Starting phenix.real_space_refine on Thu Mar 14 16:21:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/03_2024/7pr1_13607_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/03_2024/7pr1_13607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/03_2024/7pr1_13607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/03_2024/7pr1_13607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/03_2024/7pr1_13607_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/03_2024/7pr1_13607_updated.pdb" } resolution = 2.81 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= 0.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 5888 2.51 5 N 1604 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 485": "NH1" <-> "NH2" Residue "B PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 590": "NH1" <-> "NH2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 602": "OD1" <-> "OD2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B GLU 663": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9222 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4579 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 17, 'TRANS': 569} Chain: "B" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4579 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 17, 'TRANS': 569} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.32, per 1000 atoms: 0.58 Number of scatterers: 9222 At special positions: 0 Unit cell: (74.048, 90.688, 139.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 6 15.00 Mg 2 11.99 O 1696 8.00 N 1604 7.00 C 5888 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: 3.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 65.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 93 through 103 removed outlier: 4.182A pdb=" N ARG A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 148 Proline residue: A 134 - end of helix removed outlier: 3.676A pdb=" N ASP A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 204 removed outlier: 4.152A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 216 through 239 removed outlier: 3.925A pdb=" N THR A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 258 Processing helix chain 'A' and resid 261 through 308 removed outlier: 5.180A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 319 through 371 removed outlier: 3.573A pdb=" N PHE A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 399 Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 401 through 419 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 531 through 538 removed outlier: 4.488A pdb=" N GLY A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 580 through 594 Processing helix chain 'A' and resid 610 through 627 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 661 through 667 Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'B' and resid 93 through 103 removed outlier: 4.183A pdb=" N ARG B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 148 Proline residue: B 134 - end of helix removed outlier: 3.677A pdb=" N ASP B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 204 removed outlier: 4.152A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 216 through 239 removed outlier: 3.925A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 261 through 308 removed outlier: 5.179A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 319 through 371 removed outlier: 3.574A pdb=" N PHE B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 399 Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 401 through 419 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 531 through 538 removed outlier: 4.488A pdb=" N GLY B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 610 through 627 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 661 through 667 Processing helix chain 'B' and resid 670 through 676 Processing sheet with id= A, first strand: chain 'A' and resid 441 through 444 Processing sheet with id= B, first strand: chain 'A' and resid 654 through 657 removed outlier: 7.185A pdb=" N VAL A 649 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 631 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 472 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE A 633 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY A 474 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 441 through 444 Processing