Starting phenix.real_space_refine on Thu Mar 14 14:54:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhv_23351/03_2024/7lhv_23351_neut_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.162 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 32 5.16 5 C 5976 2.51 5 N 1452 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 629": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9094 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 4544 Chain: "B" Number of atoms: 4465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 575, 4454 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 549} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 4544 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'LBN': 1, 'S1P': 2, 'SO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'LBN': 1, 'S1P': 2, 'SO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE A 391 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 391 " occ=0.50 residue: pdb=" N APHE B 391 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 391 " occ=0.50 Time building chain proxies: 9.57, per 1000 atoms: 1.05 Number of scatterers: 9094 At special positions: 0 Unit cell: (123.6, 104.03, 94.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 6 15.00 O 1628 8.00 N 1452 7.00 C 5976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 3.3 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 2 sheets defined 66.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 72 through 79 removed outlier: 3.758A pdb=" N ASP A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 91 through 119 removed outlier: 4.191A pdb=" N LYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.835A pdb=" N TYR A 129 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL A 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) Proline residue: A 134 - end of helix removed outlier: 3.767A pdb=" N ALA A 139 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 173 through 194 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 206 through 229 removed outlier: 4.616A pdb=" N LYS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 252 removed outlier: 5.025A pdb=" N ASP A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 283 through 301 removed outlier: 3.770A pdb=" N ALA A 288 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.841A pdb=" N GLY A 292 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR A 297 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 346 removed outlier: 4.726A pdb=" N LYS A 331 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Proline residue: A 335 - end of helix removed outlier: 4.013A pdb=" N ALA A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 340 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 365 through 381 removed outlier: 3.674A pdb=" N LEU A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.581A pdb=" N ALA A 395 " --> pdb=" O BPHE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.827A pdb=" N ILE A 410 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.861A pdb=" N LYS A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.114A pdb=" N GLY A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 459 through 474 Processing helix chain 'A' and resid 477 through 496 Processing helix chain 'A' and resid 542 through 560 removed outlier: 4.299A pdb=" N TYR A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 599 Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 635 through 643 Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.758A pdb=" N ASP B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 91 through 119 removed outlier: 4.191A pdb=" N LYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 124 through 141 removed outlier: 3.835A pdb=" N TYR B 129 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL B 133 " --> pdb=" O SER B 130 " (cutoff:3.500A) Proline residue: B 134 - end of helix removed outlier: 3.767A pdb=" N ALA B 139 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 173 through 194 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 206 through 229 removed outlier: 4.616A pdb=" N LYS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 252 removed outlier: 5.025A pdb=" N ASP B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 283 through 301 removed outlier: 3.770A pdb=" N ALA B 288 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.841A pdb=" N GLY B 292 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 297 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 346 removed outlier: 4.726A pdb=" N LYS B 331 