Starting phenix.real_space_refine on Fri Jan 19 17:45:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahh_11786/01_2024/7ahh_11786_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahh_11786/01_2024/7ahh_11786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahh_11786/01_2024/7ahh_11786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahh_11786/01_2024/7ahh_11786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahh_11786/01_2024/7ahh_11786_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahh_11786/01_2024/7ahh_11786_updated.pdb" } resolution = 3.5 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 60 5.16 5 C 7763 2.51 5 N 2024 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 173": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 382": "NH1" <-> "NH2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D ARG 318": "NH1" <-> "NH2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D ARG 382": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12125 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4011 Classifications: {'peptide': 526} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "C" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'BET': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'ANP': 1} Classifications: {'RNA': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 6.57, per 1000 atoms: 0.54 Number of scatterers: 12125 At special positions: 0 Unit cell: (93.104, 100.188, 150.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 8 15.00 O 2270 8.00 N 2024 7.00 C 7763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.1 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 8 sheets defined 55.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 Processing helix chain 'A' and resid 27 through 50 Processing helix chain 'A' and resid 53 through 67 Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 92 through 120 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 123 through 137 removed outlier: 3.739A pdb=" N LYS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.754A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 156 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 205 through 233 removed outlier: 6.240A pdb=" N GLY A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N MET A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 252 through 274 Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.582A pdb=" N ALA A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 451 through 454 removed outlier: 4.191A pdb=" N ASP A 454 " --> pdb=" O ASN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 524 through 531 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.759A pdb=" N LEU A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP A 546 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 547 " --> pdb=" O MET A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.576A pdb=" N ILE A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.680A pdb=" N TRP A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 27 through 50 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 92 through 121 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 123 through 137 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 141 through 151 removed outlier: 3.948A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 157 through 180 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 205 through 233 removed outlier: 5.619A pdb=" N GLY B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 252 through 275 Processing helix chain 'C' and resid 19 through 27 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 123 through 134 removed outlier: 4.679A pdb=" N GLY C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 152 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 167 through 181 removed outlier: 4.316A pdb=" N ASN C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 removed outlier: 3.950A pdb=" N ALA C 194 " --> pdb=" O ALA C 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 197 through 213 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 355 through 362 Proline residue: C 358 - end of helix Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'D' and resid 19 through 27 Processing helix chain 'D' and resid 31 through 38 Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 123 through 134 removed outlier: 4.680A pdb=" N GLY D 130 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 134 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 167 through 181 removed outlier: 4.316A pdb=" N ASN D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 removed outlier: 3.950A pdb=" N ALA D 194 " --> pdb=" O ALA D 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 194' Processing helix chain 'D' and resid 197 through 213 Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 293 through 303 