sheet with id= D, first strand: chain 'B' and resid 654 through 657 removed outlier: 7.185A pdb=" N VAL B 649 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA B 631 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B 472 " --> pdb=" O ALA B 631 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE B 633 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLY B 474 " --> pdb=" O PHE B 633 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1746 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: 2.62 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2905 1.34 - 1.45: 1236 1.45 - 1.57: 5197 1.57 - 1.69: 10 1.69 - 1.80: 48 Bond restraints: 9396 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.98e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.96e+01 bond pdb=" C5 ATP B 801 " pdb=" N7 ATP B 801 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.33e+01 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.81: 161 105.81 - 113.25: 5270 113.25 - 120.68: 4391 120.68 - 128.12: 2862 128.12 - 135.56: 76 Bond angle restraints: 12760 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 117.65 22.22 1.00e+00 1.00e+00 4.94e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 120.00 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 120.02 16.81 1.00e+00 1.00e+00 2.82e+02 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.53 8.27 1.00e+00 1.00e+00 6.84e+01 ... (remaining 12755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5105 17.30 - 34.60: 438 34.60 - 51.90: 69 51.90 - 69.19: 16 69.19 - 86.49: 22 Dihedral angle restraints: 5650 sinusoidal: 2248 harmonic: 3402 Sorted by residual: dihedral pdb=" CA ARG B 489 " pdb=" C ARG B 489 " pdb=" N SER B 490 " pdb=" CA SER B 490 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A 489 " pdb=" C ARG A 489 " pdb=" N SER A 490 " pdb=" CA SER A 490 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" N GLU A 412 " pdb=" C GLU A 412 " pdb=" CA GLU A 412 " pdb=" CB GLU A 412 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1159 0.057 - 0.113: 278 0.113 - 0.170: 39 0.170 - 0.226: 6 0.226 - 0.283: 4 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CB ILE A 171 " pdb=" CA ILE A 171 " pdb=" CG1 ILE A 171 " pdb=" CG2 ILE A 171 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 171 " pdb=" CA ILE B 171 " pdb=" CG1 ILE B 171 " pdb=" CG2 ILE B 171 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA GLU A 412 " pdb=" N GLU A 412 " pdb=" C GLU A 412 " pdb=" CB GLU A 412 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1483 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.053 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO B 428 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 427 " 0.053 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO A 428 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 596 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 597 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " -0.021 5.00e-02 4.00e+02 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 110 2.62 - 3.19: 8470 3.19 - 3.76: 15390 3.76 - 4.33: 20626 4.33 - 4.90: 34328 Nonbonded interactions: 78924 Sorted by model distance: nonbonded pdb=" NE2 GLN B 522 " pdb="MG MG B 802 " model vdw 2.053 2.250 nonbonded pdb=" OD2 ASP A 207 " pdb=" OG1 THR A 423 " model vdw 2.215 2.440 nonbonded pdb=" OD2 ASP B 207 " pdb=" OG1 THR B 423 " model vdw 2.215 2.440 nonbonded pdb=" OG SER B 306 " pdb=" OE1 GLU B 322 " model vdw 2.229 2.440 nonbonded pdb=" OG SER A 306 " pdb=" OE1 GLU A 322 " model vdw 2.229 2.440 ... (remaining 78919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.010 Extract box with map and model: 7.210 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.320 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 0.082 9396 Z= 0.435 Angle : 0.951 22.218 12760 Z= 0.607 Chirality : 0.051 0.283 1486 Planarity : 0.005 0.078 1608 Dihedral : 14.353 86.493 3458 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.18 (0.23), residues: 1170 helix: 0.36 (0.17), residues: 788 sheet: -1.18 (0.55), residues: 66 loop : -0.80 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 675 HIS 0.007 0.001 HIS A 132 PHE 0.013 0.002 PHE A 259 TYR 0.014 0.002 TYR A 274 ARG 0.009 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.093 Fit side-chains REVERT: A 190 LYS