Starting phenix.real_space_refine on Thu Feb 15 11:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai7_11793/02_2024/7ai7_11793_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai7_11793/02_2024/7ai7_11793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai7_11793/02_2024/7ai7_11793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai7_11793/02_2024/7ai7_11793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai7_11793/02_2024/7ai7_11793_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai7_11793/02_2024/7ai7_11793_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 31 5.49 5 S 53 5.16 5 C 7492 2.51 5 N 2160 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 511": "OD1" <-> "OD2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 740": "OE1" <-> "OE2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B ARG 788": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12085 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6218 Classifications: {'peptide': 791} Link IDs: {'PTRANS': 35, 'TRANS': 755} Chain: "B" Number of atoms: 5261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5261 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain: "C" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "D" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.33, per 1000 atoms: 0.61 Number of scatterers: 12085 At special positions: 0 Unit cell: (112.32, 114.66, 120.51, 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 53 16.00 P 31 15.00 O 2349 8.00 N 2160 7.00 C 7492 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: 5.40 Conformation dependent library (CDL) restraints added in 2.5 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 11 sheets defined 47.0% alpha, 11.2% beta 8 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.577A pdb=" N GLN A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.690A pdb=" N GLN A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.608A pdb=" N LYS A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 231 through 248 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 301 through 311 removed outlier: 4.226A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 345 removed outlier: 4.728A pdb=" N ASP A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLY A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 3.846A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 362 through 384 Proline residue: A 376 - end of helix removed outlier: 3.714A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 431 through 458 removed outlier: 3.531A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 504 through 564 removed outlier: 3.593A pdb=" N GLU A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Proline residue: A 537 - end of helix removed outlier: 4.847A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.674A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 635 removed outlier: 3.599A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 removed outlier: 3.506A pdb=" N GLU A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 Processing helix chain 'A' and resid 732 through 738 Proline residue: A 736 - end of helix Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 783 through 797 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.624A pdb=" N ARG B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 247 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.793A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 345 removed outlier: 4.662A pdb=" N ASP B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLY B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Proline residue: B 340 - end of helix removed outlier: 3.869A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 362 through 384 Proline residue: B 376 - end of helix removed outlier: 3.718A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 431 through 458 removed outlier: 3.680A pdb=" N GLU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 504 through 564 removed outlier: 3.793A pdb=" N PHE B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Proline residue: B 537 - end of helix removed outlier: 4.823A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 3.544A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 636 removed outlier: 4.022A pdb=" N THR B 