Starting phenix.real_space_refine on Thu Feb 15 03:34:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph3_13405/02_2024/7ph3_13405_neut_updated.pdb" } resolution = 2.8 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= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Gd 2 15.26 5 P 8 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 6918 2.51 5 N 1884 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 530": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 552": "OE1" <-> "OE2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 530": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 552": "OE1" <-> "OE2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10968 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4477 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 13, 'TRANS': 563} Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4477 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 13, 'TRANS': 563} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 849 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "D" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 849 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {' MG': 1, '3PE': 1, 'ANP': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {' MG': 1, '3PE': 1, 'ANP': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Ad-hoc single atom residues: {' GD': 1} Unusual residues: {'88T': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Ad-hoc single atom residues: {' GD': 1} Unusual residues: {'88T': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C10 88T C 200 " occ=0.09 ... (35 atoms not shown) pdb=" O9 88T C 200 " occ=0.09 residue: pdb=" C10 88T D 200 " occ=0.09 ... (35 atoms not shown) pdb=" O9 88T D 200 " occ=0.09 Time building chain proxies: 6.13, per 1000 atoms: 0.56 Number of scatterers: 10968 At special positions: 0 Unit cell: (79.515, 96.255, 157.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Gd 2 63.96 S 64 16.00 P 8 15.00 Mg 2 11.99 O 2090 8.00 N 1884 7.00 C 6918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.91 Conformation dependent library (CDL) restraints added in 6.7 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 8 sheets defined 54.3% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 9 through 46 Proline residue: A 18 - end of helix Proline residue: A 22 - end of helix removed outlier: 6.011A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 64 through 110 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 121 through 163 removed outlier: 3.914A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 212 removed outlier: 4.880A pdb=" N ILE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 223 through 271 Proline residue: A 253 - end of helix removed outlier: 3.738A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 322 removed outlier: 4.212A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.031A pdb=" N ARG A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.899A pdb=" N GLN A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.744A pdb=" N GLU A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'B' and resid 9 through 46 Proline residue: B 18 - end of helix Proline residue: B 22 - end of helix removed outlier: 6.011A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY B 26 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 61 through 110 removed outlier: 3.689A pdb=" N MET B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 121 through 163 removed outlier: 3.913A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 212 removed outlier: 4.879A pdb=" N ILE B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 223 through 271 Proline residue: B 253 - end of helix removed outlier: 3.737A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 322 removed outlier: 3.907A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 4.031A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 412 through 418 removed outlier: 3.900A pdb=" N GLN B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.759A pdb=" N GLU B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 571 through 578 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 364 through 366 Processing sheet with id= B, first strand: chain 'A' and resid 555 through 560 removed outlier: 6.823A pdb=" N VAL A 550 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 559 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER A 532 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU A 374 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 534 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY A 376 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 399 through 402 removed outlier: 5.230A pdb=" N ILE B 362 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 555 through 560 removed outlier: 6.822A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 532 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 374 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 534 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY B 376 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= F, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.031A pdb=" N ARG C 38 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= H, first strand: chain 'D' and resid 108 through 110 removed outlier: 6.030A pdb=" N ARG D 38 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASN D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1692 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: 2.25 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1787 1.32 - 1.45: 2889 1.45 - 1.58: 6324 1.58 - 1.72: 14 1.72 - 1.85: 118 Bond restraints: 11132 Sorted by residual: bond pdb=" C11 88T D 200 " pdb=" N4 88T D 200 " ideal model delta sigma weight residual 1.837 1.505 0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb=" C11 88T C 200 " pdb=" N4 88T C 200 " ideal model delta sigma weight residual 1.837 1.505 0.332 2.00e-02 2.50e+03 2.75e+02 bond pdb=" C12 88T C 200 " pdb=" N4 88T C 200 " ideal model delta sigma weight residual 1.814 1.494 0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C12 88T D 200 " pdb=" N4 88T D 200 " ideal model delta sigma weight residual 1.814 1.494 0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C10 88T C 200 " pdb=" O4 88T C 200 " ideal model delta sigma weight residual 1.429 1.184 0.245 2.00e-02 2.50e+03 1.50e+02 ... (remaining 11127 not shown) Histogram of bond angle deviations from ideal: 95.48 - 109.42: 1066 109.42 - 123.36: 13505 123.36 - 137.30: 459 137.30 - 151.24: 2 151.24 - 165.17: 2 Bond angle restraints: 15034 Sorted by residual: angle pdb=" C10 88T D 200 " pdb=" O4 88T D 200 " pdb=" O8 88T D 200 " ideal model delta sigma weight residual 109.57 165.17 -55.60 3.00e+00 1.11e-01 3.44e+02 angle pdb=" C10 88T C 200 " pdb=" O4 88T C 200 " pdb=" O8 88T C 200 " ideal model delta sigma weight residual 109.57 165.12 -55.55 3.00e+00 1.11e-01 3.43e+02 angle pdb=" C15 88T C 200 " pdb=" O6 88T C 200 " pdb=" O9 88T C 200 " ideal model delta sigma weight residual 109.36 137.66 -28.30 3.00e+00 1.11e-01 8.90e+01 angle pdb=" C15 88T D 200 " pdb=" O6 88T D 200 " pdb=" O9 88T D 200 " ideal model delta sigma weight residual 109.36 137.66 -28.30 3.00e+00 1.11e-01 8.90e+01 angle pdb=" C21 88T C 200 " pdb=" O8 88T C 200 " pdb=" O4 88T C 200 " ideal model delta sigma weight residual 105.77 131.41 -25.64 3.00e+00 1.11e-01 7.30e+01 ... (remaining 15029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 6526 35.78 - 71.57: 307 71.57 - 107.35: 55 107.35 - 143.13: 18 143.13 - 178.91: 8 Dihedral angle restraints: 6914 sinusoidal: 2940 harmonic: 3974 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 12.13 80.87 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 12.20 80.80 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" C LYS A 5 " pdb=" N LYS A 5 " pdb=" CA LYS A 5 " pdb=" CB LYS A 5 " ideal model delta harmonic sigma weight residual -122.60 -109.03 -13.57 0 2.50e+00 1.60e-01 2.95e+01 ... (remaining 6911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.399: 1752 1.399 - 2.798: 0 2.798 - 4.196: 0 4.196 - 5.595: 2 5.595 - 6.994: 2 Chirality restraints: 1756 Sorted by residual: chirality pdb=" N4 88T C 200 " pdb=" C11 88T C 200 " pdb=" C12 88T C 200 " pdb=" C22 88T C 200 " both_signs ideal model delta sigma weight residual False 4.34 -2.66 6.99 2.00e-01 2.50e+01 1.22e+03 chirality pdb=" N4 88T D 200 " pdb=" C11 88T D 200 " pdb=" C12 88T D 200 " pdb=" C22 88T D 200 " both_signs ideal model delta sigma weight residual False 4.34 -2.65 6.99 2.00e-01 2.50e+01 1.22e+03 chirality pdb=" N7 88T C 200 " pdb=" C19 88T C 200 " pdb=" C20 88T C 200 " pdb=" C23 88T C 200 " both_signs ideal model delta sigma weight residual False 2.45 -2.46 4.91 2.00e-01 2.50e+01 6.03e+02 ... (remaining 1753 not shown) Planarity restraints: 1876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 279 " -0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C