cc_start: 0.7544 (mttm) cc_final: 0.7213 (mtpm) REVERT: A 425 ARG cc_start: 0.8006 (ptp-110) cc_final: 0.7737 (ptp90) REVERT: B 190 LYS cc_start: 0.7544 (mttm) cc_final: 0.7204 (mtpm) REVERT: B 425 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7747 (ptp90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 1.6295 time to fit residues: 197.9664 Evaluate side-chains 75 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.1980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 552 GLN B 495 GLN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9396 Z= 0.217 Angle : 0.574 12.104 12760 Z= 0.290 Chirality : 0.042 0.152 1486 Planarity : 0.003 0.045 1608 Dihedral : 6.507 59.620 1348 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.23 % Allowed : 10.80 % Favored : 87.96 % 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: 0.71 (0.24), residues: 1170 helix: 1.06 (0.18), residues: 786 sheet: -1.00 (0.58), residues: 66 loop : -0.49 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 675 HIS 0.003 0.001 HIS A 557 PHE 0.010 0.001 PHE B 601 TYR 0.015 0.001 TYR A 642 ARG 0.003 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.066 Fit side-chains REVERT: A 190 LYS cc_start: 0.7436 (mttm) cc_final: 0.7137 (mtpm) REVERT: A 248 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.8022 (mp) REVERT: A 289 ARG cc_start: 0.6884 (ttp80) cc_final: 0.6611 (ttp-110) REVERT: A 425 ARG cc_start: 0.7987 (ptp-110) cc_final: 0.7630 (ptp90) REVERT: A 673 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: B 190 LYS cc_start: 0.7424 (mttm) cc_final: 0.7119 (mtpm) REVERT: B 248 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8018 (mp) REVERT: B 289 ARG cc_start: 0.6914 (ttp80) cc_final: 0.6629 (ttp-110) REVERT: B 425 ARG cc_start: 0.7985 (ptp-110) cc_final: 0.7591 (ptp90) REVERT: B 605 THR cc_start: 0.8514 (p) cc_final: 0.8214 (p) REVERT: B 662 ARG cc_start: 0.7196 (ttp80) cc_final: 0.6837 (ttp-110) REVERT: B 673 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7774 (mt-10) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 1.2476 time to fit residues: 120.5347 Evaluate side-chains 84 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 0.0020 chunk 93 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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: 0.7823 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9396 Z= 0.182 Angle : 0.542 10.591 12760 Z= 0.273 Chirality : 0.041 0.146 1486 Planarity : 0.003 0.035 1608 Dihedral : 6.137 58.968 1348 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.57 % Allowed : 11.73 % Favored : 85.70 % 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: 1.16 (0.24), residues: 1170 helix: 1.45 (0.18), residues: 786 sheet: -1.07 (0.58), residues: 66 loop : -0.40 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.005 0.001 HIS B 557 PHE 0.008 0.001 PHE A 601 TYR 0.016 0.001 TYR A 642 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.7433 (mttm) cc_final: 0.7129 (mtpm) REVERT: A 248 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 289 ARG cc_start: 0.6791 (ttp80) cc_final: 0.6589 (ttp-110) REVERT: A 425 ARG cc_start: 0.8060 (ptp-110) cc_final: 0.7682 (ptp90) REVERT: A 515 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7718 (mttt) REVERT: B 190 LYS cc_start: 0.7422 (mttm) cc_final: 0.7163 (mtpt) REVERT: B 248 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7945 (mp) REVERT: B 289 ARG cc_start: 0.6815 (ttp80) cc_final: 0.6593 (ttp-110) REVERT: B 425 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7696 (ptp90) outliers start: 25 outliers final: 4 residues processed: 103 average time/residue: 1.2554 time to fit residues: 138.4641 Evaluate side-chains 84 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9396 Z= 0.182 Angle : 0.538 12.417 12760 Z= 0.268 Chirality : 0.040 0.158 1486 Planarity : 0.003 0.052 1608 Dihedral : 5.987 59.660 1348 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.37 % Allowed : 13.17 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1170 helix: 1.73 (0.18), residues: 786 sheet: -1.10 (0.57), residues: 66 loop : -0.34 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 675 HIS 0.002 0.001 HIS B 661 PHE 0.008 0.001 PHE B 601 TYR 0.017 0.001 TYR A 642 ARG 0.007 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.7435 (mttm) cc_final: 0.7180 (mtpt) REVERT: A 289 ARG cc_start: 0.6690 (ttp80) cc_final: 0.6482 (ttp-110) REVERT: A 515 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7708 (mttt) REVERT: B 190 LYS cc_start: 0.7413 (mttm) cc_final: 0.7147 (mtpt) REVERT: B 289 ARG cc_start: 0.6711 (ttp80) cc_final: 0.6496 (ttp-110) REVERT: B 425 ARG cc_start: 0.8012 (ptp-110) cc_final: 0.7554 (ptp90) REVERT: B 515 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7729 (mttt) REVERT: B 605 THR cc_start: 0.8508 (p) cc_final: 0.8218 (p) outliers start: 23 outliers final: 8 residues processed: 98 average time/residue: 1.1626 time to fit residues: 122.5924 Evaluate side-chains 85 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 614 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9396 Z= 0.200 Angle : 0.539 11.024 12760 Z= 0.271 Chirality : 0.040 0.166 1486 Planarity : 0.003 0.027 1608 Dihedral : 6.013 58.916 1348 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.88 % Allowed : 13.79 % Favored : 83.33 % 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: 1.64 (0.24), residues: 1170 helix: 1.83 (0.18), residues: 788 sheet: -1.10 (0.56), residues: 66 loop : -0.24 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 364 HIS 0.002 0.000 HIS A 661 PHE 0.008 0.001 PHE A 601 TYR 0.018 0.001 TYR A 642 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.7442 (mttm) cc_final: 0.7181 (mtpt) REVERT: A 411 MET cc_start: 0.4939 (mmp) cc_final: 0.4692 (mmt) REVERT: A 541 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7956 (m-40) REVERT: B 190 LYS cc_start: 0.7421 (mttm) cc_final: 0.7148 (mtpt) REVERT: B 271 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5582 (mtt) REVERT: B 425 ARG cc_start: 0.8035 (ptp-110) cc_final: 0.7544 (ptp90) REVERT: B 541 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7958 (m-40) REVERT: B 605 THR cc_start: 0.8496 (p) cc_final: 0.8204 (p) outliers start: 28 outliers final: 15 residues processed: 98 average time/residue: 1.1260 time to fit residues: 119.3374 Evaluate side-chains 96 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7874 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9396 Z= 0.275 Angle : 0.583 11.264 12760 Z= 0.291 Chirality : 0.042 0.183 1486 Planarity : 0.003 0.039 1608 Dihedral : 6.318 59.585 1348 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.19 % Allowed : 14.20 % Favored : 82.61 % 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: 1.59 (0.25), residues: 1170 helix: 1.77 (0.18), residues: 788 sheet: -1.13 (0.55), residues: 66 loop : -0.18 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 675 HIS 0.002 0.001 HIS B 661 PHE 0.010 0.001 PHE A 316 TYR 0.018 0.001 TYR A 642 ARG 0.012 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 84 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5677 (mtt) REVERT: A 662 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7112 (mmm160) REVERT: B 271 MET cc_start: 0.5827 (OUTLIER) cc_final: 0.5609 (mtt) REVERT: B 605 THR cc_start: 0.8491 (p) cc_final: 0.8202 (p) outliers start: 31 outliers final: 17 residues processed: 104 average time/residue: 1.1466 time to fit residues: 128.8064 Evaluate side-chains 86 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9396 Z= 0.215 Angle : 0.562 10.962 12760 Z= 0.281 Chirality : 0.041 0.174 1486 Planarity : 0.003 0.042 1608 Dihedral : 6.082 59.410 1348 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.09 % Allowed : 15.33 % Favored : 81.58 % 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: 1.71 (0.25), residues: 1170 helix: 1.86 (0.18), residues: 788 sheet: -0.92 (0.57), residues: 66 loop : -0.16 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 364 HIS 0.001 0.000 HIS B 211 PHE 0.007 0.001 PHE A 259 TYR 0.019 0.001 TYR A 642 ARG 0.008 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 1.013 Fit side-chains REVERT: A 190 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7260 (mtpm) REVERT: B 190 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7248 (mtpm) REVERT: B 605 THR cc_start: 0.8499 (p) cc_final: 0.8207 (p) outliers start: 30 outliers final: 16 residues processed: 94 average time/residue: 1.1136 time to fit residues: 113.1792 Evaluate side-chains 89 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 97 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7837 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9396 