627 " --> pdb=" O TYR B 623 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 701 through 717 Processing helix chain 'B' and resid 732 through 738 Proline residue: B 736 - end of helix Processing helix chain 'B' and resid 772 through 779 Processing helix chain 'B' and resid 783 through 797 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.502A pdb=" N TYR A 31 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN A 95 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 112 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.848A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 177 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.501A pdb=" N GLN A 493 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 502 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG A 491 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 601 through 604 Processing sheet with id= E, first strand: chain 'A' and resid 609 through 612 removed outlier: 3.789A pdb=" N GLN A 763 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 653 through 657 removed outlier: 6.717A pdb=" N LEU A 689 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ARG A 656 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU A 691 " --> pdb=" O ARG A 656 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 722 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N MET A 692 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 724 " --> pdb=" O MET A 692 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.849A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU B 177 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 181 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLN B 138 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 464 through 468 removed outlier: 3.537A pdb=" N GLN B 493 " --> pdb=" O ARG B 500 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 502 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 601 through 604 Processing sheet with id= J, first strand: chain 'B' and resid 610 through 612 removed outlier: 7.531A pdb=" N ALA B 743 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 763 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 653 through 656 removed outlier: 6.545A pdb=" N LEU B 689 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ARG B 656 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 691 " --> pdb=" O ARG B 656 " (cutoff:3.500A) No H-bonds generated for sheet with id= K 514 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.29: 1984 1.29 - 1.44: 3218 1.44 - 1.59: 6995 1.59 - 1.74: 53 1.74 - 1.89: 95 Bond restraints: 12345 Sorted by residual: bond pdb=" C PRO A 314 " pdb=" O PRO A 314 " ideal model delta sigma weight residual 1.235 1.144 0.092 1.30e-02 5.92e+03 4.96e+01 bond pdb=" C VAL A 745 " pdb=" O VAL A 745 " ideal model delta sigma weight residual 1.235 1.305 -0.070 1.02e-02 9.61e+03 4.71e+01 bond pdb=" C LEU A 307 " pdb=" O LEU A 307 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.29e-02 6.01e+03 4.05e+01 bond pdb=" C LYS A 464 " pdb=" O LYS A 464 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.14e-02 7.69e+03 3.72e+01 bond pdb=" C SER A 770 " pdb=" O SER A 770 " ideal model delta sigma weight residual 1.236 1.310 -0.074 1.22e-02 6.72e+03 3.69e+01 ... (remaining 12340 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.33: 384 105.33 - 112.71: 5864 112.71 - 120.09: 6029 120.09 - 127.47: 4427 127.47 - 134.84: 129 Bond angle restraints: 16833 Sorted by residual: angle pdb=" N ILE A 636 " pdb=" CA ILE A 636 " pdb=" C ILE A 636 " ideal model delta sigma weight residual 112.29 105.02 7.27 9.40e-01 1.13e+00 5.99e+01 angle pdb=" N GLU A 451 " pdb=" CA GLU A 451 " pdb=" C GLU A 451 " ideal model delta sigma weight residual 112.23 104.14 8.09 1.26e+00 6.30e-01 4.12e+01 angle pdb=" CA SER B 478 " pdb=" C SER B 478 " pdb=" O SER B 478 " ideal model delta sigma weight residual 121.56 114.62 6.94 1.09e+00 8.42e-01 4.05e+01 angle pdb=" N CYS A 297 " pdb=" CA CYS A 297 " pdb=" C CYS A 297 " ideal model delta sigma weight residual 112.92 105.17 7.75 1.23e+00 6.61e-01 3.97e+01 angle pdb=" CA GLY A 658 " pdb=" C GLY A 658 " pdb=" O GLY A 658 " ideal model delta sigma weight residual 122.29 117.19 5.10 8.10e-01 1.52e+00 3.96e+01 ... (remaining 