LEU A 279 " 0.078 2.00e-02 2.50e+03 pdb=" O LEU A 279 " -0.029 2.00e-02 2.50e+03 pdb=" N THR A 280 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 331 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C GLY B 331 " 0.044 2.00e-02 2.50e+03 pdb=" O GLY B 331 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 332 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 523 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C LEU A 523 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 523 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 524 " -0.013 2.00e-02 2.50e+03 ... (remaining 1873 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 77 2.57 - 3.15: 9100 3.15 - 3.74: 17624 3.74 - 4.32: 25232 4.32 - 4.90: 40236 Nonbonded interactions: 92269 Sorted by model distance: nonbonded pdb=" O2B ANP B 601 " pdb="MG MG B 602 " model vdw 1.990 2.170 nonbonded pdb=" OE1 GLN A 424 " pdb="MG MG A 602 " model vdw 2.033 2.170 nonbonded pdb=" O1G ANP B 601 " pdb="MG MG B 602 " model vdw 2.049 2.170 nonbonded pdb="MG MG A 602 " pdb=" O HOH A 701 " model vdw 2.060 2.170 nonbonded pdb="MG MG B 602 " pdb=" O HOH B 701 " model vdw 2.062 2.170 ... (remaining 92264 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' and (resid 3 through 579 or resid 601 through 602)) selection = (chain 'B' and (resid 3 through 579 or resid 601 through 602)) } ncs_group { reference = 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=0.09 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.000 Extract box with map and model: 7.010 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.700 Find NCS groups from input model: 0.410 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:14.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.332 11132 Z= 0.881 Angle : 1.233 55.605 15034 Z= 0.595 Chirality : 0.294 6.994 1756 Planarity : 0.005 0.063 1876 Dihedral : 22.880 178.913 4348 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.10 % Favored : 94.83 % Rotamer: Outliers : 0.34 % Allowed : 24.10 % Favored : 75.56 % Cbeta Deviations : 0.08 % 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: 0.63 (0.22), residues: 1372 helix: 1.34 (0.19), residues: 734 sheet: 0.28 (0.40), residues: 164 loop : -0.94 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 10 HIS 0.006 0.002 HIS B 214 PHE 0.020 0.002 PHE A 462 TYR 0.031 0.003 TYR C 93 ARG 0.007 0.001 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 263 time to evaluate : 1.045 Fit side-chains REVERT: A 5 LYS cc_start: 0.6694 (tptp) cc_final: 0.6478 (ttmt) REVERT: A 64 LEU cc_start: 0.8228 (mt) cc_final: 0.8026 (tp) REVERT: A 318 LEU cc_start: 0.7832 (tp) cc_final: 0.7321 (mm) REVERT: A 431 ASP cc_start: 0.7116 (t0) cc_final: 0.6882 (t0) REVERT: B 431 ASP cc_start: 0.7174 (t0) cc_final: 0.6869 (t0) REVERT: C 56 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7265 (ttm110) outliers start: 4 outliers final: 1 residues processed: 266 average time/residue: 1.2473 time to fit residues: 355.0554 Evaluate side-chains 174 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 0.0170 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 197 GLN A 468 ASN A 574 GLN A 576 HIS B 11 GLN B 197 GLN B 468 ASN B 574 GLN B 576 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11132 Z= 0.199 Angle : 0.654 15.348 15034 Z= 0.319 Chirality : 0.043 0.315 1756 Planarity : 0.005 0.036 1876 Dihedral : 20.127 179.515 1846 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 5.40 % Allowed : 25.99 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.22), residues: 1372 helix: 1.70 (0.18), residues: 756 sheet: 0.28 (0.38), residues: 164 loop : -0.84 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 17 HIS 0.004 0.001 HIS B 568 PHE 0.018 0.002 PHE A 161 TYR 0.013 0.001 TYR C 103 ARG 0.005 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 1.188 Fit side-chains REVERT: A 261 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7805 (mp) REVERT: A 265 PHE cc_start: 0.8264 (t80) cc_final: 0.7983 (t80) REVERT: A 335 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 431 ASP cc_start: 0.7118 (t0) cc_final: 0.6829 (t0) REVERT: A 443 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: B 161 PHE cc_start: 0.6576 (t80) cc_final: 0.5902 (t80) REVERT: B 285 THR cc_start: 0.7947 (t) cc_final: 0.7597 (p) REVERT: B 431 ASP cc_start: 0.7183 (t0) cc_final: 0.6863 (t0) REVERT: B 443 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: C 56 