Starting phenix.real_space_refine on Wed Jun 26 19:49:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624_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/7y5t_33624/06_2024/7y5t_33624_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5t_33624/06_2024/7y5t_33624_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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 42 5.16 5 Cl 1 4.86 5 C 7109 2.51 5 N 1707 2.21 5 O 1978 1.98 5 F 5 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10844 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2444 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'IGD': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.64, per 1000 atoms: 0.61 Number of scatterers: 10844 At special positions: 0 Unit cell: (110.415, 95.26, 133.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 42 16.00 P 2 15.00 F 5 9.00 O 1978 8.00 N 1707 7.00 C 7109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.01 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 1.9 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 4 sheets defined 51.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.831A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.982A pdb=" N LEU A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 482 through 502 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.838A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 666 through 692 Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 83 through 102 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 155 Processing helix chain 'B' and resid 159 through 189 removed outlier: 3.824A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 239 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.795A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 277 removed outlier: 3.742A pdb=" N GLU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 274 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 405 through 428 removed outlier: 3.613A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 15 through 23 Processing helix chain 'C' and resid 29 through 59 removed outlier: 4.022A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 101 removed outlier: 3.664A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 138 removed outlier: 3.697A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.571A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 3.998A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 232 removed outlier: 3.747A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 236 through 242 removed outlier: 3.935A pdb=" N SER C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.588A pdb=" N GLY D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 50 through 80 removed outlier: 3.516A pdb=" N ALA D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.682A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= C, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.204A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 601 through 605 removed outlier: 3.503A pdb=" N SER A 623 " --> pdb=" O GLU A 601 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1443 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: 3.02 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1935 1.33 - 1.45: 3079 1.45 - 1.58: 6039 1.58 - 1.71: 6 1.71 - 1.83: 65 Bond restraints: 11124 Sorted by residual: bond pdb=" C1 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.410 1.472 -0.062 2.00e-02 2.50e+03 9.60e+00 bond pdb=" C5 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.417 1.474 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" C1 BMA F 5 " pdb=" C2 BMA F 5 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C11 PC1 B 501 " pdb=" O13 PC1 B 501 " ideal model delta sigma weight residual 1.407 1.456 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C11 PC1 C 304 " pdb=" O13 PC1 C 304 " ideal model delta sigma weight residual 1.407 1.455 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 11119 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.09: 267 106.09 - 113.11: 6147 113.11 - 120.13: 4185 120.13 - 127.15: 4434 127.15 - 134.17: 148 Bond angle restraints: 15181 Sorted by residual: angle pdb=" C27 IGD B 502 " pdb=" C22 IGD B 502 " pdb=" F04 IGD B 502 " ideal model delta sigma weight residual 88.65 115.97 -27.32 3.00e+00 1.11e-01 8.29e+01 angle pdb=" C20 IGD B 502 " pdb=" C22 IGD B 502 " pdb=" F04 IGD B 502 " ideal model delta sigma weight residual 143.39 123.70 19.69 3.00e+00 1.11e-01 4.31e+01 angle pdb=" C29 IGD B 502 " pdb=" C26 IGD B 502 " pdb=" F05 IGD B 502 " ideal model delta sigma weight residual 104.97 120.16 -15.19 3.00e+00 1.11e-01 2.56e+01 angle pdb=" C23 IGD B 502 " pdb=" C26 IGD B 502 " pdb=" F05 IGD B 502 " ideal model delta sigma weight residual 135.02 119.97 15.05 3.00e+00 1.11e-01 2.52e+01 angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 113.53 108.93 4.60 9.80e-01 1.04e+00 2.20e+01 ... (remaining 15176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 6678 24.87 - 49.74: 174 49.74 - 74.61: 37 74.61 - 99.48: 19 99.48 - 124.34: 14 Dihedral angle restraints: 6922 sinusoidal: 3086 harmonic: 3836 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual 93.00 -178.44 -88.56 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual 93.00 