16828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 7108 33.79 - 67.58: 357 67.58 - 101.38: 17 101.38 - 135.17: 2 135.17 - 168.96: 2 Dihedral angle restraints: 7486 sinusoidal: 3250 harmonic: 4236 Sorted by residual: dihedral pdb=" C5' ADP B1801 " pdb=" O5' ADP B1801 " pdb=" PA ADP B1801 " pdb=" O2A ADP B1801 " ideal model delta sinusoidal sigma weight residual -60.00 108.97 -168.96 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP A1801 " pdb=" O3A ADP A1801 " pdb=" PA ADP A1801 " pdb=" PB ADP A1801 " ideal model delta sinusoidal sigma weight residual -60.00 94.44 -154.44 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O1B ADP B1801 " pdb=" O3A ADP B1801 " pdb=" PB ADP B1801 " pdb=" PA ADP B1801 " ideal model delta sinusoidal sigma weight residual -60.00 -179.29 119.29 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 7483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 973 0.070 - 0.140: 657 0.140 - 0.211: 212 0.211 - 0.281: 45 0.281 - 0.351: 25 Chirality restraints: 1912 Sorted by residual: chirality pdb=" CA ILE B 503 " pdb=" N ILE B 503 " pdb=" C ILE B 503 " pdb=" CB ILE B 503 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LEU A 724 " pdb=" N LEU A 724 " pdb=" C LEU A 724 " pdb=" CB LEU A 724 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB THR A 335 " pdb=" CA THR A 335 " pdb=" OG1 THR A 335 " pdb=" CG2 THR A 335 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1909 not shown) Planarity restraints: 2104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 137 " 0.001 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP A 137 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 137 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 137 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 137 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP A 137 " 0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP A 137 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 137 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 137 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 179 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C LEU A 179 " 0.075 2.00e-02 2.50e+03 pdb=" O LEU A 179 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR A 180 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 149 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ASP A 149 " 0.074 2.00e-02 2.50e+03 pdb=" O ASP A 149 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE A 150 " -0.026 2.00e-02 2.50e+03 ... (remaining 2101 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 4238 2.92 - 3.42: 12198 3.42 - 3.91: 21488 3.91 - 4.41: 24014 4.41 - 4.90: 38903 Nonbonded interactions: 100841 Sorted by model distance: nonbonded pdb=" O5' DG D 10 " pdb=" O4' DG D 10 " model vdw 2.425 2.432 nonbonded pdb=" OD1 ASP A 207 " pdb=" N THR A 208 " model vdw 2.427 2.520 nonbonded pdb=" O GLY A 442 " pdb=" OD1 ASP A 445 " model vdw 2.436 3.040 nonbonded pdb=" O5' DA C 44 " pdb=" O4' DA C 44 " model vdw 2.438 2.432 nonbonded pdb=" N TYR A 180 " pdb=" O TYR A 180 " model vdw 2.448 2.496 ... (remaining 100836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 1.820 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 40.180 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.015 0.109 12345 Z= 0.986 Angle : 1.978 12.301 16833 Z= 1.446 Chirality : 0.101 0.351 1912 Planarity : 0.008 0.043 2104 Dihedral : 18.071 168.962 4754 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.99 % Allowed : 9.83 % Favored : 89.17 % Cbeta Deviations : 0.15 % 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: -2.46 (0.19), residues: 1456 helix: -1.03 (0.17), residues: 658 sheet: -2.08 (0.34), residues: 197 loop : -2.02 (0.21), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.007 TRP A 137 HIS 0.025 0.005 HIS A 752 PHE 0.054 0.006 PHE A 204 TYR 0.039 0.005 TYR A 623 ARG 0.036 0.002 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ASN cc_start: 0.7444 (t0) cc_final: 0.6784 (t0) REVERT: A 609 MET cc_start: 0.7896 (ttm) cc_final: 0.7662 (ttm) REVERT: B 184 PHE cc_start: 0.5075 (t80) cc_final: 0.4695 (t80) REVERT: B 347 ASP cc_start: 0.7794 (p0) cc_final: 0.7109 (p0) REVERT: B 430 ASN cc_start: 0.8473 (t0) cc_final: 0.7523 (t0) REVERT: B 694 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6593 (tp30) outliers start: 12 outliers final: 0 residues processed: 183 average time/residue: 0.3029 time to fit residues: 75.2151 Evaluate side-chains 101 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 694 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 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 276 ASN A 493 GLN A 526 GLN A 557 ASN A 760 HIS B 216 GLN B 391 GLN B 476 GLN B 526 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12345 Z= 0.208 Angle : 0.655 10.028 16833 Z= 0.335 Chirality : 0.042 0.183 1912 Planarity : 0.004 0.046 2104 Dihedral : 16.604 167.134 1943 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.98 % Allowed : 13.97 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1456 helix: 0.74 (0.18), residues: 693 sheet: -1.33 (0.38), residues: 176 loop : -1.34 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 137 HIS 0.004 0.001 HIS B 760 PHE 0.020 0.002 PHE B 467 TYR 0.032 0.002 TYR A 509 ARG 0.009 0.001 ARG B 449 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.9002 (tpp) cc_final: 0.8765 (tpp) REVERT: A 430 ASN cc_start: 0.7341 (t0) cc_final: 0.6941 (t0) REVERT: A 609 MET cc_start: 0.7934 (ttm) cc_final: 0.7725 (ttm) REVERT: A 775 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8023 (p) REVERT: B 166 MET cc_start: 0.8072 (mmm) cc_final: 0.7686 (mmm) REVERT: B 184 PHE cc_start: 0.5968 (t80) cc_final: 0.5221 (t80) REVERT: B 347 ASP cc_start: 0.8012 (p0) cc_final: 0.7384 (p0) REVERT: B 430 ASN cc_start: 0.8561 (t0) cc_final: 0.8160 (t0) outliers start: 24 outliers final: 8 residues processed: 126 average time/residue: 0.2858 time to fit residues: 50.9752 Evaluate side-chains 94 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.0060 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 493 GLN A 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12345 Z= 0.183 Angle : 0.615 11.818 16833 Z= 0.306 Chirality : 0.040 0.173 1912 Planarity : 0.004 0.048 2104 Dihedral : 16.157 159.671 1940 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.65 % Allowed : 15.37 % Favored : 82.98 % 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: 0.05 (0.21), residues: 1456 helix: 1.23 (0.19), residues: 695 sheet: -0.93 (0.41), residues: 151 loop : -1.10 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 709 HIS 0.005 0.001 HIS B 760 PHE 0.012 0.001 PHE B 467 TYR 0.033 0.002 TYR B 509 ARG 0.007 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8979 (tpp) cc_final: 0.8717 (tpp) REVERT: A 430 ASN cc_start: 0.7177 (t0) cc_final: 0.6614 (t0) REVERT: B 166 MET cc_start: 0.8276 (mmm) cc_final: 0.7820 (mmm) REVERT: B 347 ASP cc_start: 0.8011 (p0) cc_final: 0.7421 (p0) REVERT: B 430 ASN cc_start: 0.8523 (t0) cc_final: 0.7933 (t0) REVERT: B 432 GLU cc_start: 0.8810 (mp0) cc_final: 0.8488 (mp0) outliers start: 20 outliers final: 9 residues processed: 106 average time/residue: 0.2857 time to fit residues: 42.4530 Evaluate side-chains 87 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 557 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12345 Z= 0.310 Angle : 0.669 9.593 16833 Z= 0.335 Chirality : 0.042 0.167 1912 Planarity : 0.005 0.050 2104 Dihedral : 16.025 149.667 1940 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.40 % Allowed : 16.78 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1456 helix: 1.12 (0.19), residues: 699 sheet: -0.63 (0.39), residues: 178 loop : -1.23 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.010 0.001 HIS B 760 PHE 0.008 0.002 PHE A 40 TYR 0.026 0.002 TYR A 635 ARG 0.013 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 77 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8951 (tpp) cc_final: 0.8737 (tpp) REVERT: B 166 MET cc_start: 0.8546 (mmm) cc_final: 0.8025 (mmm) REVERT: B 347 ASP cc_start: 0.8194 (p0) cc_final: 0.7628 (p0) REVERT: B 430 ASN cc_start: 0.8575 (t0) cc_final: 0.8158 (t0) REVERT: B 432 GLU cc_start: 0.8829 (mp0) cc_final: 0.8523 (mp0) REVERT: B 792 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.8990 (tppt) outliers start: 29 outliers final: 13 residues processed: 100 average time/residue: 0.2710 time to fit residues: 39.6738 Evaluate side-chains 85 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12345 Z= 0.189 Angle : 0.607 10.162 16833 Z= 0.301 Chirality : 0.041 0.192 1912 Planarity : 