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7338 (mtm-85) REVERT: D 21 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8105 (p) outliers start: 63 outliers final: 21 residues processed: 218 average time/residue: 1.0406 time to fit residues: 248.0269 Evaluate side-chains 183 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 468 ASN A 520 GLN A 574 GLN B 214 HIS B 468 ASN B 520 GLN B 574 GLN D 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11132 Z= 0.190 Angle : 0.564 11.553 15034 Z= 0.288 Chirality : 0.042 0.378 1756 Planarity : 0.004 0.040 1876 Dihedral : 20.084 178.943 1846 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 5.06 % Allowed : 26.42 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1372 helix: 1.80 (0.18), residues: 758 sheet: 0.33 (0.38), residues: 164 loop : -0.74 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.004 0.001 HIS A 568 PHE 0.019 0.002 PHE B 265 TYR 0.007 0.001 TYR A 87 ARG 0.006 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 161 time to evaluate : 1.116 Fit side-chains REVERT: A 261 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7908 (mp) REVERT: A 265 PHE cc_start: 0.8174 (t80) cc_final: 0.7963 (t80) REVERT: A 431 ASP cc_start: 0.7153 (t0) cc_final: 0.6856 (t0) REVERT: A 443 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 45 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8164 (tt) REVERT: B 285 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7590 (p) REVERT: B 345 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7503 (ttp-170) REVERT: B 431 ASP cc_start: 0.7196 (t0) cc_final: 0.6874 (t0) REVERT: C 56 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7382 (mtm-85) REVERT: D 109 PRO cc_start: 0.8357 (Cg_endo) cc_final: 0.8088 (Cg_exo) outliers start: 59 outliers final: 23 residues processed: 197 average time/residue: 1.1481 time to fit residues: 244.8935 Evaluate side-chains 183 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 0.0770 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 109 optimal weight: 0.0980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 485 GLN A 520 GLN A 574 GLN B 361 ASN B 468 ASN B 520 GLN B 527 GLN B 574 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11132 Z= 0.155 Angle : 0.523 7.924 15034 Z= 0.269 Chirality : 0.040 0.280 1756 Planarity : 0.004 0.038 1876 Dihedral : 19.499 177.791 1844 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 4.46 % Allowed : 27.02 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1372 helix: 1.94 (0.19), residues: 760 sheet: 0.41 (0.39), residues: 164 loop : -0.66 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 17 HIS 0.003 0.001 HIS B 568 PHE 0.015 0.001 PHE A 462 TYR 0.007 0.001 TYR D 37 ARG 0.003 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 177 time to evaluate : 1.179 Fit side-chains REVERT: A 45 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 169 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5847 (pp) REVERT: A 431 ASP cc_start: 0.7207 (t0) cc_final: 0.6873 (t0) REVERT: A 516 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6876 (tt0) REVERT: B 45 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 285 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7661 (p) REVERT: B 431 ASP cc_start: 0.7177 (t0) cc_final: 0.6840 (t0) REVERT: C 56 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7410 (mtm-85) REVERT: D 109 PRO cc_start: 0.8345 (Cg_endo) cc_final: 0.8072 (Cg_exo) outliers start: 52 outliers final: 19 residues processed: 206 average time/residue: 1.1166 time to fit residues: 250.1044 Evaluate side-chains 187 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 0.1980 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 468 ASN A 520 GLN A 527 GLN A 574 GLN B 468 ASN B 520 GLN B 574 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11132 Z= 0.183 Angle : 0.538 7.806 15034 Z= 0.276 Chirality : 0.041 0.207 1756 Planarity : 0.004 0.037 1876 Dihedral : 19.327 174.791 1844 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 4.12 % Allowed : 27.44 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1372 helix: 1.92 (0.19), residues: 760 sheet: 0.49 (0.39), residues: 164 loop : -0.65 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.004 0.001 HIS B 568 PHE 0.021 0.002 PHE B 43 TYR 0.007 0.001 TYR A 87 ARG 0.007 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 1.124 Fit side-chains REVERT: A 45 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 