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 355 through 362 Proline residue: D 358 - end of helix Processing helix chain 'D' and resid 384 through 388 Processing sheet with id= A, first strand: chain 'A' and resid 322 through 327 removed outlier: 5.924A pdb=" N ASP A 350 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 325 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LYS A 352 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR A 327 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A 354 " --> pdb=" O TYR A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 376 through 378 removed outlier: 3.691A pdb=" N ALA A 376 " --> pdb=" O ASN A 512 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 405 through 409 removed outlier: 3.612A pdb=" N GLY A 406 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 428 through 430 removed outlier: 7.199A pdb=" N LYS A 456 " --> pdb=" O ILE A 429 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 185 through 187 removed outlier: 7.045A pdb=" N THR C 217 " --> pdb=" O LEU C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 285 through 287 removed outlier: 8.376A pdb=" N THR C 286 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET C 309 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 185 through 187 removed outlier: 7.045A pdb=" N THR D 217 " --> pdb=" O LEU D 186 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 285 through 287 removed outlier: 8.376A pdb=" N THR D 286 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET D 309 " --> pdb=" O THR D 286 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1560 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: 3.21 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3432 1.33 - 1.45: 1700 1.45 - 1.57: 7057 1.57 - 1.69: 16 1.69 - 1.81: 120 Bond restraints: 12325 Sorted by residual: bond pdb=" N3B ANP C 501 " pdb=" PG ANP C 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" N3B ANP D 501 " pdb=" PG ANP D 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" O3A ANP D 501 " pdb=" PB ANP D 501 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ANP C 501 " pdb=" PB ANP C 501 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C5' 2BA D 502 " pdb=" O5' 2BA D 502 " ideal model delta sigma weight residual 1.433 1.359 0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 12320 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.45: 275 105.45 - 112.59: 6684 112.59 - 119.73: 3983 119.73 - 126.88: 5613 126.88 - 134.02: 152 Bond angle restraints: 16707 Sorted by residual: angle pdb=" N ILE C 252 " pdb=" CA ILE C 252 " pdb=" C ILE C 252 " ideal model delta sigma weight residual 111.00 103.52 7.48 1.09e+00 8.42e-01 4.71e+01 angle pdb=" N LEU C 253 " pdb=" CA LEU C 253 " pdb=" C LEU C 253 " ideal model delta sigma weight residual 112.23 120.87 -8.64 1.26e+00 6.30e-01 4.70e+01 angle pdb=" N ILE D 252 " pdb=" CA ILE D 252 " pdb=" C ILE D 252 " ideal model delta sigma weight residual 111.00 103.64 7.36 1.09e+00 8.42e-01 4.56e+01 angle pdb=" N LEU D 253 " pdb=" CA LEU D 253 " pdb=" C LEU D 253 " ideal model delta sigma weight residual 112.23 120.06 -7.83 1.26e+00 6.30e-01 3.86e+01 angle pdb=" CA THR A 537 " pdb=" CB THR A 537 " pdb=" CG2 THR A 537 " ideal model delta sigma weight residual 110.50 119.06 -8.56 1.70e+00 3.46e-01 2.54e+01 ... (remaining 16702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.56: 6981 19.56 - 39.12: 442 39.12 - 58.68: 97 58.68 - 78.24: 20 78.24 - 97.80: 14 Dihedral angle restraints: 7554 sinusoidal: 3086 harmonic: 4468 Sorted by residual: dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N LYS A 538 " pdb=" CA LYS A 538 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA SER C 109 " pdb=" C SER C 109 " pdb=" N MET C 110 " pdb=" CA MET C 110 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER D 109 " pdb=" C SER D 109 " pdb=" N MET D 110 " pdb=" CA MET D 110 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1984 0.230 - 0.460: 7 0.460 - 0.691: 8 0.691 - 0.921: 0 0.921 - 1.151: 1 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CB THR A 537 " pdb=" CA THR A 537 " pdb=" OG1 THR A 537 " pdb=" CG2 THR A 537 " both_signs ideal model delta sigma weight residual False 2.55 1.40 1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CG LEU C 101 " pdb=" CB LEU C 101 " pdb=" CD1 LEU C 101 " pdb=" CD2 LEU C 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CG LEU D 101 " pdb=" CB LEU D 101 " pdb=" CD1 LEU D 101 " pdb=" CD2 LEU D 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.57e+00 ... (remaining 1997 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 214 " 0.029 2.00e-02 2.50e+03 3.42e-02 2.04e+01 pdb=" CG PHE C 214 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE C 214 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 214 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 214 