Z= 0.211 Angle : 0.571 10.844 12760 Z= 0.284 Chirality : 0.041 0.185 1486 Planarity : 0.003 0.050 1608 Dihedral : 6.024 59.130 1348 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.37 % Allowed : 16.36 % Favored : 81.28 % 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: 1.78 (0.25), residues: 1170 helix: 1.89 (0.18), residues: 788 sheet: -0.64 (0.60), residues: 66 loop : -0.15 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 675 HIS 0.003 0.000 HIS B 661 PHE 0.007 0.001 PHE A 316 TYR 0.019 0.001 TYR A 642 ARG 0.014 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.112 Fit side-chains REVERT: A 190 LYS cc_start: 0.7575 (ttmm) cc_final: 0.7172 (mtpt) REVERT: B 190 LYS cc_start: 0.7563 (ttmm) cc_final: 0.7161 (mtpt) REVERT: B 605 THR cc_start: 0.8493 (p) cc_final: 0.8193 (p) REVERT: B 662 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7127 (mmm160) outliers start: 23 outliers final: 12 residues processed: 96 average time/residue: 1.0502 time to fit residues: 109.6497 Evaluate side-chains 89 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9396 Z= 0.261 Angle : 0.589 10.393 12760 Z= 0.295 Chirality : 0.042 0.195 1486 Planarity : 0.004 0.057 1608 Dihedral : 6.230 58.828 1348 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.75 % Allowed : 16.98 % Favored : 81.28 % 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: 1.69 (0.25), residues: 1170 helix: 1.80 (0.18), residues: 788 sheet: -0.55 (0.59), residues: 66 loop : -0.13 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.003 0.001 HIS A 661 PHE 0.009 0.001 PHE A 316 TYR 0.019 0.001 TYR B 642 ARG 0.014 0.001 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.058 Fit side-chains REVERT: A 190 LYS cc_start: 0.7580 (ttmm) cc_final: 0.7172 (mtpt) REVERT: A 662 ARG cc_start: 0.7655 (mmm160) cc_final: 0.7102 (mmm160) REVERT: B 190 LYS cc_start: 0.7568 (ttmm) cc_final: 0.7161 (mtpt) REVERT: B 605 THR cc_start: 0.8476 (p) cc_final: 0.8183 (p) REVERT: B 662 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7100 (mmm160) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 1.2514 time to fit residues: 122.3678 Evaluate side-chains 86 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN B 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9396 Z= 0.284 Angle : 0.601 12.046 12760 Z= 0.300 Chirality : 0.043 0.203 1486 Planarity : 0.004 0.069 1608 Dihedral : 6.440 59.443 1348 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.75 % Allowed : 17.39 % Favored : 80.86 % 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: 1.65 (0.25), residues: 1170 helix: 1.74 (0.18), residues: 790 sheet: -0.49 (0.60), residues: 66 loop : -0.10 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 284 HIS 0.002 0.001 HIS B 661 PHE 0.010 0.001 PHE A 316 TYR 0.020 0.001 TYR A 642 ARG 0.015 0.001 ARG A 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.065 Fit side-chains REVERT: A 190 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7172 (mtpt) REVERT: A 662 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7061 (mmm160) REVERT: B 100 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7392 (tmm) REVERT: B 190 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7145 (mtpt) REVERT: B 605 THR cc_start: 0.8456 (p) cc_final: 0.8176 (p) REVERT: B 662 ARG cc_start: 0.7677 (mmm160) cc_final: 0.7135 (mmm-85) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 1.3036 time to fit residues: 126.5913 Evaluate side-chains 85 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116925 restraints weight = 11465.770| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.29 r_work: 0.3284 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9396 Z= 0.204 Angle : 0.571 11.511 12760 Z= 0.286 Chirality : 0.041 0.188 1486 Planarity : 0.004 0.056 1608 Dihedral : 6.083 55.996 1348 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.44 % Allowed : 17.80 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1170 helix: 1.87 (0.18), residues: 788 sheet: -0.38 (0.61), residues: 66 loop : -0.15 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.002 0.000 HIS B 211 PHE 0.007 0.001 PHE A 316 TYR 0.021 0.001 TYR A 642 ARG 0.014 0.001 ARG A 662 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.90 seconds wall clock time: 54 minutes 53.90 seconds (3293.90 seconds total)