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 334 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Proline residue: B 335 - end of helix removed outlier: 4.013A pdb=" N ALA B 338 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 340 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 365 through 381 removed outlier: 3.674A pdb=" N LEU B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.581A pdb=" N ALA B 395 " --> pdb=" O BPHE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.827A pdb=" N ILE B 410 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.861A pdb=" N LYS B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 428 " --> pdb=" O MET B 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 424 through 428' Processing helix chain 'B' and resid 431 through 445 removed outlier: 4.114A pdb=" N GLY B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'B' and resid 459 through 474 Processing helix chain 'B' and resid 477 through 496 Processing helix chain 'B' and resid 542 through 560 removed outlier: 4.299A pdb=" N TYR B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 599 Processing helix chain 'B' and resid 611 through 620 Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 628 through 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 635 through 643 Processing sheet with id= A, first strand: chain 'A' and resid 501 through 504 removed outlier: 4.693A pdb=" N ILE A 530 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 529 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 572 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 531 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 574 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE A 533 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN A 603 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 574 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 605 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 501 through 504 removed outlier: 4.693A pdb=" N ILE B 530 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 529 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 572 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 531 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 574 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 533 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN B 603 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU B 574 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA B 605 " --> pdb=" O LEU B 574 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1230 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: 2.48 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1392 1.31 - 1.43: 2426 1.43 - 1.56: 5418 1.56 - 1.68: 8 1.68 - 1.81: 50 Bond restraints: 9294 Sorted by residual: bond pdb=" O2 LBN B1004 " pdb=" P1 LBN B1004 " ideal model delta sigma weight residual 1.650 1.480 0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" O2 LBN A1003 " pdb=" P1 LBN A1003 " ideal model delta sigma weight residual 1.650 1.480 0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" O4 LBN B1004 " pdb=" P1 LBN B1004 " ideal model delta sigma weight residual 1.497 1.592 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" O4 LBN A1003 " pdb=" P1 LBN A1003 " ideal model delta sigma weight residual 1.497 1.592 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" O1 S1P A1001 " pdb=" P22 S1P A1001 " ideal model delta sigma weight residual 1.661 1.575 0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 9289 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.08: 278 107.08 - 113.83: 5428 113.83 - 120.57: 3744 120.57 - 127.31: 3070 127.31 - 134.05: 106 Bond angle restraints: 12626 Sorted by residual: angle pdb=" O1 LBN A1003 " pdb=" P1 LBN A1003 " pdb=" O2 LBN A1003 " ideal model delta sigma weight residual 93.45 110.76 -17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O1 LBN B1004 " pdb=" P1 LBN B1004 " pdb=" O2 LBN B1004 " ideal model delta sigma weight residual 93.45 110.76 -17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O3 LBN B1004 " pdb=" P1 LBN B1004 " pdb=" O4 LBN B1004 " ideal model delta sigma weight residual 119.36 104.85 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" O3 LBN A1003 " pdb=" P1 LBN A1003 " pdb=" O4 LBN A1003 " ideal model delta sigma weight residual 119.36 104.85 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C4 S1P B1002 " pdb=" C5 S1P B1002 " pdb=" C6 S1P B1002 " ideal model delta sigma weight residual 119.98 131.01 -11.03 3.00e+00 1.11e-01 1.35e+01 ... (remaining 12621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 5394 35.93 - 71.87: 66 71.87 - 107.80: 12 107.80 - 143.73: 12 143.73 - 179.67: 6 Dihedral angle restraints: 5490 sinusoidal: 2158 harmonic: 3332 Sorted by residual: dihedral pdb=" C39 LBN A1003 " pdb=" C40 LBN A1003 " pdb=" C41 LBN A1003 " pdb=" C42 LBN A1003 " ideal model delta sinusoidal sigma weight residual 178.66 -1.67 -179.