431 ASP cc_start: 0.7215 (t0) cc_final: 0.6876 (t0) REVERT: A 516 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: B 45 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8097 (tt) REVERT: B 285 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7625 (p) REVERT: B 431 ASP cc_start: 0.7193 (t0) cc_final: 0.6849 (t0) REVERT: C 56 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7441 (mtm-85) outliers start: 48 outliers final: 19 residues processed: 187 average time/residue: 1.1124 time to fit residues: 226.2949 Evaluate side-chains 178 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 485 GLN A 520 GLN A 574 GLN B 468 ASN B 520 GLN B 574 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11132 Z= 0.272 Angle : 0.599 7.699 15034 Z= 0.302 Chirality : 0.043 0.196 1756 Planarity : 0.004 0.038 1876 Dihedral : 19.530 171.439 1844 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 4.20 % Allowed : 27.19 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1372 helix: 1.79 (0.18), residues: 752 sheet: 0.37 (0.38), residues: 164 loop : -0.69 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 17 HIS 0.005 0.001 HIS B 568 PHE 0.026 0.002 PHE A 462 TYR 0.008 0.001 TYR A 87 ARG 0.003 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 160 time to evaluate : 1.377 Fit side-chains REVERT: A 45 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8360 (tt) REVERT: A 431 ASP cc_start: 0.7181 (t0) cc_final: 0.6851 (t0) REVERT: A 516 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7053 (tt0) REVERT: B 285 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7583 (p) REVERT: B 431 ASP cc_start: 0.7195 (t0) cc_final: 0.6857 (t0) outliers start: 49 outliers final: 25 residues processed: 193 average time/residue: 1.0847 time to fit residues: 228.6357 Evaluate side-chains 181 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 520 GLN A 574 GLN B 468 ASN B 520 GLN B 574 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11132 Z= 0.196 Angle : 0.554 7.572 15034 Z= 0.282 Chirality : 0.041 0.182 1756 Planarity : 0.004 0.037 1876 Dihedral : 19.251 166.161 1844 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.30 % Rotamer: Outliers : 3.86 % Allowed : 28.13 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1372 helix: 1.82 (0.19), residues: 758 sheet: 0.42 (0.38), residues: 164 loop : -0.67 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.004 0.001 HIS B 568 PHE 0.025 0.002 PHE B 265 TYR 0.007 0.001 TYR A 87 ARG 0.006 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.319 Fit side-chains REVERT: A 45 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 431 ASP cc_start: 0.7204 (t0) cc_final: 0.6872 (t0) REVERT: A 516 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: B 285 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7591 (p) REVERT: B 431 ASP cc_start: 0.7202 (t0) cc_final: 0.6863 (t0) REVERT: B 461 ASP cc_start: 0.7514 (m-30) cc_final: 0.7241 (p0) REVERT: D 82 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: D 109 PRO cc_start: 0.8360 (Cg_endo) cc_final: 0.8101 (Cg_exo) outliers start: 45 outliers final: 22 residues processed: 180 average time/residue: 1.1100 time to fit residues: 217.7691 Evaluate side-chains 175 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 103 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 520 GLN A 574 GLN B 468 ASN B 520 GLN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11132 Z= 0.163 Angle : 0.533 7.424 15034 Z= 0.271 Chirality : 0.040 0.159 1756 Planarity : 0.004 0.036 1876 Dihedral : 18.985 162.220 1844 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 3.34 % Allowed : 28.47 % Favored : 68.18 % 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: 1.38 (0.23), residues: 1372 helix: 1.93 (0.19), residues: 760 sheet: 0.53 (0.38), residues: 164 loop : -0.69 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.004 0.001 HIS A 568 PHE 0.023 0.002 PHE B 265 TYR 0.007 0.001 TYR C 93 ARG 0.007 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 1.117 Fit side-chains REVERT: A 45 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 431 ASP cc_start: 0.7189 (t0) cc_final: 0.6850 (t0) REVERT: A 516 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: A 538 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7215 (mtt180) REVERT: B 285 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7566 (p) REVERT: B 431 ASP cc_start: 0.7184 (t0) cc_final: 0.6853 (t0) REVERT: B 461 ASP