179.32 -86.32 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -147.26 -32.74 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 6919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.122: 1810 1.122 - 2.245: 0 2.245 - 3.367: 0 3.367 - 4.490: 0 4.490 - 5.612: 2 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C14 IGD B 502 " pdb=" C15 IGD B 502 " pdb=" C16 IGD B 502 " pdb=" C20 IGD B 502 " both_signs ideal model delta sigma weight residual False 2.73 -2.88 5.61 2.00e-01 2.50e+01 7.87e+02 chirality pdb=" C17 IGD B 502 " pdb=" C18 IGD B 502 " pdb=" C19 IGD B 502 " pdb=" N13 IGD B 502 " both_signs ideal model delta sigma weight residual False 2.59 -2.71 5.30 2.00e-01 2.50e+01 7.03e+02 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 464 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 1809 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 464 " -0.007 2.00e-02 2.50e+03 2.44e-01 7.47e+02 pdb=" CG ASN A 464 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 464 " 0.261 2.00e-02 2.50e+03 pdb=" ND2 ASN A 464 " -0.424 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.029 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP C 227 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO A 560 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.041 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2667 2.79 - 3.32: 9764 3.32 - 3.85: 17695 3.85 - 4.37: 20855 4.37 - 4.90: 36001 Nonbonded interactions: 86982 Sorted by model distance: nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.265 2.440 nonbonded pdb=" O LYS B 216 " pdb=" OH TYR D 18 " model vdw 2.288 2.440 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.301 2.440 nonbonded pdb=" OH TYR A 148 " pdb=" OD1 ASP A 381 " model vdw 2.302 2.440 nonbonded pdb=" OE1 GLU A 595 " pdb=" OH TYR A 602 " model vdw 2.309 2.440 ... (remaining 86977 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 7.500 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.770 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.007 0.098 11124 Z= 0.447 Angle : 1.016 27.318 15181 Z= 0.512 Chirality : 0.191 5.612 1812 Planarity : 0.007 0.073 1829 Dihedral : 14.014 124.344 4438 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.18 % Allowed : 1.86 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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: -3.37 (0.18), residues: 1304 helix: -1.82 (0.15), residues: 689 sheet: -1.40 (0.47), residues: 121 loop : -2.91 (0.22), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP C 227 HIS 0.017 0.003 HIS C 197 PHE 0.047 0.004 PHE C 132 TYR 0.040 0.003 TYR A 565 ARG 0.012 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.9140 (mmm) cc_final: 0.8883 (tpp) REVERT: A 242 ILE cc_start: 0.7871 (tt) cc_final: 0.7612 (tp) REVERT: A 617 LEU cc_start: 0.8196 (mt) cc_final: 0.7923 (tp) REVERT: B 112 GLN cc_start: 0.7891 (tt0) cc_final: 0.7686 (tt0) REVERT: B 184 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 270 MET cc_start: 0.6764 (mmm) cc_final: 0.6561 (mmm) REVERT: C 28 ASP cc_start: 0.8295 (t0) cc_final: 0.8041 (t0) REVERT: C 99 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6968 (pp20) REVERT: C 104 LEU cc_start: 0.7085 (mt) cc_final: 0.6842 (mm) REVERT: C 159 THR cc_start: 0.8889 (m) cc_final: 0.8595 (p) REVERT: C 180 ASP cc_start: 0.8546 (t0) cc_final: 0.8282 (t70) REVERT: D 17 LYS cc_start: 0.8184 (mttm) cc_final: 0.7817 (ttmm) REVERT: D 54 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7303 (tttp) outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 1.2429 time to fit residues: 275.0166 Evaluate side-chains 111 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 436 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 163 GLN A 355 GLN A 358 ASN A 385 GLN A 531 ASN A 552 GLN A 606 GLN B 204 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11124 Z= 0.264 Angle : 0.765 27.269 15181 Z= 0.354 Chirality : 0.067 2.104 1812 Planarity : 0.005 0.046 1829 Dihedral : 14.025 140.962 2130 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.95 % Allowed : 8.78 % Favored : 89.26 % 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: -1.17 (0.22), residues: 1304 helix: 0.35 (0.19), residues: 701 sheet: -0.97 (0.48), residues: 116 loop : -2.41 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 227 HIS 0.005 0.001 HIS C 197 PHE 0.028 0.002 PHE A 302 TYR 0.015 0.002 TYR A 645 ARG 0.011 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9181 (mmm) cc_final: 0.8972 (tpp) REVERT: A 617 LEU cc_start: 0.8122 (mt) cc_final: 0.7876 (tp) REVERT: B 270 MET cc_start: 0.6766 (mmm) cc_final: 0.6530 (mmm) REVERT: C 28 ASP cc_start: 0.8182 (t0) cc_final: 0.7889 (t0) REVERT: C 159 THR cc_start: 0.8881 (m) cc_final: 0.8620 (p) REVERT: C 186 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7032 (mtp180) REVERT: D 17 LYS cc_start: 0.8144 (mttm) cc_final: 0.7800 (ttmm) REVERT: D 40 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: D 91 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7378 (m-80) outliers start: 22 outliers final: 11 residues processed: 132 average time/residue: 1.0455 time to fit residues: 150.8679 Evaluate side-chains 112 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 11124 Z= 0.325 Angle : 0.775 25.796 15181 Z= 0.356 Chirality : 0.070 