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C39 LBN B1004 " pdb=" C40 LBN B1004 " pdb=" C41 LBN B1004 " pdb=" C42 LBN B1004 " ideal model delta sinusoidal sigma weight residual 178.66 -1.67 -179.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 S1P B1001 " pdb=" C2 S1P B1001 " pdb=" C3 S1P B1001 " pdb=" C4 S1P B1001 " ideal model delta sinusoidal sigma weight residual 192.71 15.43 177.28 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1304 0.062 - 0.123: 176 0.123 - 0.185: 6 0.185 - 0.246: 0 0.246 - 0.308: 2 Chirality restraints: 1488 Sorted by residual: chirality pdb=" C2 S1P B1002 " pdb=" C1 S1P B1002 " pdb=" C3 S1P B1002 " pdb=" N2 S1P B1002 " both_signs ideal model delta sigma weight residual False -2.62 -2.31 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C2 S1P A1001 " pdb=" C1 S1P A1001 " pdb=" C3 S1P A1001 " pdb=" N2 S1P A1001 " both_signs ideal model delta sigma weight residual False -2.62 -2.31 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA THR A 423 " pdb=" N THR A 423 " pdb=" C THR A 423 " pdb=" CB THR A 423 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1485 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C34 LBN A1003 " -0.030 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C35 LBN A1003 " 0.008 2.00e-02 2.50e+03 pdb=" O7 LBN A1003 " 0.009 2.00e-02 2.50e+03 pdb=" O8 LBN A1003 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C34 LBN B1004 " 0.030 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C35 LBN B1004 " -0.008 2.00e-02 2.50e+03 pdb=" O7 LBN B1004 " -0.009 2.00e-02 2.50e+03 pdb=" O8 LBN B1004 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 418 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C SER B 418 " -0.028 2.00e-02 2.50e+03 pdb=" O SER B 418 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 419 " 0.010 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2672 2.82 - 3.34: 8903 3.34 - 3.86: 15341 3.86 - 4.38: 17550 4.38 - 4.90: 30442 Nonbonded interactions: 74908 Sorted by model distance: nonbonded pdb=" O SER A 160 " pdb=" NH2 ARG A 235 " model vdw 2.299 2.520 nonbonded pdb=" O SER B 160 " pdb=" NH2 ARG B 235 " model vdw 2.299 2.520 nonbonded pdb=" N2 S1P B1001 " pdb=" O1 S1P B1001 " model vdw 2.302 2.496 nonbonded pdb=" N2 S1P A1004 " pdb=" O1 S1P A1004 " model vdw 2.302 2.496 nonbonded pdb=" N2 S1P B1001 " pdb=" O3 S1P B1001 " model vdw 2.303 2.496 ... (remaining 74903 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 70 through 390 or resid 392 through 644 or (resid 1001 and \ (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name N2 or name O1 or name O23 or name O24 or name O25 \ or name O3 or name P22)))) selection = (chain 'B' and (resid 70 through 390 or resid 392 through 644 or resid 1001)) } 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=0.50 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: 0.350 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: 2.110 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.780 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.170 9294 Z= 0.429 Angle : 0.755 17.314 12626 Z= 0.323 Chirality : 0.042 0.308 1488 Planarity : 0.004 0.033 1546 Dihedral : 17.053 179.668 3354 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: 0.97 (0.25), residues: 1152 helix: 1.40 (0.19), residues: 784 sheet: 3.34 (0.85), residues: 34 loop : -1.51 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 91 HIS 0.003 0.001 HIS A 636 PHE 0.011 0.001 PHE A 491 TYR 0.015 0.001 TYR B 385 ARG 0.002 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.982 Fit side-chains REVERT: A 364 ASP cc_start: 0.7148 (p0) cc_final: 0.6700 (p0) REVERT: A 557 ASP cc_start: 0.6185 (m-30) cc_final: 0.5710 (m-30) REVERT: B 70 MET cc_start: 0.4051 (ttm) cc_final: 0.3740 (ttp) REVERT: B 96 LYS cc_start: 0.7230 (ptmm) cc_final: 0.6945 (mmtm) REVERT: B 276 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7897 (ptmm) outliers start: 0 outliers final: 1 residues processed: 147 average time/residue: 1.0502 time to fit residues: 166.2345 Evaluate side-chains 84 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9294 Z= 0.218 Angle : 0.540 6.669 12626 Z= 0.268 Chirality : 0.041 0.147 1488 Planarity : 