Starting phenix.real_space_refine on Tue Feb 20 01:24:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhw_29172/02_2024/8fhw_29172_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhw_29172/02_2024/8fhw_29172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhw_29172/02_2024/8fhw_29172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhw_29172/02_2024/8fhw_29172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhw_29172/02_2024/8fhw_29172_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhw_29172/02_2024/8fhw_29172_neut_trim_updated.pdb" } resolution = 3.2 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= -0.002 sd= 0.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 8772 2.51 5 N 2312 2.21 5 O 2488 1.98 5 H 12732 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D GLU 458": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26376 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.60, per 1000 atoms: 0.44 Number of scatterers: 26376 At special positions: 0 Unit cell: (115.56, 104.76, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 12 15.00 O 2488 8.00 N 2312 7.00 C 8772 6.00 H 12732 1.00 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: 23.82 Conformation dependent library (CDL) restraints added in 3.1 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 12 sheets defined 46.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 87 through 90 No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 165 through 184 removed outlier: 3.714A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 322 through 331 removed outlier: 4.069A pdb=" N GLN A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.540A pdb=" N GLU A 386 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.612A pdb=" N ARG A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 457 through 477 removed outlier: 3.737A pdb=" N ASP A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 557 through 569 Processing helix chain 'A' and resid 572 through 588 Processing helix chain 'A' and resid 591 through 603 Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 115 through 125 Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 165 through 184 removed outlier: 3.714A pdb=" N LEU B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 313 through 316 No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 322 through 331 removed outlier: 4.069A pdb=" N GLN B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 Processing helix chain 'B' and resid 381 through 388 removed outlier: 3.540A pdb=" N GLU B 386 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 403 removed outlier: 3.612A pdb=" N ARG B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 435 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 457 through 477 removed outlier: 3.737A pdb=" N ASP B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'B' and resid 557 through 569 Processing helix chain 'B' and resid 572 through 588 Processing helix chain 'B' and resid 591 through 603 Processing helix chain 'C' and resid 87 through 90 No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 165 through 184 removed outlier: 3.716A pdb=" N LEU C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 313 through 316 No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 322 through 331 removed outlier: 4.069A pdb=" N GLN C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 353 Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.541A pdb=" N GLU C 386 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 403 removed outlier: 3.611A pdb=" N ARG C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 435 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.737A pdb=" N ASP C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 503 Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 557 through 569 Processing helix chain 'C' and resid 572 through 588 Processing helix chain 'C' and resid 591 through 603 Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'D' and resid 142 through 148 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 165 through 184 removed outlier: 3.715A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 313 through 316 No H-bonds generated for 'chain 'D' and resid 313 through 316' Processing helix chain 'D' and resid 322 through 331 removed outlier: 4.069A pdb=" N GLN D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 353 Processing helix chain 'D' and resid 381 through 388 removed outlier: 3.541A pdb=" N GLU D 386 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 403 removed outlier: 3.611A pdb=" N ARG D 396 " --> pdb=" O SER D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 435 Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 457 through 477 removed outlier: 3.738A pdb=" N ASP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 503 Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 557 