0.004 0.049 2104 Dihedral : 15.765 142.268 1940 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.98 % Allowed : 17.52 % Favored : 80.50 % 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: 0.12 (0.22), residues: 1456 helix: 1.31 (0.20), residues: 698 sheet: -0.70 (0.37), residues: 199 loop : -1.17 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.004 0.001 HIS B 760 PHE 0.014 0.001 PHE A 184 TYR 0.024 0.001 TYR B 509 ARG 0.005 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.1727 (m-80) cc_final: -0.0101 (m-80) REVERT: A 187 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7761 (mmt) REVERT: B 166 MET cc_start: 0.8588 (mmm) cc_final: 0.8005 (mmm) REVERT: B 347 ASP cc_start: 0.8155 (p0) cc_final: 0.7541 (p0) REVERT: B 430 ASN cc_start: 0.8526 (t0) cc_final: 0.8098 (t0) REVERT: B 432 GLU cc_start: 0.8798 (mp0) cc_final: 0.8462 (mp0) outliers start: 24 outliers final: 11 residues processed: 94 average time/residue: 0.2396 time to fit residues: 33.5755 Evaluate side-chains 87 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12345 Z= 0.271 Angle : 0.649 10.837 16833 Z= 0.324 Chirality : 0.042 0.162 1912 Planarity : 0.004 0.050 2104 Dihedral : 15.675 135.643 1940 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.48 % Allowed : 18.10 % Favored : 79.42 % 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: 0.01 (0.21), residues: 1456 helix: 1.19 (0.19), residues: 701 sheet: -0.69 (0.36), residues: 206 loop : -1.24 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 137 HIS 0.008 0.001 HIS B 760 PHE 0.012 0.002 PHE A 670 TYR 0.022 0.002 TYR A 473 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 75 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.1685 (m-80) cc_final: 0.0717 (m-10) REVERT: A 187 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7877 (mmt) REVERT: B 166 MET cc_start: 0.8641 (mmm) cc_final: 0.8015 (mmm) REVERT: B 347 ASP cc_start: 0.8265 (p0) cc_final: 0.7673 (p0) REVERT: B 430 ASN cc_start: 0.8614 (t0) cc_final: 0.8108 (t0) REVERT: B 432 GLU cc_start: 0.8778 (mp0) cc_final: 0.8427 (mp0) REVERT: B 792 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8989 (tppt) outliers start: 30 outliers final: 16 residues processed: 98 average time/residue: 0.2676 time to fit residues: 38.1097 Evaluate side-chains 90 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12345 Z= 0.319 Angle : 0.695 12.820 16833 Z= 0.343 Chirality : 0.043 0.169 1912 Planarity : 0.005 0.050 2104 Dihedral : 15.685 128.436 1940 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.81 % Allowed : 18.76 % Favored : 78.43 % 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: -0.14 (0.21), residues: 1456 helix: 1.04 (0.19), residues: 703 sheet: -0.67 (0.36), residues: 201 loop : -1.30 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 709 HIS 0.008 0.001 HIS B 760 PHE 0.017 0.002 PHE B 143 TYR 0.020 0.002 TYR B 635 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.1603 (m-80) cc_final: 0.0916 (m-10) REVERT: A 187 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7895 (mmt) REVERT: B 166 MET cc_start: 0.8711 (mmm) cc_final: 0.8080 (mmm) REVERT: B 347 ASP cc_start: 0.8350 (p0) cc_final: 0.7821 (p0) REVERT: B 430 ASN cc_start: 0.8606 (t0) cc_final: 0.8104 (t0) REVERT: B 432 GLU cc_start: 0.8777 (mp0) cc_final: 0.8439 (mp0) REVERT: B 624 MET cc_start: 0.8163 (mmm) cc_final: 0.7911 (mmm) REVERT: B 792 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9001 (tppt) outliers start: 34 outliers final: 21 residues processed: 97 average time/residue: 0.2621 time to fit residues: 37.5690 Evaluate side-chains 93 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12345 Z= 0.185 Angle : 0.623 13.234 16833 Z= 0.303 Chirality : 0.040 0.178 1912 Planarity : 0.004 0.049 2104 Dihedral : 15.527 120.691 1940 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 19.92 % Favored : 78.60 % 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: 0.16 (0.22), residues: 1456 helix: 1.36 (0.20), residues: 699 sheet: -0.50 (0.37), residues: 199 loop : -1.27 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 202 HIS 0.004 0.001 HIS B 760 PHE 0.024 0.001 PHE B 143 TYR 0.019 0.001 TYR B 509 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.1991 (m-80) cc_final: 0.1481 (m-10) REVERT: A 187 