Starting phenix.real_space_refine on Fri Jul 19 22:51:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/07_2024/8tve_41639.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/07_2024/8tve_41639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/07_2024/8tve_41639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/07_2024/8tve_41639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/07_2024/8tve_41639.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tve_41639/07_2024/8tve_41639.cif" } resolution = 3.9 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= 0.016 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5799 2.51 5 N 1536 2.21 5 O 1707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9090 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3002 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3002 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3002 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 73 Chain: "A" 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: "B" 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: "C" 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 Time building chain proxies: 7.02, per 1000 atoms: 0.77 Number of scatterers: 9090 At special positions: 0 Unit cell: (84.96, 85.845, 171.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1707 8.00 N 1536 7.00 C 5799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.06 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.06 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.06 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.04 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 NAG-ASN " NAG A 601 " - " ASN A 65 " " NAG A 602 " - " ASN A 459 " " NAG B 601 " - " ASN B 65 " " NAG B 602 " - " ASN B 459 " " NAG C 601 " - " ASN C 65 " " NAG C 602 " - " ASN C 459 " Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.7 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 18 sheets defined 42.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 4.997A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 92 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 141 through 178 Processing helix chain 'A' and resid 178 through 207 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 344 through 353 removed outlier: 4.237A pdb=" N CYS A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 476 Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.997A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 92 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 141 through 178 Processing helix chain 'B' and resid 178 through 207 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 344 through 353 removed outlier: 4.237A pdb=" N CYS B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 476 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.997A pdb=" N LYS C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 92 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 141 through 178 Processing helix chain 'C' and resid 178 through 207 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'C' and resid 344 through 353 removed outlier: 4.237A pdb=" N CYS C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 476 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 removed outlier: 5.344A pdb=" N GLU A 290 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR A 38 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 288 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 310 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 321 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 removed outlier: 7.012A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 264 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR A 270 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLY B 431 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 51 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR B 433 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 53 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374 removed outlier: 4.031A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.526A pdb=" N THR A 394 " --> pdb=" O CYS A 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 removed outlier: 6.900A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 38 removed outlier: 5.345A pdb=" N GLU B 290 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR B 38 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 288 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 310 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 