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 214 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 214 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 214 " 0.028 2.00e-02 2.50e+03 3.38e-02 2.00e+01 pdb=" CG PHE D 214 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE D 214 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE D 214 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 214 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE D 214 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 214 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 169 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO A 170 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.043 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1872 2.75 - 3.29: 13273 3.29 - 3.83: 19607 3.83 - 4.36: 24098 4.36 - 4.90: 40999 Nonbonded interactions: 99849 Sorted by model distance: nonbonded pdb=" O GLU C 250 " pdb=" N LEU C 253 " model vdw 2.213 2.520 nonbonded pdb=" O GLU A 541 " pdb=" N LEU A 545 " model vdw 2.215 2.520 nonbonded pdb=" O ALA A 472 " pdb=" N HIS A 476 " model vdw 2.216 2.520 nonbonded pdb=" OD1 ASP D 91 " pdb=" N VAL D 92 " model vdw 2.226 2.520 nonbonded pdb=" OD1 ASP C 91 " pdb=" N VAL C 92 " model vdw 2.227 2.520 ... (remaining 99844 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 'C' selection = (chain 'D' and (resid 3 through 391 or resid 501)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 4.310 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 33.740 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.008 0.164 12325 Z= 0.517 Angle : 0.967 10.253 16707 Z= 0.534 Chirality : 0.067 1.151 2000 Planarity : 0.005 0.076 2084 Dihedral : 14.623 97.804 4660 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.23 % Allowed : 2.27 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.56 (0.21), residues: 1548 helix: 0.24 (0.18), residues: 870 sheet: -4.26 (0.33), residues: 124 loop : -2.24 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 535 HIS 0.004 0.001 HIS D 9 PHE 0.077 0.003 PHE C 214 TYR 0.013 0.002 TYR A 327 ARG 0.017 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 1.322 Fit side-chains REVERT: A 119 MET cc_start: 0.8231 (ttm) cc_final: 0.7932 (mtp) REVERT: A 198 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7554 (ttp-110) REVERT: D 45 TYR cc_start: 0.7776 (t80) cc_final: 0.7342 (t80) REVERT: D 109 SER cc_start: 0.8889 (t) cc_final: 0.8683 (t) REVERT: D 189 ASP cc_start: 0.7543 (t0) cc_final: 0.7277 (t0) outliers start: 3 outliers final: 0 residues processed: 239 average time/residue: 0.2570 time to fit residues: 85.9661 Evaluate side-chains 153 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 0.0670 chunk 47 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 140 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 451 ASN B 8 GLN C 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12325 Z= 0.194 Angle : 0.628 11.336 16707 Z= 0.318 Chirality : 0.044 0.167 2000 Planarity : 0.004 0.052 2084 Dihedral : 7.629 59.288 1753 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.44 % Allowed : 7.49 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.68 (0.22), residues: 1548 helix: 0.91 (0.18), residues: 878 sheet: -3.79 (0.33), residues: 134 loop : -1.78 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 535 HIS 0.001 0.001 HIS D 9 PHE 0.015 0.001 PHE A 74 TYR 0.017 0.001 TYR A 412 ARG 0.006 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 1.370 Fit side-chains REVERT: A 198 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.7451 (ttp-110) REVERT: B 205 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7387 (mm-30) REVERT: D 45 TYR cc_start: 0.7653 (t80) cc_final: 0.7286 (t80) REVERT: D 314 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8101 (tptm) outliers start: 19 outliers final: 11 residues processed: 197 average time/residue: 0.2084 time to fit residues: 62.1157 Evaluate side-chains 158 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 354 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 0.0470 chunk 139 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 overall best weight: 2.