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7977 (mmt) REVERT: B 166 MET cc_start: 0.8753 (mmm) cc_final: 0.8209 (mmm) REVERT: B 347 ASP cc_start: 0.8240 (p0) cc_final: 0.7641 (p0) REVERT: B 430 ASN cc_start: 0.8556 (t0) cc_final: 0.8092 (t0) REVERT: B 432 GLU cc_start: 0.8780 (mp0) cc_final: 0.8450 (mp0) REVERT: B 624 MET cc_start: 0.8374 (mmm) cc_final: 0.8132 (mmm) REVERT: B 792 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9024 (tptt) outliers start: 18 outliers final: 13 residues processed: 88 average time/residue: 0.2682 time to fit residues: 34.6627 Evaluate side-chains 86 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 135 optimal weight: 0.0870 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 493 GLN B 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12345 Z= 0.168 Angle : 0.614 13.404 16833 Z= 0.296 Chirality : 0.040 0.175 1912 Planarity : 0.004 0.049 2104 Dihedral : 15.327 115.272 1940 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.57 % Allowed : 20.00 % Favored : 78.43 % 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: 0.32 (0.22), residues: 1456 helix: 1.51 (0.20), residues: 698 sheet: -0.49 (0.37), residues: 194 loop : -1.17 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.000 HIS B 760 PHE 0.023 0.001 PHE B 143 TYR 0.019 0.001 TYR B 509 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7065 (mtm) cc_final: 0.6755 (mpp) REVERT: A 671 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: B 166 MET cc_start: 0.8742 (mmm) cc_final: 0.8173 (mmm) REVERT: B 347 ASP cc_start: 0.8140 (p0) cc_final: 0.7502 (p0) REVERT: B 430 ASN cc_start: 0.8546 (t0) cc_final: 0.8109 (t0) REVERT: B 432 GLU cc_start: 0.8738 (mp0) cc_final: 0.8412 (mp0) REVERT: B 624 MET cc_start: 0.8340 (mmm) cc_final: 0.8077 (mmm) REVERT: B 792 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9064 (tptt) outliers start: 19 outliers final: 11 residues processed: 89 average time/residue: 0.2632 time to fit residues: 34.3542 Evaluate side-chains 85 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 146 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12345 Z= 0.278 Angle : 0.666 13.806 16833 Z= 0.324 Chirality : 0.041 0.189 1912 Planarity : 0.004 0.048 2104 Dihedral : 15.499 121.544 1940 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.57 % Allowed : 20.00 % Favored : 78.43 % 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: 0.22 (0.22), residues: 1456 helix: 1.41 (0.20), residues: 697 sheet: -0.48 (0.37), residues: 199 loop : -1.22 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 709 HIS 0.007 0.001 HIS B 760 PHE 0.022 0.002 PHE B 143 TYR 0.018 0.002 TYR A 243 ARG 0.004 0.000 ARG A 790 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7220 (mtm) cc_final: 0.6966 (mpp) REVERT: B 166 MET cc_start: 0.8765 (mmm) cc_final: 0.8195 (mmm) REVERT: B 347 ASP cc_start: 0.8320 (p0) cc_final: 0.7756 (p0) REVERT: B 430 ASN cc_start: 0.8562 (t0) cc_final: 0.8125 (t0) REVERT: B 432 GLU cc_start: 0.8744 (mp0) cc_final: 0.8425 (mp0) REVERT: B 624 MET cc_start: 0.8334 (mmm) cc_final: 0.8060 (mmm) outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.2591 time to fit residues: 31.4105 Evaluate side-chains 85 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 692 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.079637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059046 restraints weight = 48087.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059561 restraints weight = 30992.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059828 restraints weight = 21399.920| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12345 Z= 0.206 Angle : 0.627 13.914 16833 Z= 0.303 Chirality : 0.040 0.157 1912 Planarity : 0.004 0.049 2104 Dihedral : 15.465 120.128 1940 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.49 % Allowed : 19.83 % Favored : 78.68 % 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: 0.24 (0.22), residues: 1456 helix: 1.49 (0.20), residues: 689 sheet: -0.53 (0.36), residues: 206 loop : -1.25 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.005 0.001 HIS B 760 PHE 0.023 0.001 PHE B 143 TYR 0.017 0.002 TYR B 509 ARG 0.003 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.35 seconds wall clock time: 38 minutes 42.02 seconds (2322.02 seconds total)