321 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220 removed outlier: 7.012A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLY C 431 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 51 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR C 433 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 53 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 374 removed outlier: 4.032A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.525A pdb=" N THR B 394 " --> pdb=" O CYS B 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 38 removed outlier: 5.344A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE C 310 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 321 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AB8, first strand: chain 'C' and resid 371 through 374 removed outlier: 4.031A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.525A pdb=" N THR C 394 " --> pdb=" O CYS C 389 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 4.01 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: 2310 1.33 - 1.46: 2146 1.46 - 1.59: 4691 1.59 - 1.71: 3 1.71 - 1.84: 66 Bond restraints: 9216 Sorted by residual: bond pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB LEU B 23 " pdb=" CG LEU B 23 " ideal model delta sigma weight residual 1.530 1.601 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB LEU C 23 " pdb=" CG LEU C 23 " ideal model delta sigma weight residual 1.530 1.601 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" NE ARG C 171 " pdb=" CZ ARG C 171 " ideal model delta sigma weight residual 1.326 1.362 -0.036 1.10e-02 8.26e+03 1.07e+01 bond pdb=" NE ARG A 171 " pdb=" CZ ARG A 171 " ideal model delta sigma weight residual 1.326 1.362 -0.036 1.10e-02 8.26e+03 1.05e+01 ... (remaining 9211 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.34: 350 107.34 - 113.90: 5049 113.90 - 120.46: 3864 120.46 - 127.03: 3283 127.03 - 133.59: 27 Bond angle restraints: 12573 Sorted by residual: angle pdb=" N ASN C 464 " pdb=" CA ASN C 464 " pdb=" C ASN C 464 " ideal model delta sigma weight residual 111.36 101.68 9.68 1.09e+00 8.42e-01 7.89e+01 angle pdb=" N ASN B 464 " pdb=" CA ASN B 464 " pdb=" C ASN B 464 " ideal model delta sigma weight residual 111.36 101.68 9.68 1.09e+00 8.42e-01 7.88e+01 angle pdb=" N ASN A 464 " pdb=" CA ASN A 464 " pdb=" C ASN A 464 " ideal model delta sigma weight residual 111.36 101.69 9.67 1.09e+00 8.42e-01 7.88e+01 angle pdb=" N MET C 142 " pdb=" CA MET C 142 " pdb=" C MET C 142 " ideal model delta sigma weight residual 111.28 101.66 9.62 1.09e+00 8.42e-01 7.79e+01 angle pdb=" N MET A 142 " pdb=" CA MET A 142 " pdb=" C MET A 142 " ideal model delta sigma weight residual 111.28 101.67 9.61 1.09e+00 8.42e-01 7.77e+01 ... (remaining 12568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 5451 16.38 - 32.75: 183 32.75 - 49.13: 33 49.13 - 65.50: 21 65.50 - 81.88: 12 Dihedral angle restraints: 5700 sinusoidal: 2118 harmonic: 3582 Sorted by residual: dihedral pdb=" CB CYS B 389 " pdb=" SG CYS B 389 " pdb=" SG CYS B 412 " pdb=" CB CYS B 412 " ideal model delta sinusoidal sigma weight residual -86.00 -167.88 81.88 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 389 " pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -167.87 81.87 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 412 " pdb=" CB CYS A 412 " ideal model delta sinusoidal sigma weight residual -86.00 -167.87 81.87 1 1.00e+01 1.00e-02 8.24e+01 ... (remaining 5697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 940 0.070 - 0.139: 466 0.139 - 0.208: 118 0.208 - 0.278: 30 0.278 - 0.347: 9 Chirality restraints: 1563 Sorted by residual: chirality pdb=" C2 NAG B 602 " pdb=" C1 NAG B 602 " pdb=" C3 NAG B 602 " pdb=" N2 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C2 NAG A 602 " pdb=" C1 NAG A 602 " pdb=" C3 NAG A 602 " pdb=" N2 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 NAG C 602 " pdb=" C1 NAG C 602 " pdb=" C3 NAG C 602 " pdb=" N2 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1560 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 65 " 0.028 2.00e-02 2.50e+03 2.98e-02 1.11e+01 pdb=" CG ASN B 65 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 65 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 65 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG B 601 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 65 " 0.028 2.00e-02 2.50e+03 2.97e-02 1.11e+01 pdb=" CG ASN A 65 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 65 