0.004 0.036 1546 Dihedral : 18.259 174.444 1349 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.24 % Allowed : 8.26 % Favored : 90.50 % 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: 0.90 (0.25), residues: 1152 helix: 1.36 (0.19), residues: 784 sheet: 3.36 (0.86), residues: 34 loop : -1.55 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 91 HIS 0.002 0.001 HIS B 174 PHE 0.024 0.001 PHE A 95 TYR 0.015 0.001 TYR A 385 ARG 0.005 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.792 Fit side-chains REVERT: A 364 ASP cc_start: 0.7590 (p0) cc_final: 0.7111 (p0) REVERT: A 557 ASP cc_start: 0.6164 (m-30) cc_final: 0.5737 (m-30) REVERT: B 70 MET cc_start: 0.4138 (ttm) cc_final: 0.3837 (ttp) REVERT: B 428 TYR cc_start: 0.8135 (m-80) cc_final: 0.7716 (m-80) REVERT: B 495 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7518 (tm-30) outliers start: 12 outliers final: 4 residues processed: 108 average time/residue: 1.0520 time to fit residues: 122.5458 Evaluate side-chains 92 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 598 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 102 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9294 Z= 0.150 Angle : 0.478 6.584 12626 Z= 0.239 Chirality : 0.039 0.142 1488 Planarity : 0.004 0.033 1546 Dihedral : 15.071 154.884 1346 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.93 % Allowed : 10.33 % Favored : 88.74 % 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: 1.14 (0.25), residues: 1152 helix: 1.54 (0.19), residues: 786 sheet: 2.48 (0.92), residues: 38 loop : -1.41 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 91 HIS 0.002 0.000 HIS B 636 PHE 0.018 0.001 PHE A 95 TYR 0.015 0.001 TYR B 385 ARG 0.007 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.844 Fit side-chains REVERT: A 364 ASP cc_start: 0.7610 (p0) cc_final: 0.7253 (p0) REVERT: A 557 ASP cc_start: 0.6163 (m-30) cc_final: 0.5706 (m-30) REVERT: B 70 MET cc_start: 0.4135 (ttm) cc_final: 0.3741 (ttp) REVERT: B 428 TYR cc_start: 0.8053 (m-80) cc_final: 0.7670 (m-80) REVERT: B 495 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: B 553 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6545 (mt-10) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 1.2183 time to fit residues: 126.7471 Evaluate side-chains 90 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 598 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7322 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9294 Z= 0.271 Angle : 0.546 6.694 12626 Z= 0.279 Chirality : 0.042 0.151 1488 Planarity : 0.004 0.038 1546 Dihedral : 13.924 156.184 1346 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.24 % Allowed : 10.54 % Favored : 88.22 % 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: 0.84 (0.25), residues: 1152 helix: 1.35 (0.19), residues: 782 sheet: 2.75 (0.84), residues: 34 loop : -1.58 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.003 0.001 HIS A 636 PHE 0.013 0.001 PHE B 491 TYR 0.018 0.002 TYR A 126 ARG 0.009 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.107 Fit side-chains REVERT: A 251 ASP cc_start: 0.7458 (t0) cc_final: 0.7044 (m-30) REVERT: A 557 ASP cc_start: 0.6258 (m-30) cc_final: 0.5826 (m-30) REVERT: A 569 ILE cc_start: 0.7854 (mm) cc_final: 0.7484 (mm) REVERT: B 70 MET cc_start: 0.4042 (ttm) cc_final: 0.3565 (ttp) REVERT: B 267 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7117 (mt) REVERT: B 364 ASP cc_start: 0.7280 (p0) cc_final: 0.6564 (p0) REVERT: B 428 TYR cc_start: 0.8261 (m-80) cc_final: 0.7929 (m-80) REVERT: B 495 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7843 (tm-30) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 1.1830 time to fit residues: 135.9869 Evaluate side-chains 97 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 598 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.5980 chunk 62 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9294 Z= 0.172 Angle : 0.481 6.576 12626 Z= 0.243 Chirality : 0.039 0.140 1488 Planarity : 0.004 0.036 1546 Dihedral : 13.285 155.555 1346 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.52 % Allowed : 11.98 % Favored : 87.50 % 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: 1.03 (0.25), residues: 1152 helix: 1.48 (0.19), residues: 784 sheet: 1.99 (0.89), residues: 38 loop : -1.44 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 91 HIS 0.002 0.000 HIS B 174 PHE 0.026 0.001 PHE A 95 TYR 0.016 0.001 TYR B 385 ARG 0.006 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.004 Fit side-chains REVERT: A 251 ASP cc_start: 0.7303 (t0) cc_final: 0.6932 (m-30) REVERT: A 267 ILE cc_start: 0.7453 (mp) cc_final: 0.7193 (mp) REVERT: A 557 ASP cc_start: 0.6231 (m-30) cc_final: 0.5794 (m-30) REVERT: A 569 ILE cc_start: 0.7735 (mm) cc_final: 0.7400 (mm) REVERT: B 70 MET cc_start: 0.4049 (ttm) cc_final: 0.3641 (ttp) REVERT: B 267 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7082 (mp) REVERT: B 428 TYR cc_start: 0.8210 (m-80) cc_final: 0.7930 (m-80) REVERT: B 495 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7854 (tm-30) outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 1.1641 time to fit residues: 120.1099 Evaluate side-chains 93 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 598 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.7361 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9294 Z= 0.238 Angle : 0.524 6.717 12626 Z= 0.265 Chirality : 0.040 0.141 1488 Planarity : 0.004 0.036 1546 Dihedral : 13.126 158.313 1346 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.62 % Allowed : 12.81 % Favored : 86.57 % 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: 0.85 (0.25), residues: 1152 helix: 1.36 (0.19), residues: 782 sheet: 1.41 (0.89), residues: 38 loop : -1.47 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 91 HIS 0.005 0.001 HIS A 636 PHE 0.010 0.001 PHE A 95 TYR 0.017 0.001 TYR A 126 ARG 0.011 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.022 Fit side-chains REVERT: A 100 MET cc_start: 0.7227 (mmp) cc_final: 0.7001 (mmm) REVERT: A 251 ASP cc_start: 0.7309 (t0) cc_final: 0.7044 (m-30) REVERT: A 517 LYS cc_start: 0.7036 (mmpt) cc_final: 0.6751 (mppt) REVERT: A 557 ASP cc_start: 0.6252 (m-30) cc_final: 0.5926 (m-30) REVERT: B 70 MET cc_start: 0.4114 (ttm) cc_final: 0.3668 (ttp) REVERT: B 172 GLU cc_start: 0.7593 (tp30) cc_final: 0.7315 (tp30) REVERT: B 267 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7065 (mp) REVERT: B 364 ASP cc_start: 0.7412 (p0) cc_final: 0.6568 (p0) REVERT: B 495 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (tm-30) outliers start: 6 outliers final: 2 residues processed: 99 average time/residue: 1.2162 time to fit residues: 129.2316 Evaluate side-chains 93 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 495 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7335 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9294 Z= 0.168 Angle : 0.484 6.579 12626 Z= 0.244 Chirality : 0.039 0.141 1488 Planarity : 0.004 0.034 1546 Dihedral : 12.940 157.261 1346 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.62 % Allowed : 13.12 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1152 helix: 1.48 (0.19), residues: 782 sheet: 2.29 (0.87), residues: 34 loop : -1.44 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 91 HIS 0.002 0.000 HIS A 636 PHE 0.023 0.001 PHE A 95 TYR 0.016 0.001 TYR B 385 ARG 0.007 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.063 Fit side-chains REVERT: A 100 MET cc_start: 0.7224 (mmp) cc_final: 0.6997 (mmm) REVERT: A 251 ASP cc_start: 0.7245 (t0) cc_final: 0.7026 (m-30) REVERT: A 517 LYS cc_start: 0.7122 (mmpt) cc_final: 0.6840 (mppt) REVERT: A 557 ASP cc_start: 0.6196 (m-30) cc_final: 0.5806 (m-30) REVERT: A 569 ILE cc_start: 0.7806 (mm) cc_final: 0.7574 (mm) REVERT: B 70 MET cc_start: 0.4073 (ttm) cc_final: 0.3577 (ttp) REVERT: B 267 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7077 (mp) REVERT: B 428 TYR cc_start: 0.8255 (m-80) cc_final: 0.8024 (m-80) REVERT: B 495 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7961 (tm-30) outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 1.2014 time to fit residues: 126.6631 Evaluate side-chains 94 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 495 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.7380 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9294 Z= 0.293 Angle : 0.539 6.784 12626 Z= 0.272 Chirality : 0.041 0.151 1488 Planarity : 0.004 0.037 1546 Dihedral : 13.034 159.921 1346 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.93 % Allowed : 13.33 % Favored : 85.74 % 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: 0.81 (0.25), residues: 1152 helix: 1.31 (0.19), residues: 782 sheet: 2.14 (0.88), residues: 34 loop : -1.47 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 91 HIS 0.004 0.001 HIS A 636 PHE 0.010 0.001 PHE A 95 TYR 0.019 0.002 TYR A 126 ARG 0.008 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.989 Fit side-chains REVERT: A 100 MET cc_start: 0.7234 (mmp) cc_final: 0.6940 (mmm) REVERT: A 251 ASP cc_start: 0.7349 (t0) cc_final: 0.7114 (m-30) REVERT: A 517 LYS cc_start: 0.7255 (mmpt) cc_final: 0.6966 (mppt) REVERT: A 557 ASP cc_start: 0.6234 (m-30) cc_final: 0.5898 (m-30) REVERT: A 569 ILE cc_start: 0.7843 (mm) cc_final: 0.7512 (mm) REVERT: B 70 MET cc_start: 0.4066 (ttm) cc_final: 0.3420 (ttp) REVERT: B 267 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7067 (mp) REVERT: B 428 TYR cc_start: 0.8281 (m-80) cc_final: 0.7981 (m-80) REVERT: B 495 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7932 (tm-30) outliers start: 9 outliers final: 7 residues processed: 100 average time/residue: 1.1579 time to fit residues: 124.6302 Evaluate side-chains 104 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 495 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7345 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9294 Z= 0.191 Angle : 0.493 6.611 12626 Z= 0.248 Chirality : 0.039 0.141 1488 Planarity : 0.004 0.034 1546 Dihedral : 12.829 159.434 1346 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.62 % Allowed : 13.84 % Favored : 85.54 % 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: 1.00 (0.25), residues: 1152 helix: 1.46 (0.19), residues: 782 sheet: 2.15 (0.87), residues: 34 loop : -1.39 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 465 HIS 0.002 0.000 HIS B 636 PHE 0.009 0.001 PHE B 95 TYR 0.014 0.001 TYR B 385 ARG 0.006 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.011 Fit side-chains REVERT: A 100 MET cc_start: 0.7217 (mmp) cc_final: 0.6928 (mmm) REVERT: A 251 ASP cc_start: 0.7388 (t0) cc_final: 0.7185 (m-30) REVERT: A 517 LYS cc_start: 0.7228 (mmpt) cc_final: 0.6963 (mppt) REVERT: A 557 ASP cc_start: 0.6211 (m-30) cc_final: 0.5876 (m-30) REVERT: A 569 ILE cc_start: 0.7797 (mm) cc_final: 0.7571 (mm) REVERT: B 70 MET cc_start: 0.4070 (ttm) cc_final: 0.3532 (ttp) REVERT: B 172 GLU cc_start: 0.7436 (tp30) cc_final: 0.7231 (tp30) REVERT: B 267 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7079 (mp) REVERT: B 428 TYR cc_start: 0.8262 (m-80) cc_final: 0.8021 (m-80) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 1.1471 time to fit residues: 122.2559 Evaluate side-chains 97 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7343 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9294 Z= 0.183 Angle : 0.498 6.588 12626 Z= 0.250 Chirality : 0.039 0.141 1488 Planarity : 0.004 0.034 1546 Dihedral : 12.750 159.371 1346 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.52 % Allowed : 13.95 % Favored : 85.54 % 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: 1.03 (0.25), residues: 1152 helix: 1.45 (0.19), residues: 784 sheet: 2.20 (0.87), residues: 34 loop : -1.35 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 465 HIS 0.002 0.000 HIS B 636 PHE 0.009 0.001 PHE B 95 TYR 0.015 0.001 TYR B 385 ARG 0.007 0.000 ARG B 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.952 Fit side-chains REVERT: A 100 MET cc_start: 0.7207 (mmp) cc_final: 0.6931 (mmm) REVERT: A 251 ASP cc_start: 0.7391 (t0) cc_final: 0.7183 (m-30) REVERT: A 267 ILE cc_start: 0.7462 (mp) cc_final: 0.7221 (mt) REVERT: A 517 LYS cc_start: 0.7088 (mmpt) cc_final: 0.6867 (mppt) REVERT: A 557 ASP cc_start: 0.6223 (m-30) cc_final: 0.5895 (m-30) REVERT: A 569 ILE cc_start: 0.7803 (mm) cc_final: 0.7575 (mm) REVERT: B 70 MET cc_start: 0.4074 (ttm) cc_final: 0.3200 (ttp) REVERT: B 267 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7080 (mp) REVERT: B 428 TYR cc_start: 0.8261 (m-80) cc_final: 0.8022 (m-80) outliers start: 5 outliers final: 4 residues processed: 94 average time/residue: 1.1740 time to fit residues: 118.7615 Evaluate side-chains 96 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 93 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.172291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133606 restraints weight = 16553.960| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.74 r_work: 0.3505 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9294 Z= 0.145 Angle : 0.475 6.493 12626 Z= 0.238 Chirality : 0.038 0.142 1488 Planarity : 0.004 0.033 1546 Dihedral : 12.330 155.890 1346 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.31 % Allowed : 14.36 % Favored : 85.33 % 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: 1.21 (0.25), residues: 1152 helix: 1.60 (0.19), residues: 784 sheet: 2.23 (0.88), residues: 34 loop : -1.31 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 465 HIS 0.001 0.000 HIS A 329 PHE 0.007 0.001 PHE B 95 TYR 0.016 0.001 TYR A 385 ARG 0.008 0.000 ARG B 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.41 seconds wall clock time: 53 minutes 41.54 seconds (3221.54 seconds total)