Starting phenix.real_space_refine on Fri Feb 16 16:01:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/02_2024/7l2o_23135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/02_2024/7l2o_23135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/02_2024/7l2o_23135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/02_2024/7l2o_23135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/02_2024/7l2o_23135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/02_2024/7l2o_23135_updated.pdb" } resolution = 3.64 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= 0.004 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10416 2.51 5 N 2492 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "C ASP 654": "OD1" <-> "OD2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 651": "OE1" <-> "OE2" Residue "D ASP 654": "OD1" <-> "OD2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B ASP 654": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.88, per 1000 atoms: 0.50 Number of scatterers: 15800 At special positions: 0 Unit cell: (126.5, 125.35, 108.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2796 8.00 N 2492 7.00 C 10416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.02 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.02 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.02 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: 6.50 Conformation dependent library (CDL) restraints added in 2.8 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 4 sheets defined 59.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 287 through 293 removed outlier: 3.582A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 4.357A pdb=" N LEU A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.661A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 4.597A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.692A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.995A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 689 Processing helix chain 'A' and resid 692 through 711 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 4.312A pdb=" N LEU C 421 " --> pdb=" O PRO C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.683A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 4.688A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 598 removed outlier: 3.914A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.991A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 689 Processing helix chain 'C' and resid 692 through 711 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 293 removed outlier: 3.647A pdb=" N VAL D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.963A pdb=" N LEU D 421 " --> pdb=" O PRO D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.645A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 575 removed outlier: 4.911A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.010A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 689 Processing helix chain 'D' and resid 692 through 711 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 4.136A pdb=" N LEU B 421 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 536 through 556 removed outlier: 4.040A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 543 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 removed outlier: 4.762A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 630 through 640 removed outlier: 4.048A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 692 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 745 removed outlier: 3.736A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 742 through 745 removed outlier: 6.448A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 742 through 745 removed outlier: 6.471A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 742 through 746 removed outlier: 3.680A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2214 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: 4.72 Time building geometry restraints manager: 6.