through 569 Processing helix chain 'D' and resid 572 through 588 Processing helix chain 'D' and resid 591 through 603 Processing sheet with id= A, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.293A pdb=" N ARG A 301 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 194 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY A 303 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 334 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE A 335 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN A 371 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE A 337 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A 373 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 408 through 415 Processing sheet with id= C, first strand: chain 'A' and resid 506 through 508 removed outlier: 6.786A pdb=" N SER A 533 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A 550 " --> pdb=" O LEU A 536 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.291A pdb=" N ARG B 301 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL B 194 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY B 303 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 334 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE B 335 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN B 371 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE B 337 " --> pdb=" O GLN B 371 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY B 373 " --> pdb=" O PHE B 337 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 408 through 415 Processing sheet with id= F, first strand: chain 'B' and resid 506 through 508 removed outlier: 6.787A pdb=" N SER B 533 " --> pdb=" O CYS B 507 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU B 550 " --> pdb=" O LEU B 536 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.292A pdb=" N ARG C 301 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL C 194 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY C 303 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU C 334 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE C 335 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN C 371 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE C 337 " --> pdb=" O GLN C 371 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY C 373 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 408 through 415 Processing sheet with id= I, first strand: chain 'C' and resid 506 through 508 removed outlier: 6.786A pdb=" N SER C 533 " --> pdb=" O CYS C 507 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU C 550 " --> pdb=" O LEU C 536 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 101 through 103 removed outlier: 6.292A pdb=" N ARG D 301 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL D 194 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY D 303 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU D 334 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE D 335 " --> pdb=" O TYR D 369 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN D 371 " --> pdb=" O ILE D 335 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 337 " --> pdb=" O GLN D 371 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY D 373 " --> pdb=" O PHE D 337 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 408 through 415 Processing sheet with id= L, first strand: chain 'D' and resid 506 through 508 removed outlier: 6.786A pdb=" N SER D 533 " --> pdb=" O CYS D 507 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU D 550 " --> pdb=" O LEU D 536 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 564 hydrogen bonds defined for protein. 1620 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: 10.20 Time building geometry restraints manager: 23.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12712 1.03 - 1.22: 27 1.22 - 1.42: 5981 1.42 - 1.61: 7884 1.61 - 1.80: 104 Bond restraints: 26708 Sorted by residual: bond pdb=" O1B UDP B 701 " pdb=" PB UDP B 701 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.00e-02 1.00e+04 2.45e+01 bond pdb=" O1B UDP D 701 " pdb=" PB UDP D 701 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.00e-02 1.00e+04 2.39e+01 bond pdb=" C1 G6P D 702 " pdb=" O5 G6P D 702 " ideal model delta sigma weight residual 1.401 1.492 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 G6P C 702 " pdb=" O5 G6P C 702 " ideal model delta sigma weight residual 1.401 1.492 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 G6P B 702 " pdb=" O5 G6P B 702 " ideal model delta sigma weight residual 1.401 1.492 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 26703 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.88: 508 106.88 - 113.68: 30587 113.68 - 120.47: 9257 120.47 - 127.27: 7304 127.27 - 134.06: 204 Bond angle restraints: 47860 Sorted by residual: angle pdb=" O1B UDP D 701 " pdb=" PB UDP D 701 " pdb=" O3A UDP D 701 " ideal model delta