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN C 135 ASN D 9 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12325 Z= 0.365 Angle : 0.656 6.918 16707 Z= 0.331 Chirality : 0.046 0.176 2000 Planarity : 0.004 0.049 2084 Dihedral : 6.926 60.588 1753 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.04 % Allowed : 10.82 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.58 (0.22), residues: 1548 helix: 0.75 (0.18), residues: 886 sheet: -3.39 (0.34), residues: 134 loop : -1.41 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 535 HIS 0.003 0.001 HIS C 223 PHE 0.016 0.002 PHE D 49 TYR 0.015 0.001 TYR A 327 ARG 0.003 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.430 Fit side-chains REVERT: A 72 ILE cc_start: 0.7561 (tp) cc_final: 0.7335 (tp) REVERT: A 356 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7564 (pp) REVERT: C 60 MET cc_start: 0.8232 (mtp) cc_final: 0.7899 (mtp) REVERT: D 45 TYR cc_start: 0.7860 (t80) cc_final: 0.7258 (t80) REVERT: D 244 MET cc_start: 0.7846 (ptp) cc_final: 0.7573 (ptp) REVERT: D 314 LYS cc_start: 0.8447 (ptpp) cc_final: 0.8226 (tppt) outliers start: 27 outliers final: 14 residues processed: 175 average time/residue: 0.2103 time to fit residues: 56.5234 Evaluate side-chains 156 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 134 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 329 ASN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12325 Z= 0.171 Angle : 0.547 7.531 16707 Z= 0.275 Chirality : 0.042 0.154 2000 Planarity : 0.004 0.052 2084 Dihedral : 6.539 59.778 1753 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.27 % Allowed : 12.48 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.06 (0.22), residues: 1548 helix: 1.16 (0.18), residues: 873 sheet: -2.91 (0.37), residues: 134 loop : -1.19 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 PHE 0.015 0.001 PHE A 349 TYR 0.016 0.001 TYR A 527 ARG 0.003 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.531 Fit side-chains REVERT: A 72 ILE cc_start: 0.7502 (tp) cc_final: 0.7282 (tp) REVERT: A 119 MET cc_start: 0.8619 (ttm) cc_final: 0.8230 (mtp) REVERT: A 356 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7497 (pp) REVERT: B 144 TYR cc_start: 0.8198 (m-80) cc_final: 0.7118 (m-80) REVERT: B 185 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: D 45 TYR cc_start: 0.7856 (t80) cc_final: 0.7252 (t80) outliers start: 30 outliers final: 20 residues processed: 186 average time/residue: 0.2045 time to fit residues: 57.9286 Evaluate side-chains 168 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 334 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 274 GLN C 126 ASN C 135 ASN D 126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12325 Z= 0.166 Angle : 0.533 8.314 16707 Z= 0.268 Chirality : 0.042 0.139 2000 Planarity : 0.004 0.048 2084 Dihedral : 6.304 60.952 1753 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.57 % Allowed : 14.15 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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 (0.22), residues: 1548 helix: 1.34 (0.18), residues: 877 sheet: -2.58 (0.40), residues: 134 loop : -1.13 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 PHE 0.011 0.001 PHE A 349 TYR 0.010 0.001 TYR A 412 ARG 0.004 0.000 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.689 Fit side-chains REVERT: A 72 ILE cc_start: 0.7477 (tp) cc_final: 0.7270 (tp) REVERT: A 119 MET cc_start: 0.8609 (ttm) cc_final: 0.8218 (mtp) REVERT: A 356 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7474 (pp) REVERT: B 144 TYR cc_start: 0.8206 (m-80) cc_final: 0.7155 (m-80) REVERT: B 185 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: C 60 MET cc_start: 0.8103 (mtp) cc_final: 0.7796 (mtp) REVERT: D 45 TYR cc_start: 0.7813 (t80) cc_final: 0.7258 (t80) outliers start: 34 outliers final: 21 residues processed: 182 average time/residue: 0.2007 time to fit residues: 56.3701 Evaluate side-chains 176 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.1980 chunk 36 optimal weight: 0.3980 chunk 149 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12325 Z= 0.158 Angle : 0.535 8.626 16707 Z= 0.265 Chirality : 0.041 0.139 2000 Planarity : 0.004 0.046 2084 Dihedral : 6.125 61.023 1753 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.65 % Allowed : 15.51 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1548 helix: 1.54 (0.18), residues: 874 sheet: -2.24 (0.43), residues: 134 loop : -1.10 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 PHE 0.009 0.001 PHE A 349 TYR 0.010 0.001 TYR A 412 ARG 0.003 0.000 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8611 (ttm) cc_final: 0.8213 (mtp) REVERT: A 356 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7458 (pp) REVERT: B 144 TYR cc_start: 0.8066 (m-80) cc_final: 0.7061 (m-80) REVERT: B 185 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: C 60 MET cc_start: 0.8104 (mtp) cc_final: 0.7761 (mtp) REVERT: D 45 TYR cc_start: 0.7785 (t80) cc_final: 0.7176 (t80) outliers start: 35 outliers final: 24 residues processed: 189 average time/residue: 0.1940 time to fit residues: 56.5754 Evaluate side-chains 177 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 381 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.4980 chunk 85 optimal weight: 0.0570 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12325 Z= 0.164 Angle : 0.551 16.007 16707 Z= 0.268 Chirality : 0.041 0.174 2000 Planarity : 0.004 0.048 2084 Dihedral : 6.046 61.115 1753 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.34 % Allowed : 16.57 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.56 (0.23), residues: 1548 helix: 1.62 (0.18), residues: 871 sheet: -2.02 (0.44), residues: 134 loop : -1.02 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 PHE 0.007 0.001 PHE A 135 TYR 0.008 0.001 TYR D 361 ARG 0.002 0.000 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8597 (ttm) cc_final: 0.8154 (mtp) REVERT: A 356 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7432 (pp) REVERT: B 144 TYR cc_start: 0.8087 (m-80) cc_final: 0.7114 (m-80) REVERT: C 60 MET cc_start: 0.8132 (mtp) cc_final: 0.7778 (mtp) REVERT: D 45 TYR cc_start: 0.7889 (t80) cc_final: 0.7208 (t80) REVERT: D 60 MET cc_start: 0.8498 (mtp) cc_final: 0.7737 (mtm) REVERT: D 225 LEU cc_start: 0.8664 (tp) cc_final: 0.8384 (tp) outliers start: 31 outliers final: 23 residues processed: 176 average time/residue: 0.1964 time to fit residues: 53.5423 Evaluate side-chains 179 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.0370 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12325 Z= 0.200 Angle : 0.568 15.681 16707 Z= 0.276 Chirality : 0.042 0.183 2000 Planarity : 0.004 0.049 2084 Dihedral : 5.999 62.139 1753 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.50 % Allowed : 17.17 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.56 (0.23), residues: 1548 helix: 1.57 (0.18), residues: 873 sheet: -1.92 (0.44), residues: 134 loop : -0.97 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 535 HIS 0.002 0.000 HIS A 487 PHE 0.009 0.001 PHE D 49 TYR 0.013 0.001 TYR D 361 ARG 0.002 0.000 ARG D 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8636 (ttm) cc_final: 0.8180 (mtp) REVERT: A 274 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6913 (pp30) REVERT: A 356 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7411 (pp) REVERT: A 369 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 144 TYR cc_start: 0.8116 (m-80) cc_final: 0.7130 (m-80) REVERT: B 185 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: C 60 MET cc_start: 0.8177 (mtp) cc_final: 0.7799 (mtp) REVERT: D 45 TYR cc_start: 0.7954 (t80) cc_final: 0.7225 (t80) REVERT: D 60 MET cc_start: 0.8519 (mtp) cc_final: 0.7723 (mtm) REVERT: D 225 LEU cc_start: 0.8761 (tp) cc_final: 0.8508 (tp) outliers start: 33 outliers final: 24 residues processed: 176 average time/residue: 0.1995 time to fit residues: 53.7816 Evaluate side-chains 182 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 67.0355 > 50: distance: 43 - 48: 16.387 distance: 48 - 49: 10.298 distance: 49 - 50: 18.891 distance: 49 - 52: 10.800 distance: 50 - 51: 14.033 distance: 50 - 56: 11.293 distance: 52 - 53: 6.855 distance: 53 - 54: 9.546 distance: 54 - 55: 13.168 distance: 56 - 57: 11.411 distance: 56 - 139: 11.609 distance: 57 - 58: 32.435 distance: 57 - 60: 27.831 distance: 58 - 59: 32.797 distance: 58 - 61: 21.305 distance: 59 - 136: 26.364 distance: 61 - 62: 29.262 distance: 62 - 63: 41.174 distance: 62 - 65: 30.896 distance: 63 - 64: 42.888 distance: 63 - 68: 32.206 distance: 65 - 66: 38.069 distance: 65 - 67: 49.798 distance: 68 - 69: 28.578 distance: 69 - 70: 16.121 distance: 69 - 72: 35.704 distance: 70 - 71: 25.110 distance: 70 - 76: 38.428 distance: 72 - 73: 5.936 distance: 73 - 74: 9.415 distance: 73 - 75: 17.617 distance: 76 - 77: 55.305 distance: 77 - 78: 31.374 distance: 77 - 80: 46.066 distance: 78 - 79: 43.953 distance: 78 - 85: 55.542 distance: 80 - 81: 47.765 distance: 81 - 82: 26.008 distance: 82 - 83: 17.906 distance: 83 - 84: 27.508 distance: 85 - 86: 17.707 distance: 86 - 87: 32.651 distance: 86 - 89: 42.412 distance: 87 - 88: 14.506 distance: 87 - 94: 37.809 distance: 89 - 90: 41.942 distance: 90 - 91: 40.865 distance: 91 - 92: 20.571 distance: 92 - 93: 17.344 distance: 94 - 95: 32.234 distance: 95 - 96: 37.709 distance: 95 - 98: 33.556 distance: 96 - 97: 17.782 distance: 96 - 105: 39.392 distance: 98 - 99: 20.615 distance: 99 - 100: 32.144 distance: 100 - 101: 30.456 distance: 101 - 102: 4.464 distance: 102 - 103: 29.158 distance: 102 - 104: 29.062 distance: 105 - 106: 31.402 distance: 106 - 107: 32.234 distance: 106 - 109: 61.113 distance: 107 - 108: 30.021 distance: 107 - 114: 15.802 distance: 109 - 110: 51.567 distance: 110 - 111: 12.025 distance: 111 - 112: 28.231 distance: 111 - 113: 24.715 distance: 114 - 115: 36.708 distance: 115 - 116: 23.698 distance: 115 - 118: 54.905 distance: 116 - 117: 44.888 distance: 116 - 125: 41.300 distance: 118 - 119: 56.327 distance: 119 - 120: 23.318 distance: 119 - 121: 14.139 distance: 120 - 122: 46.848 distance: 121 - 123: 38.352 distance: 122 - 124: 19.745 distance: 123 - 124: 21.953 distance: 125 - 126: 39.941 distance: 126 - 127: 38.371 distance: 126 - 129: 57.319 distance: 127 - 128: 56.718 distance: 127 - 136: 27.739 distance: 129 - 130: 40.384 distance: 130 - 131: 33.674 distance: 131 - 132: 32.451 distance: 132 - 133: 10.167 distance: 133 - 134: 36.217 distance: 133 - 135: 19.630