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3839 1.33 - 1.45: 3619 1.45 - 1.57: 8590 1.57 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 16204 Sorted by residual: bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C PHE D 649 " pdb=" N THR D 650 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.29e-02 6.01e+03 5.97e+00 ... (remaining 16199 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.64: 231 104.64 - 112.00: 7690 112.00 - 119.35: 5773 119.35 - 126.70: 8122 126.70 - 134.05: 168 Bond angle restraints: 21984 Sorted by residual: angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER C 711 " pdb=" N PHE C 712 " pdb=" CA PHE C 712 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C SER D 711 " pdb=" N PHE D 712 " pdb=" CA PHE D 712 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 110.53 115.72 -5.19 1.32e+00 5.74e-01 1.55e+01 ... (remaining 21979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 8950 17.44 - 34.89: 675 34.89 - 52.33: 143 52.33 - 69.77: 35 69.77 - 87.22: 9 Dihedral angle restraints: 9812 sinusoidal: 4140 harmonic: 5672 Sorted by residual: dihedral pdb=" CA PHE C 712 " pdb=" C PHE C 712 " pdb=" N LEU C 713 " pdb=" CA LEU C 713 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1947 0.057 - 0.115: 468 0.115 - 0.172: 53 0.172 - 0.230: 4 0.230 - 0.287: 4 Chirality restraints: 2476 Sorted by residual: chirality pdb=" CA ASN A 652 " pdb=" N ASN A 652 " pdb=" C ASN A 652 " pdb=" CB ASN A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN B 652 " pdb=" N ASN B 652 " pdb=" C ASN B 652 " pdb=" CB ASN B 652 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASN C 652 " pdb=" N ASN C 652 " pdb=" C ASN C 652 " pdb=" CB ASN C 652 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2473 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 548 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.48e+00 pdb=" C GLY D 548 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY D 548 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP D 549 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 548 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C GLY A 548 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY A 548 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP A 549 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLY B 548 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY B 548 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP B 549 " -0.015 2.00e-02 2.50e+03 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 163 2.57 - 3.15: 13798 3.15 - 3.74: 23715 3.74 - 4.32: 32020 4.32 - 4.90: 53649 Nonbonded interactions: 123345 Sorted by model distance: nonbonded pdb=" OH TYR D 495 " pdb=" OG SER D 510 " model vdw 1.989 2.440 nonbonded pdb=" OH TYR B 495 " pdb=" OG SER B 510 " model vdw 2.022 2.440 nonbonded pdb=" O LEU A 384 " pdb=" NH2 ARG A 721 " model vdw 2.130 2.520 nonbonded pdb=" OG SER A 379 " pdb=" OD1 ASP A 745 " model vdw 2.139 2.440 nonbonded pdb=" OH TYR A 495 " pdb=" OG SER A 510 " model vdw 2.140 2.440 ... (remaining 123340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.590 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: 3.360 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 42.330 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.010 0.119 16204 Z= 0.626 Angle : 0.892 9.360 21984 Z= 0.483 Chirality : 0.050 0.287 2476 Planarity : 0.004 0.028 2692 Dihedral : 13.303 87.217 6152 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.87 % Allowed : 5.67 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 1904 helix: 0.49 (0.14), residues: 1184 sheet: -4.24 (0.61), residues: 40 loop : -2.20 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 697 HIS 0.005 0.002 HIS D 410 PHE 0.034 0.003 PHE C 649 TYR 0.016 0.003 TYR C 511 ARG 0.006 0.001 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 620 time to evaluate : 1.795 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8350 (mt) cc_final: 0.7801 (tp) REVERT: A 305 VAL cc_start: 0.7629 (t) cc_final: 0.7113 (m) REVERT: A 311 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 345 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7836 (mmtm) REVERT: A 351 TYR cc_start: 0.7701 (t80) cc_final: 0.7386 (t80) REVERT: A 388 ASP cc_start: 0.7961 (p0) cc_final: 0.7739 (p0) REVERT: A 424 ASP cc_start: 0.8766 (t70) cc_final: 0.8467 (t0) REVERT: A 425 LYS cc_start: 0.8787 (mttm) cc_final: 0.8565 (mtpp) REVERT: A 428 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8387 (mtp180) REVERT: A 432 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7621 (mtt90) REVERT: A 439 PHE cc_start: 0.8502 (t80) cc_final: 0.8259 (t80) REVERT: A 496 PHE cc_start: 0.8337 (t80) cc_final: 0.7918 (m-80) REVERT: A 503 LEU cc_start: 0.8698 (mt) cc_final: 0.8494 (mm) REVERT: A 547 MET cc_start: 0.8756 (mtm) cc_final: 0.8411 (mtp) REVERT: A 551 ASN cc_start: 0.9109 (m-40) cc_final: 0.8631 (m110) REVERT: A 568 MET cc_start: 