sigma weight residual 102.95 112.15 -9.20 1.00e+00 1.00e+00 8.46e+01 angle pdb=" O1B UDP B 701 " pdb=" PB UDP B 701 " pdb=" O3A UDP B 701 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.43e+01 angle pdb=" O3A UDP B 701 " pdb=" PB UDP B 701 " pdb=" O3B UDP B 701 " ideal model delta sigma weight residual 112.01 103.01 9.00 1.00e+00 1.00e+00 8.11e+01 angle pdb=" O3A UDP D 701 " pdb=" PB UDP D 701 " pdb=" O3B UDP D 701 " ideal model delta sigma weight residual 112.01 103.09 8.92 1.00e+00 1.00e+00 7.96e+01 angle pdb=" O5' UDP A 701 " pdb=" PA UDP A 701 " pdb=" O1A UDP A 701 " ideal model delta sigma weight residual 106.70 111.18 -4.48 1.00e+00 1.00e+00 2.01e+01 ... (remaining 47855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11530 17.89 - 35.78: 935 35.78 - 53.67: 251 53.67 - 71.56: 74 71.56 - 89.45: 14 Dihedral angle restraints: 12804 sinusoidal: 6784 harmonic: 6020 Sorted by residual: dihedral pdb=" CA MET A 500 " pdb=" C MET A 500 " pdb=" N TYR A 501 " pdb=" CA TYR A 501 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET B 500 " pdb=" C MET B 500 " pdb=" N TYR B 501 " pdb=" CA TYR B 501 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET C 500 " pdb=" C MET C 500 " pdb=" N TYR C 501 " pdb=" CA TYR C 501 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 12801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1863 0.064 - 0.128: 258 0.128 - 0.192: 11 0.192 - 0.255: 0 0.255 - 0.319: 4 Chirality restraints: 2136 Sorted by residual: chirality pdb=" C1 G6P C 702 " pdb=" C2 G6P C 702 " pdb=" O1 G6P C 702 " pdb=" O5 G6P C 702 " both_signs ideal model delta sigma weight residual False -2.03 -2.35 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C1 G6P B 702 " pdb=" C2 G6P B 702 " pdb=" O1 G6P B 702 " pdb=" O5 G6P B 702 " both_signs ideal model delta sigma weight residual False -2.03 -2.35 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C1 G6P A 702 " pdb=" C2 G6P A 702 " pdb=" O1 G6P A 702 " pdb=" O5 G6P A 702 " both_signs ideal model delta sigma weight residual False -2.03 -2.35 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2133 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 422 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO A 423 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 422 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 423 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 422 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 423 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.018 5.00e-02 4.00e+02 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 667 2.13 - 2.75: 47425 2.75 - 3.37: 73734 3.37 - 3.98: 97613 3.98 - 4.60: 154811 Nonbonded interactions: 374250 Sorted by model distance: nonbonded pdb=" HG SER A 312 " pdb=" HG SER D 312 " model vdw 1.517 2.100 nonbonded pdb=" HG SER B 312 " pdb=" HG SER C 312 " model vdw 1.524 2.100 nonbonded pdb=" HE ARG D 453 " pdb=" O3P G6P D 702 " model vdw 1.638 1.850 nonbonded pdb=" HE ARG C 453 " pdb=" O2P G6P C 702 " model vdw 1.638 1.850 nonbonded pdb=" HE ARG B 453 " pdb=" O3P G6P B 702 " model vdw 1.638 1.850 ... (remaining 374245 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.380 Extract box with map and model: 10.910 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 85.990 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.006 0.091 13976 Z= 0.380 Angle : 0.641 9.198 19028 Z= 0.354 Chirality : 0.046 0.319 2136 Planarity : 0.003 0.032 2392 Dihedral : 14.679 89.454 5080 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.81 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.11 (0.20), residues: 1680 helix: 0.96 (0.17), residues: 852 sheet: 0.39 (0.36), residues: 212 loop : -1.73 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS A 198 PHE 0.013 0.002 PHE D 310 TYR 0.010 0.002 TYR D 589 ARG 0.006 0.001 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.6391 time to fit residues: 92.7470 Evaluate side-chains 76 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.0000 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 345 HIS C 345 HIS D 345 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 13976 Z= 0.132 Angle : 0.454 4.095 19028 Z= 0.232 Chirality : 0.041 0.146 2136 Planarity : 0.003 0.028 2392 Dihedral : 7.183 81.316 2092 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.10 % Favored : 96.67 % Rotamer: Outliers : 0.29 % Allowed : 4.94 % Favored : 94.77 % 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: 0.62 (0.21), residues: 1680 helix: 1.70 (0.18), residues: 848 sheet: 0.49 (0.35), residues: 212 loop : -1.48 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 168 HIS 0.003 0.001 HIS C 141 PHE 0.010 0.001 PHE B 384 TYR 0.007 0.001 TYR C 171 ARG 0.002 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 2.217 Fit side-chains REVERT: A 534 MET cc_start: 0.8638 (tpt) cc_final: 0.8214 (tpt) REVERT: B 534 MET cc_start: 