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 65 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 65 " -0.027 2.00e-02 2.50e+03 2.97e-02 1.10e+01 pdb=" CG ASN C 65 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 65 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 65 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " -0.036 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3860 2.93 - 3.42: 8456 3.42 - 3.91: 14542 3.91 - 4.41: 15317 4.41 - 4.90: 25936 Nonbonded interactions: 68111 Sorted by model distance: nonbonded pdb=" N THR B 392 " pdb=" N ASP B 393 " model vdw 2.433 2.560 nonbonded pdb=" N THR C 392 " pdb=" N ASP C 393 " model vdw 2.433 2.560 nonbonded pdb=" N THR A 392 " pdb=" N ASP A 393 " model vdw 2.433 2.560 nonbonded pdb=" N SER B 356 " pdb=" O SER B 356 " model vdw 2.513 2.496 nonbonded pdb=" N SER C 356 " pdb=" O SER C 356 " model vdw 2.513 2.496 ... (remaining 68106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 18.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 29.510 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.013 0.072 9216 Z= 0.828 Angle : 1.522 11.409 12573 Z= 1.074 Chirality : 0.087 0.347 1563 Planarity : 0.005 0.020 1614 Dihedral : 9.806 79.964 3345 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.34 % 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 (0.21), residues: 1209 helix: 0.53 (0.20), residues: 504 sheet: 0.73 (0.40), residues: 159 loop : -0.14 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.005 TRP A 303 HIS 0.002 0.001 HIS C 253 PHE 0.016 0.004 PHE B 230 TYR 0.027 0.005 TYR B 202 ARG 0.004 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 0.986 Fit side-chains REVERT: B 217 VAL cc_start: 0.9116 (t) cc_final: 0.8912 (m) REVERT: B 404 VAL cc_start: 0.8501 (t) cc_final: 0.8275 (t) REVERT: B 473 GLU cc_start: 0.7893 (tt0) cc_final: 0.7653 (tt0) REVERT: C 463 GLN cc_start: 0.7851 (mm110) cc_final: 0.7644 (mm110) outliers start: 3 outliers final: 0 residues processed: 159 average time/residue: 0.2619 time to fit residues: 54.3586 Evaluate side-chains 85 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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: 61.5729 > 50: distance: 97 - 100: 3.913 distance: 100 - 101: 4.175 distance: 101 - 102: 5.186 distance: 101 - 104: 10.440 distance: 102 - 103: 9.777 distance: 102 - 106: 6.487 distance: 104 - 105: 13.776 distance: 107 - 108: 5.855 distance: 107 - 110: 9.572 distance: 108 - 109: 9.773 distance: 108 - 112: 4.871 distance: 110 - 111: 15.192 distance: 112 - 113: 18.066 distance: 113 - 114: 30.969 distance: 113 - 116: 14.396 distance: 114 - 115: 26.588 distance: 114 - 124: 25.763 distance: 116 - 117: 6.514 distance: 117 - 118: 5.445 distance: 117 - 119: 3.859 distance: 118 - 120: 8.177 distance: 119 - 121: 5.699 distance: 120 - 122: 11.496 distance: 121 - 122: 10.782 distance: 122 - 123: 6.394 distance: 124 - 125: 22.942 distance: 125 - 126: 6.382 distance: 125 - 128: 19.030 distance: 126 - 127: 11.149 distance: 126 - 131: 9.223 distance: 128 - 129: 16.802 distance: 128 - 130: 8.006 distance: 131 - 132: 16.644 distance: 131 - 137: 22.704 distance: 132 - 133: 36.556 distance: 132 - 135: 19.400 distance: 133 - 134: 50.361 distance: 133 - 138: 27.225 distance: 135 - 136: 11.876 distance: 136 - 137: 11.067 distance: 138 - 139: 42.969 distance: 139 - 140: 36.067 distance: 139 - 142: 41.595 distance: 140 - 141: 18.579 distance: 140 - 149: 18.221 distance: 142 - 143: 35.780 distance: 143 - 144: 19.578 distance: 144 - 145: 23.467 distance: 145 - 146: 23.517 distance: 146 - 147: 26.511 distance: 146 - 148: 9.647 distance: 149 - 150: 19.856 distance: 150 - 151: 18.397 distance: 150 - 153: 11.730 distance: 151 - 152: 10.170 distance: 151 - 160: 14.206 distance: 153 - 154: 7.439 distance: 154 - 155: 6.582 distance: 154 - 156: 12.970 distance: 155 - 157: 5.998 distance: 156 - 158: 30.424 distance: 158 - 159: 15.973 distance: 160 - 161: 13.532 distance: 160 - 203: 6.100 distance: 161 - 162: 8.440 distance: 161 - 164: 12.367 distance: 162 - 163: 5.867 distance: 162 - 165: 6.967 distance: 163 - 200: 6.458 distance: 165 - 166: 9.087 distance: 166 - 167: 11.988 distance: 166 - 169: 11.724 distance: 167 - 168: 9.612 distance: 167 - 173: 17.057 distance: 169 - 170: 6.136 distance: 170 - 171: 5.570 distance: 170 - 172: 12.131 distance: 173 - 174: 9.683 distance: 173 - 190: 19.317 distance: 174 - 175: 12.000 distance: 174 - 177: 3.153 distance: 175 - 176: 16.611 distance: 175 - 179: 11.180 distance: 176 - 187: 15.821 distance: 177 - 178: 14.847