0.8510 (mmt) cc_final: 0.8194 (mmt) REVERT: A 650 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7665 (p) REVERT: A 669 LEU cc_start: 0.9332 (mt) cc_final: 0.9046 (mt) REVERT: A 677 MET cc_start: 0.8978 (mmm) cc_final: 0.8513 (tpp) REVERT: A 697 TRP cc_start: 0.9228 (t60) cc_final: 0.8918 (t60) REVERT: A 718 LYS cc_start: 0.8202 (mttt) cc_final: 0.7468 (pttt) REVERT: C 305 VAL cc_start: 0.7783 (t) cc_final: 0.7529 (m) REVERT: C 311 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 345 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8082 (mmtm) REVERT: C 378 HIS cc_start: 0.5994 (m90) cc_final: 0.5751 (m90) REVERT: C 425 LYS cc_start: 0.8814 (mttm) cc_final: 0.8538 (mtpp) REVERT: C 439 PHE cc_start: 0.8491 (t80) cc_final: 0.8262 (t80) REVERT: C 478 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8555 (mt-10) REVERT: C 496 PHE cc_start: 0.8315 (t80) cc_final: 0.8045 (m-80) REVERT: C 503 LEU cc_start: 0.8692 (mt) cc_final: 0.8486 (mm) REVERT: C 536 GLU cc_start: 0.7797 (pm20) cc_final: 0.7256 (pm20) REVERT: C 551 ASN cc_start: 0.9085 (m-40) cc_final: 0.8545 (m110) REVERT: C 572 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7795 (mtt) REVERT: C 644 MET cc_start: 0.8992 (mmm) cc_final: 0.8760 (mmp) REVERT: C 650 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7648 (p) REVERT: C 669 LEU cc_start: 0.9342 (mt) cc_final: 0.9033 (mt) REVERT: C 672 ILE cc_start: 0.9294 (mm) cc_final: 0.8955 (mt) REVERT: C 697 TRP cc_start: 0.9206 (t60) cc_final: 0.8927 (t60) REVERT: C 718 LYS cc_start: 0.8314 (mttt) cc_final: 0.7774 (pttt) REVERT: D 257 CYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5644 (m) REVERT: D 311 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8326 (mm-30) REVERT: D 318 LYS cc_start: 0.8217 (mttm) cc_final: 0.7903 (mmmt) REVERT: D 345 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8172 (mmtm) REVERT: D 423 GLN cc_start: 0.8956 (tp40) cc_final: 0.8673 (tp40) REVERT: D 424 ASP cc_start: 0.8789 (m-30) cc_final: 0.8437 (t70) REVERT: D 439 PHE cc_start: 0.8468 (t80) cc_final: 0.8264 (t80) REVERT: D 478 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8553 (mt-10) REVERT: D 496 PHE cc_start: 0.8210 (t80) cc_final: 0.7932 (m-80) REVERT: D 503 LEU cc_start: 0.8700 (mt) cc_final: 0.8476 (mm) REVERT: D 547 MET cc_start: 0.8729 (mtm) cc_final: 0.8416 (mtp) REVERT: D 551 ASN cc_start: 0.9138 (m-40) cc_final: 0.8606 (m110) REVERT: D 561 GLN cc_start: 0.6863 (pm20) cc_final: 0.6639 (mp10) REVERT: D 628 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6631 (t0) REVERT: D 650 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7542 (p) REVERT: D 707 ASP cc_start: 0.8583 (t70) cc_final: 0.8182 (t70) REVERT: D 718 LYS cc_start: 0.8376 (mttt) cc_final: 0.7918 (pttt) REVERT: B 309 TYR cc_start: 0.9053 (t80) cc_final: 0.8669 (t80) REVERT: B 345 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8140 (mmtm) REVERT: B 423 GLN cc_start: 0.8989 (tp40) cc_final: 0.8712 (mm-40) REVERT: B 424 ASP cc_start: 0.8750 (m-30) cc_final: 0.8307 (t0) REVERT: B 439 PHE cc_start: 0.8450 (t80) cc_final: 0.8245 (t80) REVERT: B 536 GLU cc_start: 0.7668 (pm20) cc_final: 0.7173 (pm20) REVERT: B 547 MET cc_start: 0.8758 (mtm) cc_final: 0.8433 (mtp) REVERT: B 551 ASN cc_start: 0.9096 (m-40) cc_final: 0.8512 (m110) REVERT: B 572 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7427 (mtt) REVERT: B 581 MET cc_start: 0.7784 (mmm) cc_final: 0.7379 (ptt) REVERT: B 669 LEU cc_start: 0.9301 (mt) cc_final: 0.8987 (mt) REVERT: B 677 MET cc_start: 0.8994 (mmm) cc_final: 0.8555 (mmm) outliers start: 32 outliers final: 10 residues processed: 634 average time/residue: 0.3124 time to fit residues: 276.5829 Evaluate side-chains 464 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 447 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 150 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16204 Z= 0.167 Angle : 0.572 8.565 21984 Z= 0.296 Chirality : 0.038 0.163 2476 Planarity : 0.003 0.023 2692 Dihedral : 6.623 53.431 2513 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.16 % Allowed : 13.49 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.26 (0.19), residues: 1904 helix: 1.54 (0.15), residues: 1168 sheet: -2.72 (0.66), residues: 60 loop : -2.08 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 697 HIS 0.002 0.000 HIS A 410 PHE 0.021 0.001 PHE D 742 TYR 0.021 0.001 TYR D 565 ARG 0.007 0.000 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 503 