0.8619 (tpt) cc_final: 0.8236 (tpt) REVERT: C 534 MET cc_start: 0.8645 (tpt) cc_final: 0.8198 (tpt) REVERT: D 534 MET cc_start: 0.8648 (tpt) cc_final: 0.8216 (tpt) outliers start: 4 outliers final: 1 residues processed: 84 average time/residue: 0.5741 time to fit residues: 73.2206 Evaluate side-chains 79 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS D 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13976 Z= 0.254 Angle : 0.489 4.274 19028 Z= 0.250 Chirality : 0.042 0.150 2136 Planarity : 0.004 0.030 2392 Dihedral : 7.218 79.161 2092 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 0.86 % Allowed : 7.38 % Favored : 91.76 % 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: 0.55 (0.20), residues: 1680 helix: 1.62 (0.18), residues: 852 sheet: 0.46 (0.34), residues: 212 loop : -1.51 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.002 0.000 HIS D 167 PHE 0.012 0.002 PHE B 310 TYR 0.011 0.001 TYR C 171 ARG 0.003 0.000 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 2.349 Fit side-chains REVERT: A 534 MET cc_start: 0.8658 (tpt) cc_final: 0.8341 (tpt) REVERT: B 534 MET cc_start: 0.8650 (tpt) cc_final: 0.8329 (tpt) REVERT: C 534 MET cc_start: 0.8655 (tpt) cc_final: 0.8283 (tpt) REVERT: D 534 MET cc_start: 0.8657 (tpt) cc_final: 0.8352 (tpt) outliers start: 12 outliers final: 12 residues processed: 86 average time/residue: 0.5136 time to fit residues: 67.8539 Evaluate side-chains 87 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13976 Z= 0.339 Angle : 0.534 4.485 19028 Z= 0.275 Chirality : 0.044 0.153 2136 Planarity : 0.004 0.045 2392 Dihedral : 7.450 78.081 2092 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.50 % Allowed : 8.67 % Favored : 89.83 % 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: 0.31 (0.20), residues: 1680 helix: 1.38 (0.18), residues: 852 sheet: 0.42 (0.33), residues: 212 loop : -1.57 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 168 HIS 0.003 0.001 HIS B 198 PHE 0.016 0.002 PHE B 100 TYR 0.011 0.001 TYR A 171 ARG 0.009 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 2.176 Fit side-chains REVERT: A 351 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8119 (t) REVERT: B 351 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8115 (t) REVERT: C 351 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8122 (t) REVERT: D 351 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8122 (t) outliers start: 21 outliers final: 16 residues processed: 94 average time/residue: 0.4439 time to fit residues: 67.4060 Evaluate side-chains 94 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13976 Z= 0.210 Angle : 0.471 4.229 19028 Z= 0.240 Chirality : 0.042 0.149 2136 Planarity : 0.003 0.032 2392 Dihedral : 7.228 76.378 2092 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.93 % Allowed : 9.31 % Favored : 89.76 % 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: 0.54 (0.20), residues: 1680 helix: 1.62 (0.18), residues: 856 sheet: 0.40 (0.33), residues: 212 loop : -1.53 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.002 0.001 HIS D 141 PHE 0.010 0.001 PHE D 310 TYR 0.009 0.001 TYR C 171 ARG 0.005 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 2.382 Fit side-chains REVERT: A 351 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8113 (t) REVERT: B 351 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8113 (t) REVERT: C 351 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8116 (t) REVERT: D 351 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8112 (t) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.4328 time to fit residues: 58.6886 Evaluate side-chains 84 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 chunk 87 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13976 Z= 0.308 Angle : 0.511 4.729 19028 Z= 0.262 Chirality : 0.043 0.152 2136 Planarity : 0.004 0.032 2392 Dihedral : 7.416 75.883 2092 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.72 % Allowed : 8.88 % Favored : 89.40 % 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: 0.38 (0.20), residues: 1680 helix: 1.46 (0.18), residues: 856 sheet: 0.39 (0.33), residues: 212 loop : -1.57 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.001 HIS D 198 PHE 0.012 0.002 PHE C 100 TYR 0.011 0.001 TYR D 171 ARG 0.004 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 2.091 Fit side-chains REVERT: A 351 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8105 (t) REVERT: B 351 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8105 (t) REVERT: C 351 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8106 (t) REVERT: D 351 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8104 (t) outliers start: 24 outliers final: 20 residues processed: 92 average time/residue: 0.4571 time to fit residues: 69.6671 Evaluate side-chains 96 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13976 Z= 0.132 Angle : 0.432 4.088 