2.211 1812 Planarity : 0.004 0.046 1829 Dihedral : 12.537 139.134 2128 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.84 % Allowed : 10.20 % Favored : 86.96 % 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: -0.30 (0.23), residues: 1304 helix: 1.25 (0.20), residues: 696 sheet: -0.95 (0.48), residues: 124 loop : -2.22 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 209 HIS 0.006 0.002 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.017 0.002 TYR A 645 ARG 0.005 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 624 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8983 (m) REVERT: B 127 GLN cc_start: 0.5974 (pt0) cc_final: 0.5724 (pt0) REVERT: B 257 ASP cc_start: 0.8203 (t70) cc_final: 0.7233 (t0) REVERT: C 28 ASP cc_start: 0.8179 (t0) cc_final: 0.7842 (t0) REVERT: C 104 LEU cc_start: 0.7262 (mm) cc_final: 0.6798 (tp) REVERT: C 186 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7033 (mtp180) REVERT: D 17 LYS cc_start: 0.8196 (mttm) cc_final: 0.7943 (ttmm) REVERT: D 40 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7311 (tm-30) outliers start: 32 outliers final: 13 residues processed: 124 average time/residue: 0.9805 time to fit residues: 133.8976 Evaluate side-chains 110 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 0.0010 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 124 optimal weight: 0.0040 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11124 Z= 0.144 Angle : 0.666 25.949 15181 Z= 0.299 Chirality : 0.065 2.122 1812 Planarity : 0.003 0.040 1829 Dihedral : 11.744 134.925 2128 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.22 % Allowed : 11.62 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1304 helix: 1.80 (0.20), residues: 695 sheet: -0.66 (0.48), residues: 123 loop : -2.13 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 67 HIS 0.003 0.001 HIS C 58 PHE 0.024 0.001 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.004 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 481 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8586 (m) REVERT: A 624 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8982 (m) REVERT: A 683 SER cc_start: 0.8907 (m) cc_final: 0.8653 (p) REVERT: B 127 GLN cc_start: 0.5912 (pt0) cc_final: 0.5549 (pt0) REVERT: B 257 ASP cc_start: 0.8358 (t70) cc_final: 0.7586 (t0) REVERT: B 270 MET cc_start: 0.6893 (mmm) cc_final: 0.6674 (mtp) REVERT: C 104 LEU cc_start: 0.7200 (mm) cc_final: 0.6732 (tp) REVERT: C 186 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6888 (mtp180) REVERT: C 241 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6971 (tpp80) REVERT: D 17 LYS cc_start: 0.8176 (mttm) cc_final: 0.7924 (ttmm) REVERT: D 40 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7377 (tm-30) outliers start: 25 outliers final: 8 residues processed: 126 average time/residue: 0.9590 time to fit residues: 133.4139 Evaluate side-chains 107 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 65.6756 > 50: distance: 71 - 75: 34.743 distance: 77 - 78: 56.524 distance: 77 - 79: 9.762 distance: 79 - 80: 11.049 distance: 80 - 81: 6.798 distance: 80 - 83: 24.582 distance: 81 - 82: 13.348 distance: 81 - 87: 24.013 distance: 83 - 84: 6.986 distance: 84 - 86: 5.808 distance: 87 - 88: 55.079 distance: 88 - 89: 43.345 distance: 88 - 91: 41.321 distance: 89 - 90: 16.245 distance: 89 - 93: 20.042 distance: 91 - 92: 40.155 distance: 93 - 94: 6.468 distance: 94 - 95: 40.502 distance: 94 - 97: 4.546 distance: 95 - 96: 39.738 distance: 95 - 100: 31.028 distance: 97 - 98: 11.148 distance: 98 - 99: 4.401 distance: 100 - 101: 17.287 distance: 101 - 102: 11.627 distance: 101 - 104: 5.292 distance: 102 - 103: 24.631 distance: 102 - 112: 42.843 distance: 104 - 105: 21.029 distance: 105 - 107: 33.630 distance: 106 - 108: 16.112 distance: 107 - 109: 8.653 distance: 108 - 110: 30.191 distance: 109 - 110: 44.351 distance: 110 - 111: 9.019 distance: 113 - 114: 29.092 distance: 113 - 116: 33.582 distance: 114 - 115: 25.486 distance: 114 - 124: 18.123 distance: 115 - 150: 31.320 distance: 116 - 117: 27.701 distance: 117 - 118: 14.642 distance: 117 - 119: 16.581 distance: 118 - 120: 16.248 distance: 119 - 121: 17.594 distance: 120 - 122: 16.665 distance: 121 - 122: 8.403 distance: 122 - 123: 4.417 distance: 124 - 125: 30.142 distance: 125 - 126: 27.686 distance: 125 - 128: 13.392 distance: 126 - 127: 12.272 distance: 126 - 135: 11.453 distance: 127 - 156: 29.575 distance: 128 - 129: 13.992 distance: 129 - 130: 24.205 distance: 129 - 131: 23.009 distance: 130 - 132: 16.802 distance: 131 - 133: 16.615 distance: 132 - 134: 23.898 distance: 133 - 134: 30.463 distance: 135 - 136: 12.144 distance: 136 - 137: 24.217 distance: 136 - 139: 26.840 distance: 137 - 138: 20.232 distance: 137 - 143: 32.789 distance: 138 - 161: 29.506 distance: 139 - 140: 15.341 distance: 140 - 141: 19.375 distance: 140 - 142: 19.435 distance: 143 - 144: 23.512 distance: 144 - 145: 12.290 distance: 144 - 147: 15.947 distance: 145 - 146: 17.981 distance: 145 - 150: 13.357 distance: 146 - 170: 22.857 distance: 147 - 148: 4.057 distance: 147 - 149: 34.022 distance: 150 - 151: 8.041 distance: 151 - 152: 6.379 distance: 151 - 154: 20.902 distance: 152 - 153: 6.296 distance: 152 - 156: 25.983 distance: 153 - 178: 27.143 distance: 154 - 155: 12.140