cc_start: 0.7439 (m-30) cc_final: 0.7202 (p0) REVERT: D 82 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8101 (mtm) REVERT: D 109 PRO cc_start: 0.8330 (Cg_endo) cc_final: 0.8051 (Cg_exo) outliers start: 39 outliers final: 21 residues processed: 176 average time/residue: 1.1589 time to fit residues: 221.9672 Evaluate side-chains 173 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.0270 chunk 125 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 520 GLN A 574 GLN B 468 ASN B 520 GLN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11132 Z= 0.210 Angle : 0.564 9.879 15034 Z= 0.286 Chirality : 0.041 0.143 1756 Planarity : 0.004 0.037 1876 Dihedral : 19.052 162.444 1844 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 3.09 % Allowed : 29.16 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1372 helix: 1.85 (0.19), residues: 758 sheet: 0.55 (0.38), residues: 164 loop : -0.73 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 17 HIS 0.004 0.001 HIS A 568 PHE 0.023 0.002 PHE B 265 TYR 0.007 0.001 TYR A 87 ARG 0.007 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.350 Fit side-chains REVERT: A 431 ASP cc_start: 0.7178 (t0) cc_final: 0.6852 (t0) REVERT: A 516 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: A 538 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7229 (mtt180) REVERT: B 47 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7511 (mp) REVERT: B 285 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7565 (p) REVERT: B 431 ASP cc_start: 0.7209 (t0) cc_final: 0.6863 (t0) REVERT: B 461 ASP cc_start: 0.7458 (m-30) cc_final: 0.7211 (p0) REVERT: B 498 ASP cc_start: 0.6270 (t0) cc_final: 0.5996 (t0) REVERT: D 82 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8108 (mtm) outliers start: 36 outliers final: 22 residues processed: 168 average time/residue: 1.1138 time to fit residues: 203.8339 Evaluate side-chains 169 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 0.0670 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 0.0000 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 overall best weight: 0.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 520 GLN A 574 GLN B 468 ASN B 520 GLN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11132 Z= 0.154 Angle : 0.535 8.776 15034 Z= 0.271 Chirality : 0.039 0.140 1756 Planarity : 0.004 0.035 1876 Dihedral : 18.879 165.819 1844 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.40 % Allowed : 29.50 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1372 helix: 1.95 (0.19), residues: 760 sheet: 0.64 (0.38), residues: 164 loop : -0.73 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.004 0.001 HIS A 568 PHE 0.023 0.002 PHE B 265 TYR 0.007 0.001 TYR D 37 ARG 0.007 0.000 ARG D 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.420 Fit side-chains REVERT: A 431 ASP cc_start: 0.7188 (t0) cc_final: 0.6847 (t0) REVERT: A 516 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: A 538 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7184 (mtt180) REVERT: B 47 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 285 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7569 (p) REVERT: B 431 ASP cc_start: 0.7183 (t0) cc_final: 0.6842 (t0) REVERT: B 461 ASP cc_start: 0.7405 (m-30) cc_final: 0.7172 (p0) REVERT: D 82 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8102 (mtm) outliers start: 28 outliers final: 19 residues processed: 162 average time/residue: 1.2088 time to fit residues: 212.9946 Evaluate side-chains 166 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 520 GLN A 574 GLN B 468 ASN B 520 GLN B 574 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122061 restraints weight = 5671.291| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.33 r_work: 0.3251 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11132 Z= 0.178 Angle : 0.544 9.897 15034 Z= 0.277 Chirality : 0.040 0.141 1756 Planarity : 0.004 0.049 1876 Dihedral : 18.998 168.346 1844 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 2.66 % Allowed : 29.67 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1372 helix: 1.89 (0.19), residues: 762 sheet: 0.85 (0.37), residues: 174 loop : -0.75 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 HIS 0.004 0.001 HIS A 568 PHE 0.023 0.002 PHE B 265 TYR 0.007 0.001 TYR D 37 ARG 0.010 0.000 ARG B 530 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4353.40 seconds wall clock time: 88 minutes 28.13 seconds (5308.13 seconds total)