19028 Z= 0.218 Chirality : 0.041 0.146 2136 Planarity : 0.003 0.031 2392 Dihedral : 7.025 75.499 2092 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.86 % Allowed : 9.96 % Favored : 89.18 % 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: 0.93 (0.21), residues: 1680 helix: 2.03 (0.18), residues: 856 sheet: 0.47 (0.33), residues: 212 loop : -1.45 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.001 HIS D 141 PHE 0.008 0.001 PHE C 384 TYR 0.008 0.001 TYR D 171 ARG 0.006 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 2.238 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.5281 time to fit residues: 75.3649 Evaluate side-chains 80 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13976 Z= 0.279 Angle : 0.490 4.300 19028 Z= 0.250 Chirality : 0.042 0.151 2136 Planarity : 0.004 0.031 2392 Dihedral : 7.301 74.795 2092 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.22 % Allowed : 10.32 % Favored : 88.47 % 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: 0.72 (0.21), residues: 1680 helix: 1.80 (0.18), residues: 856 sheet: 0.45 (0.33), residues: 212 loop : -1.49 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.001 HIS D 198 PHE 0.011 0.002 PHE C 100 TYR 0.010 0.001 TYR D 171 ARG 0.004 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 2.276 Fit side-chains REVERT: A 351 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8085 (t) REVERT: B 351 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8096 (t) REVERT: C 351 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8084 (t) REVERT: D 351 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8084 (t) outliers start: 17 outliers final: 13 residues processed: 85 average time/residue: 0.4736 time to fit residues: 66.4763 Evaluate side-chains 89 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13976 Z= 0.217 Angle : 0.466 4.262 19028 Z= 0.237 Chirality : 0.042 0.150 2136 Planarity : 0.003 0.030 2392 Dihedral : 7.258 74.247 2092 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.50 % Allowed : 10.32 % Favored : 88.18 % 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: 0.82 (0.21), residues: 1680 helix: 1.91 (0.18), residues: 856 sheet: 0.47 (0.33), residues: 212 loop : -1.47 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.001 HIS A 198 PHE 0.009 0.001 PHE C 310 TYR 0.009 0.001 TYR B 171 ARG 0.004 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 2.260 Fit side-chains REVERT: A 351 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8057 (t) REVERT: B 351 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8069 (t) REVERT: C 351 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (t) REVERT: D 351 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8058 (t) outliers start: 21 outliers final: 13 residues processed: 89 average time/residue: 0.4791 time to fit residues: 70.7732 Evaluate side-chains 89 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13976 Z= 0.256 Angle : 0.484 4.303 19028 Z= 0.246 Chirality : 0.042 0.151 2136 Planarity : 0.004 0.030 2392 Dihedral : 7.367 74.699 2092 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.43 % Allowed : 10.39 % Favored : 88.18 % 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: 0.76 (0.21), residues: 1680 helix: 1.85 (0.18), residues: 856 sheet: 0.48 (0.33), residues: 212 loop : -1.50 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.001 HIS A 198 PHE 0.010 0.002 PHE B 100 TYR 0.010 0.001 TYR B 171 ARG 0.004 0.000 ARG D 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 2.171 Fit side-chains REVERT: A 351 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8075 (t) REVERT: B 351 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8087 (t) REVERT: C 351 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8078 (t) REVERT: D 351 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8077 (t) outliers start: 20 outliers final: 15 residues processed: 88 average time/residue: 0.4174 time to fit residues: 61.0144 Evaluate side-chains 91 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106584 restraints weight = 57751.478| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.37 r_work: 0.3326 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13976 Z= 0.189 Angle : 0.454 4.222 19028 Z= 0.230 Chirality : 0.041 0.150 2136 Planarity : 0.003 0.030 2392 Dihedral : 7.199 74.560 2092 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.29 % Allowed : 10.53 % Favored : 88.18 % 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: 0.93 (0.21), residues: 1680 helix: 2.04 (0.18), residues: 856 sheet: 0.49 (0.33), residues: 212 loop : -1.47 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 168 HIS 0.002 0.001 HIS D 141 PHE 0.009 0.001 PHE C 310 TYR 0.008 0.001 TYR B 171 ARG 0.004 0.000 ARG D 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.97 seconds wall clock time: 82 minutes 0.92 seconds (4920.92 seconds total)