time to evaluate : 1.729 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: A 267 LEU cc_start: 0.7962 (mt) cc_final: 0.7735 (tt) REVERT: A 309 TYR cc_start: 0.9084 (t80) cc_final: 0.8698 (t80) REVERT: A 311 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 404 SER cc_start: 0.8148 (m) cc_final: 0.7388 (t) REVERT: A 420 ARG cc_start: 0.8849 (tpp80) cc_final: 0.8426 (mmm-85) REVERT: A 428 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8462 (mtp180) REVERT: A 439 PHE cc_start: 0.8412 (t80) cc_final: 0.8190 (t80) REVERT: A 478 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 496 PHE cc_start: 0.8203 (t80) cc_final: 0.7928 (m-80) REVERT: A 536 GLU cc_start: 0.7917 (mp0) cc_final: 0.7675 (mp0) REVERT: A 549 TRP cc_start: 0.9036 (m100) cc_final: 0.7731 (m100) REVERT: A 551 ASN cc_start: 0.8997 (m-40) cc_final: 0.8437 (m110) REVERT: A 568 MET cc_start: 0.8551 (mmt) cc_final: 0.8254 (mmt) REVERT: A 581 MET cc_start: 0.6921 (ptt) cc_final: 0.6688 (ttp) REVERT: A 589 PHE cc_start: 0.8390 (t80) cc_final: 0.8148 (t80) REVERT: A 650 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7837 (p) REVERT: A 689 ILE cc_start: 0.8917 (pt) cc_final: 0.8030 (mm) REVERT: A 700 GLN cc_start: 0.7793 (mt0) cc_final: 0.7523 (mt0) REVERT: C 311 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 372 TRP cc_start: 0.4941 (m100) cc_final: 0.4585 (m100) REVERT: C 387 ILE cc_start: 0.7344 (mm) cc_final: 0.6859 (mp) REVERT: C 404 SER cc_start: 0.8004 (m) cc_final: 0.7344 (t) REVERT: C 420 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8440 (mmm-85) REVERT: C 441 TYR cc_start: 0.8863 (t80) cc_final: 0.8448 (t80) REVERT: C 496 PHE cc_start: 0.8222 (t80) cc_final: 0.7977 (m-80) REVERT: C 504 LYS cc_start: 0.8028 (mttp) cc_final: 0.7238 (ptpp) REVERT: C 551 ASN cc_start: 0.8927 (m-40) cc_final: 0.8342 (m110) REVERT: C 589 PHE cc_start: 0.8526 (t80) cc_final: 0.8307 (t80) REVERT: C 650 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7921 (p) REVERT: C 743 ARG cc_start: 0.8373 (ttm110) cc_final: 0.7884 (mtp85) REVERT: D 311 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 318 LYS cc_start: 0.8034 (mttm) cc_final: 0.7736 (mmmt) REVERT: D 424 ASP cc_start: 0.8642 (m-30) cc_final: 0.8346 (t0) REVERT: D 428 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8296 (mtp180) REVERT: D 439 PHE cc_start: 0.8390 (t80) cc_final: 0.8178 (t80) REVERT: D 496 PHE cc_start: 0.8119 (t80) cc_final: 0.7848 (m-80) REVERT: D 504 LYS cc_start: 0.7889 (mttp) cc_final: 0.6955 (ptpp) REVERT: D 536 GLU cc_start: 0.7932 (mp0) cc_final: 0.7669 (mp0) REVERT: D 581 MET cc_start: 0.6887 (ptt) cc_final: 0.6627 (ttp) REVERT: D 589 PHE cc_start: 0.8434 (t80) cc_final: 0.8223 (t80) REVERT: D 650 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7841 (p) REVERT: B 404 SER cc_start: 0.8117 (m) cc_final: 0.7307 (t) REVERT: B 420 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8430 (mmm-85) REVERT: B 478 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8436 (mt-10) REVERT: B 581 MET cc_start: 0.7552 (mmm) cc_final: 0.7282 (ttp) REVERT: B 589 PHE cc_start: 0.8458 (t80) cc_final: 0.8209 (t80) REVERT: B 650 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7810 (p) outliers start: 37 outliers final: 11 residues processed: 519 average time/residue: 0.2839 time to fit residues: 213.9365 Evaluate side-chains 448 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 433 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16204 Z= 0.153 Angle : 0.541 12.198 21984 Z= 0.275 Chirality : 0.038 0.185 2476 Planarity : 0.003 0.025 2692 Dihedral : 5.686 50.279 2492 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.39 % Allowed : 15.01 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.60 (0.20), residues: 1904 helix: 1.84 (0.15), residues: 1148 sheet: -2.57 (0.67), residues: 60 loop : -1.88 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 697 HIS 0.002 0.000 HIS A 410 PHE 0.023 0.001 PHE C 742 TYR 0.017 0.001 TYR D 565 ARG 0.006 0.000 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 475 time to evaluate : 1.714 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: A 309 TYR cc_start: 0.9053 (t80) cc_final: 0.8764 (t80) REVERT: A 311 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 420 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8397 (mmm-85) REVERT: A 428 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8360 (mtp180) REVERT: A 478 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8405 (mt-10) REVERT: A 496 PHE cc_start: 0.8087 (t80) cc_final: 0.7848 (m-80) REVERT: A 533 GLN cc_start: 0.8250 (tt0) cc_final: 0.7561 (tm-30) REVERT: A 584 TYR cc_start: 0.9006 (t80) cc_final: 0.8696 (t80) REVERT: A 709 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8129 (tm-30) REVERT: C 311 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 414 LEU cc_start: 0.8604 (mt) cc_final: 0.8336 (mm) REVERT: C 496 PHE cc_start: 0.8087 (t80) cc_final: 0.7836 (m-80) REVERT: C 535 LYS cc_start: 0.8794 (tppp) cc_final: 0.8426 (tppt) REVERT: C 709 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8037 (tm-30) REVERT: C 743 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8118 (mtp85) REVERT: D 311 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8360 (mm-30) REVERT: D 318 LYS cc_start: 0.8061 (mttm) cc_final: 0.7800 (mmmt) REVERT: D 504 LYS cc_start: 0.7873 (mttp) cc_final: 0.7168 (ptpp) REVERT: D 536 GLU cc_start: 0.7919 (mp0) cc_final: 0.7607 (mp0) REVERT: D 581 MET cc_start: 0.6741 (ptt) cc_final: 0.6449 (ttp) REVERT: D 589 PHE cc_start: 0.8491 (t80) cc_final: 0.8234 (t80) REVERT: D 674 LEU cc_start: 0.9149 (tp) cc_final: 0.8947 (tp) REVERT: D 743 ARG cc_start: 0.8818 (mtp180) cc_final: 0.8546 (mtp180) REVERT: B 420 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8580 (mmm-85) REVERT: B 487 TYR cc_start: 0.9057 (t80) cc_final: 0.8593 (t80) REVERT: B 496 PHE cc_start: 0.8489 (m-80) cc_final: 0.8203 (m-80) REVERT: B 581 MET cc_start: 0.7558 (mmm) cc_final: 0.7264 (ttp) REVERT: B 589 PHE cc_start: 0.8485 (t80) cc_final: 0.8281 (t80) REVERT: B 707 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8700 (t0) outliers start: 41 outliers final: 24 residues processed: 484 average time/residue: 0.2692 time to fit residues: 191.3495 Evaluate side-chains 448 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 423 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 708 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.9990 chunk 131 optimal weight: 0.0070 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16204 Z= 0.142 Angle : 0.544 12.616 21984 Z= 0.273 Chirality : 0.038 0.172 2476 Planarity : 0.003 0.056 2692 Dihedral : 5.338 47.082 2488 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.04 % Allowed : 16.36 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.20), residues: 1904 helix: 1.91 (0.15), residues: 1148 sheet: -2.42 (0.69), residues: 60 loop : -1.83 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 697 HIS 0.001 0.000 HIS A 410 PHE 0.024 0.001 PHE C 742 TYR 0.014 0.001 TYR D 565 ARG 0.004 0.000 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 455 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9082 (t80) cc_final: 0.8826 (t80) REVERT: A 311 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 420 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8451 (mmm-85) REVERT: A 428 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8342 (mtp180) REVERT: A 533 GLN cc_start: 0.8186 (tt0) cc_final: 0.7522 (tm-30) REVERT: A 568 MET cc_start: 0.8624 (mmt) cc_final: 0.8275 (mmt) REVERT: A 571 LYS cc_start: 0.8958 (ttmm) cc_final: 0.8422 (tmtt) REVERT: A 572 MET cc_start: 0.7562 (mtm) cc_final: 0.7241 (mtt) REVERT: A 584 TYR cc_start: 0.9007 (t80) cc_final: 0.8746 (t80) REVERT: A 598 LEU cc_start: 0.9311 (tt) cc_final: 0.9096 (tp) REVERT: A 709 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 309 TYR cc_start: 0.9001 (t80) cc_final: 0.8799 (t80) REVERT: C 311 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8106 (mm-30) REVERT: C 414 LEU cc_start: 0.8621 (mt) cc_final: 0.8370 (mm) REVERT: C 420 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8543 (mmm-85) REVERT: C 535 LYS cc_start: 0.8756 (tppp) cc_final: 0.8419 (tppt) REVERT: C 674 LEU cc_start: 0.9060 (tp) cc_final: 0.8679 (mp) REVERT: C 709 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 743 ARG cc_start: 0.8370 (ttm110) cc_final: 0.8063 (mtp-110) REVERT: D 300 ASP cc_start: 0.7564 (m-30) cc_final: 0.7030 (p0) REVERT: D 311 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 318 LYS cc_start: 0.8058 (mttm) cc_final: 0.7795 (mmmt) REVERT: D 581 MET cc_start: 0.6748 (ptt) cc_final: 0.6496 (ttp) REVERT: D 589 PHE cc_start: 0.8475 (t80) cc_final: 0.8246 (t80) REVERT: D 700 GLN cc_start: 0.7009 (mt0) cc_final: 0.6772 (mt0) REVERT: B 300 ASP cc_start: 0.7720 (m-30) cc_final: 0.7151 (p0) REVERT: B 487 TYR cc_start: 0.9020 (t80) cc_final: 0.8444 (t80) REVERT: B 496 