0.012 0.002 TYR A 425 ARG 0.006 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.661 Fit side-chains REVERT: A 106 PHE cc_start: 0.8949 (m-80) cc_final: 0.8713 (m-80) REVERT: A 132 SER cc_start: 0.8717 (p) cc_final: 0.8173 (m) REVERT: A 264 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: B 154 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7524 (mtt) REVERT: C 37 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7432 (mt) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 0.9884 time to fit residues: 114.0390 Evaluate side-chains 109 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 142 GLN C 19 GLN C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7226 Z= 0.203 Angle : 0.597 7.526 9810 Z= 0.288 Chirality : 0.040 0.153 1149 Planarity : 0.005 0.069 1173 Dihedral : 11.978 150.423 1785 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.51 % Allowed : 15.34 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.28), residues: 891 helix: 1.92 (0.26), residues: 383 sheet: -0.29 (0.40), residues: 174 loop : -2.22 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 95 HIS 0.002 0.001 HIS A 156 PHE 0.015 0.002 PHE B 89 TYR 0.013 0.001 TYR A 425 ARG 0.007 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.651 Fit side-chains REVERT: A 106 PHE cc_start: 0.8938 (m-80) cc_final: 0.8704 (m-80) REVERT: A 132 SER cc_start: 0.8704 (p) cc_final: 0.8171 (m) REVERT: A 263 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7819 (mmtm) REVERT: A 264 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: A 431 PHE cc_start: 0.8458 (m-80) cc_final: 0.8172 (m-80) REVERT: B 154 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7495 (mtt) REVERT: C 37 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7353 (mp) REVERT: C 61 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7520 (ttt90) outliers start: 22 outliers final: 11 residues processed: 109 average time/residue: 0.9795 time to fit residues: 113.9903 Evaluate side-chains 114 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1633 > 50: distance: 26 - 28: 7.384 distance: 28 - 29: 4.514 distance: 29 - 30: 6.070 distance: 29 - 32: 8.903 distance: 30 - 31: 8.006 distance: 30 - 34: 5.918 distance: 32 - 33: 12.803 distance: 34 - 35: 4.431 distance: 35 - 36: 3.730 distance: 35 - 38: 10.761 distance: 36 - 37: 3.394 distance: 36 - 39: 15.375 distance: 39 - 40: 9.614 distance: 40 - 41: 11.693 distance: 40 - 43: 14.389 distance: 41 - 42: 20.639 distance: 41 - 46: 16.949 distance: 43 - 44: 25.986 distance: 43 - 45: 21.527 distance: 46 - 47: 15.307 distance: 46 - 246: 22.338 distance: 47 - 48: 19.376 distance: 47 - 50: 26.928 distance: 48 - 49: 11.364 distance: 48 - 51: 27.983 distance: 49 - 243: 30.448 distance: 51 - 52: 15.006 distance: 51 - 154: 13.742 distance: 52 - 53: 6.570 distance: 52 - 55: 7.970 distance: 53 - 54: 20.964 distance: 53 - 65: 12.903 distance: 54 - 151: 18.429 distance: 55 - 56: 13.894 distance: 56 - 57: 7.323 distance: 56 - 58: 16.150 distance: 57 - 59: 18.195 distance: 58 - 60: 27.326 distance: 58 - 61: 18.140 distance: 59 - 60: 26.985 distance: 60 - 62: 29.390 distance: 61 - 63: 11.449 distance: 62 - 64: 5.373 distance: 63 - 64: 9.811 distance: 65 - 66: 7.939 distance: 65 - 229: 16.895 distance: 66 - 67: 13.628 distance: 66 - 69: 5.689 distance: 67 - 68: 12.545 distance: 67 - 76: 5.237 distance: 68 - 226: 16.765 distance: 69 - 70: 14.141 distance: 70 - 71: 8.818 distance: 70 - 72: 9.126 distance: 71 - 73: 10.755 distance: 72 - 74: 3.216 distance: 73 - 75: 14.500 distance: 74 - 75: 8.488 distance: 76 - 77: 6.354 distance: 77 - 78: 7.089 distance: 77 - 80: 10.733 distance: 78 - 79: 7.662 distance: 80 - 81: 9.939 distance: 81 - 82: 5.673 distance: 81 - 83: 10.401 distance: 84 - 85: 8.585 distance: 84 - 211: 13.694 distance: 85 - 86: 8.408 distance: 85 - 88: 12.355 distance: 86 - 87: 14.829 distance: 86 - 93: 11.785 distance: 87 - 208: 9.998 distance: 88 - 89: 7.098 distance: 90 - 91: 3.620 distance: 90 - 92: 20.016 distance: 93 - 94: 7.351 distance: 94 - 95: 3.493 distance: 94 - 97: 5.673 distance: 95 - 96: 24.808 distance: 95 - 104: 7.898 distance: 97 - 98: 6.025 distance: 98 - 99: 14.241 distance: 99 - 100: 6.662 distance: 100 - 101: 10.084 distance: 101 - 102: 3.251 distance: 101 - 103: 4.665 distance: 104 - 105: 12.529 distance: 104 - 110: 17.598 distance: 105 - 106: 4.814 distance: 105 - 108: 5.093 distance: 106 - 107: 23.360 distance: 106 - 111: 5.089 distance: 108 - 109: 13.347 distance: 109 - 110: 18.090