PHE cc_start: 0.8476 (m-80) cc_final: 0.8184 (m-80) REVERT: B 581 MET cc_start: 0.7510 (mmm) cc_final: 0.7231 (ttp) REVERT: B 689 ILE cc_start: 0.8982 (pt) cc_final: 0.8728 (mm) outliers start: 52 outliers final: 33 residues processed: 471 average time/residue: 0.2797 time to fit residues: 193.2945 Evaluate side-chains 455 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 422 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 138 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS C 551 ASN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16204 Z= 0.159 Angle : 0.553 11.642 21984 Z= 0.277 Chirality : 0.039 0.207 2476 Planarity : 0.003 0.043 2692 Dihedral : 5.198 43.207 2488 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.92 % Allowed : 17.64 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.75 (0.20), residues: 1904 helix: 1.92 (0.15), residues: 1148 sheet: -2.38 (0.68), residues: 60 loop : -1.78 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 697 HIS 0.005 0.000 HIS C 320 PHE 0.024 0.001 PHE A 742 TYR 0.011 0.001 TYR A 463 ARG 0.005 0.000 ARG D 743 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 454 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9094 (t80) cc_final: 0.8801 (t80) REVERT: A 311 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 420 ARG cc_start: 0.8896 (tpp80) cc_final: 0.8494 (mmm-85) REVERT: A 568 MET cc_start: 0.8602 (mmt) cc_final: 0.8272 (mmt) REVERT: A 581 MET cc_start: 0.6911 (ptt) cc_final: 0.6509 (ttp) REVERT: A 584 TYR cc_start: 0.9017 (t80) cc_final: 0.8760 (t80) REVERT: A 598 LEU cc_start: 0.9347 (tt) cc_final: 0.9068 (tp) REVERT: A 700 GLN cc_start: 0.7493 (mt0) cc_final: 0.7083 (mt0) REVERT: A 709 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 311 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8370 (mm-30) REVERT: C 414 LEU cc_start: 0.8650 (mt) cc_final: 0.8398 (mm) REVERT: C 420 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8508 (mmm-85) REVERT: C 473 PHE cc_start: 0.8311 (m-10) cc_final: 0.7993 (m-10) REVERT: C 496 PHE cc_start: 0.8489 (m-80) cc_final: 0.8197 (m-80) REVERT: C 535 LYS cc_start: 0.8759 (tppp) cc_final: 0.8472 (tppt) REVERT: C 551 ASN cc_start: 0.8730 (m110) cc_final: 0.8340 (m110) REVERT: C 584 TYR cc_start: 0.9038 (t80) cc_final: 0.8753 (t80) REVERT: C 674 LEU cc_start: 0.9172 (tp) cc_final: 0.8812 (mp) REVERT: C 697 TRP cc_start: 0.9071 (t60) cc_final: 0.8750 (t60) REVERT: C 709 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 743 ARG cc_start: 0.8538 (ttm110) cc_final: 0.8196 (mtp-110) REVERT: D 300 ASP cc_start: 0.7582 (m-30) cc_final: 0.7053 (p0) REVERT: D 308 MET cc_start: 0.8279 (mtm) cc_final: 0.7735 (mtt) REVERT: D 311 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8382 (mm-30) REVERT: D 318 LYS cc_start: 0.8096 (mttm) cc_final: 0.7800 (mmmt) REVERT: D 533 GLN cc_start: 0.8194 (tt0) cc_final: 0.7517 (tm-30) REVERT: D 581 MET cc_start: 0.6828 (ptt) cc_final: 0.6571 (ttp) REVERT: D 589 PHE cc_start: 0.8479 (t80) cc_final: 0.8252 (t80) REVERT: B 300 ASP cc_start: 0.7801 (m-30) cc_final: 0.7227 (p0) REVERT: B 473 PHE cc_start: 0.8294 (m-10) cc_final: 0.8050 (m-10) REVERT: B 581 MET cc_start: 0.7537 (mmm) cc_final: 0.7254 (ttp) REVERT: B 689 ILE cc_start: 0.9074 (pt) cc_final: 0.8640 (mm) outliers start: 50 outliers final: 39 residues processed: 473 average time/residue: 0.2677 time to fit residues: 186.1634 Evaluate side-chains 470 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 431 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16204 Z= 0.204 Angle : 0.579 12.509 21984 Z= 0.288 Chirality : 0.040 0.229 2476 Planarity : 0.003 0.042 2692 Dihedral : 5.207 42.242 2488 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.21 % Allowed : 18.34 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1904 helix: 1.82 (0.15), residues: 1148 sheet: -2.35 (0.68), residues: 60 loop : -1.81 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 697 HIS 0.001 0.000 HIS C 320 PHE 0.026 0.001 PHE A 742 TYR 0.017 0.001 TYR B 463 ARG 0.005 0.000 ARG C 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 458 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9093 (t80) cc_final: 0.8799 (t80) REVERT: A 311 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 432 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7367 (mtt90) REVERT: A 487 TYR cc_start: 0.9060 (t80) cc_final: 0.8552 (t80) REVERT: A 568 MET cc_start: 0.8530 (mmt) cc_final: 0.8227 (mmt) REVERT: A 572 MET cc_start: 0.7627 (mtt) cc_final: 0.7289 (mtm) REVERT: A 581 MET cc_start: 0.7083 (ptt) cc_final: 0.6681 (ttp) REVERT: A 584 TYR cc_start: 0.9037 (t80) cc_final: 0.8803 (t80) REVERT: A 709 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8200 (tm-30) REVERT: C 414 LEU cc_start: 0.8653 (mt) cc_final: 0.8386 (mm) REVERT: C 473 PHE cc_start: 0.8350 (m-10) cc_final: 0.8062 (m-10) REVERT: C 491 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8152 (mmm160) REVERT: C 496 PHE cc_start: 0.8532 (m-80) cc_final: 0.8308 (m-80) REVERT: C 499 ARG cc_start: 0.8445 (mmp80) cc_final: 0.8243 (tpp-160) REVERT: C 535 LYS cc_start: 0.8783 (tppp) cc_final: 0.8525 (tppt) REVERT: C 674 LEU cc_start: 0.9231 (tp) cc_final: 0.8882 (mp) REVERT: C 697 TRP cc_start: 0.9131 (t60) cc_final: 0.8629 (t60) REVERT: C 709 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 743 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8227 (mtp85) REVERT: D 300 ASP cc_start: 0.7568 (m-30) cc_final: 0.7036 (p0) REVERT: D 318 LYS cc_start: 0.8147 (mttm) cc_final: 0.7744 (mmmt) REVERT: D 581 MET cc_start: 0.6809 (ptt) cc_final: 0.6536 (ttp) REVERT: D 589 PHE cc_start: 0.8535 (t80) cc_final: 0.8320 (t80) REVERT: D 674 LEU cc_start: 0.9072 (tp) cc_final: 0.8693 (mp) REVERT: D 700 GLN cc_start: 0.7179 (mt0) cc_final: 0.6902 (mt0) REVERT: B 300 ASP cc_start: 0.7778 (m-30) cc_final: 0.7203 (p0) REVERT: B 432 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7470 (ptp-110) REVERT: B 473 PHE cc_start: 0.8348 (m-10) cc_final: 0.8044 (m-10) REVERT: B 504 LYS cc_start: 0.7937 (tttt) cc_final: 0.7345 (mmtp) REVERT: B 544 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8863 (p) REVERT: B 557 ARG cc_start: 0.7515 (ptp-170) cc_final: 0.7252 (ptp-170) REVERT: B 581 MET cc_start: 0.7528 (mmm) cc_final: 0.7268 (ttp) outliers start: 55 outliers final: 43 residues processed: 477 average time/residue: 0.2870 time to fit residues: 199.0064 Evaluate side-chains 478 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 434 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN A 551 ASN C 551 ASN D 354 GLN ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16204 Z= 0.169 Angle : 0.577 12.116 21984 Z= 0.288 Chirality : 0.039 0.261 2476 Planarity : 0.003 0.046 2692 Dihedral : 5.140 44.542 2488 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.80 % Allowed : 19.10 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.58 (0.20), residues: 1904 helix: 1.80 (0.15), residues: 1152 sheet: -2.30 (0.69), residues: 60 loop : -1.89 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 697 HIS 0.001 0.000 HIS D 410 PHE 0.026 0.001 PHE C 742 TYR 0.017 0.001 TYR B 463 ARG 0.005 0.000 ARG C 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 440 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9081 (t80) cc_final: 0.8831 (t80) REVERT: A 311 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8046 (mm-30) REVERT: A 432 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7214 (ptp90) REVERT: A 487 TYR cc_start: 0.9044 (t80) cc_final: 0.8534 (t80) REVERT: A 551 ASN cc_start: 0.8660 (m110) cc_final: 0.8263 (m110) REVERT: A 568 MET cc_start: 0.8583 (mmt) cc_final: 0.8239 (mmt) REVERT: A 572 MET cc_start: 0.7671 (mtt) cc_final: 0.7410 (mtm) REVERT: A 581 MET cc_start: 0.7050 (ptt) cc_final: 0.6663 (ttp) REVERT: A 674 LEU cc_start: 0.8965 (tp) cc_final: 0.8617 (mp) REVERT: A 709 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 414 LEU cc_start: 0.8640 (mt) cc_final: 0.8390 (mm) REVERT: C 432 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6735 (ptp90) REVERT: C 473 PHE cc_start: 0.8330 (m-10) cc_final: 0.8021 (m-10) REVERT: C 491 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8123 (mmm160) REVERT: C 499 ARG cc_start: 0.8374 (mmp80) cc_final: 0.8103 (mmt-90) REVERT: C 535 LYS cc_start: 0.8763 (tppp) cc_final: 0.8518 (tppt) REVERT: C 551 ASN cc_start: 0.8665 (m110) cc_final: 0.8273 (m110) REVERT: C 674 LEU cc_start: 0.9168 (tp) cc_final: 0.8814 (mp) REVERT: C 709 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8096 (tm-30) REVERT: C 743 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8228 (mtp-110) REVERT: D 300 ASP cc_start: 0.7644 (m-30) cc_final: 0.7031 (p0) REVERT: D 318 LYS cc_start: 0.8160 (mttm) cc_final: 0.7720 (mmmt) REVERT: D 487 TYR cc_start: 0.9104 (t80) cc_final: 0.7434 (t80) REVERT: D 499 ARG cc_start: 0.8696 (mmp80) cc_final: 0.8434 (mmm160) REVERT: D 581 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6459 (ttp) REVERT: D 674 LEU cc_start: 0.9077 (tp) cc_final: 0.8711 (mp) REVERT: D 700 GLN cc_start: 0.7183 (mt0) cc_final: 0.6888 (mt0) REVERT: B 300 ASP cc_start: 0.7775 (m-30) cc_final: 0.7211 (p0) REVERT: B 309 TYR cc_start: 0.9095 (t80) cc_final: 0.8893 (t80) REVERT: B 473 PHE cc_start: 0.8306 (m-10) cc_final: 0.7967 (m-10) REVERT: B 504 LYS cc_start: 0.7862 (tttt) cc_final: 0.7368 (mmtp) REVERT: B 557 ARG cc_start: 0.7487 (ptp-170) cc_final: 0.7030 (ptp-170) REVERT: B 571 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8645 (tmtt) REVERT: B 581 MET cc_start: 0.7527 (mmm) cc_final: 0.7259 (ttp) outliers start: 48 outliers final: 40 residues processed: 458 average time/residue: 0.2743 time to fit residues: 184.8246 Evaluate side-chains 460 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 419 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN A 551 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16204 Z= 0.195 Angle : 0.593 12.004 21984 Z= 0.298 Chirality : 0.040 0.249 2476 Planarity : 0.003 0.042 2692 Dihedral : 5.148 45.076 2488 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.86 % Allowed : 19.92 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.44 (0.20), residues: 1904 helix: 1.66 (0.15), residues: 1152 sheet: -2.30 (0.69), residues: 60 loop : -1.91 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 697 HIS 0.001 0.000 HIS D 410 PHE 0.025 0.001 PHE D 742 TYR 0.016 0.001 TYR B 463 ARG 0.009 0.000 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 433 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9126 (t80) cc_final: 0.8805 (t80) REVERT: A 311 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8093 (mm-30) REVERT: A 432 ARG cc_start: 0.7763 (mtt90) cc_final: 0.7357 (mtt90) REVERT: A 568 MET cc_start: 0.8547 (mmt) cc_final: 0.8255 (mmt) REVERT: A 572 MET cc_start: 0.7690 (mtt) cc_final: 0.7400 (mtm) REVERT: A 581 MET cc_start: 0.7089 (ptt) cc_final: 0.6683 (ttp) REVERT: A 584 TYR cc_start: 0.9040 (t80) cc_final: 0.8774 (t80) REVERT: A 709 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 414 LEU cc_start: 0.8630 (mt) cc_final: 0.8356 (mm) REVERT: C 473 PHE cc_start: 0.8336 (m-10) cc_final: 0.8025 (m-10) REVERT: C 499 ARG cc_start: 0.8370 (mmp80) cc_final: 0.8045 (mmt-90) REVERT: C 674 LEU cc_start: 0.9190 (tp) cc_final: 0.8844 (mp) REVERT: C 709 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8102 (tm-30) REVERT: D 267 LEU cc_start: 0.8365 (tt) cc_final: 0.8114 (mp) REVERT: D 300 ASP cc_start: 0.7617 (m-30) cc_final: 0.7009 (p0) REVERT: D 318 LYS cc_start: 0.8149 (mttm) cc_final: 0.7739 (mmmt) REVERT: D 499 ARG cc_start: 0.8714 (mmp80) cc_final: 0.8494 (mmm160) REVERT: D 581 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6541 (ttp) REVERT: D 674 LEU cc_start: 0.9093 (tp) cc_final: 0.8714 (mp) REVERT: B 300 ASP cc_start: 0.7777 (m-30) cc_final: 0.7218 (p0) REVERT: B 473 PHE cc_start: 0.8313 (m-10) cc_final: 0.7968 (m-10) REVERT: B 504 LYS cc_start: 0.7799 (tttt) cc_final: 0.7174 (tptm) REVERT: B 581 MET cc_start: 0.7564 (mmm) cc_final: 0.7295 (ttp) outliers start: 49 outliers final: 44 residues processed: 453 average time/residue: 0.2732 time to fit residues: 181.8301 Evaluate side-chains 456 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 411 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 155 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN A 551 ASN A 560 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 354 GLN D 519 GLN D 551 ASN B 519 GLN B 551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16204 Z= 0.159 Angle : 0.599 12.116 21984 Z= 0.299 Chirality : 0.039 0.204 2476 Planarity : 0.003 0.066 2692 Dihedral : 5.063 50.335 2488 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.57 % Allowed : 20.97 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.48 (0.20), residues: 1904 helix: 1.72 (0.15), residues: 1152 sheet: -2.20 (0.69), residues: 60 loop : -1.95 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 697 HIS 0.001 0.000 HIS A 320 PHE 0.026 0.001 PHE D 742 TYR 0.015 0.001 TYR B 554 ARG 0.006 0.000 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 437 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9104 (t80) cc_final: 0.8745 (t80) REVERT: A 311 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8154 (mm-30) REVERT: A 487 TYR cc_start: 0.9036 (t80) cc_final: 0.8515 (t80) REVERT: A 551 ASN cc_start: 0.8580 (m110) cc_final: 0.8182 (m110) REVERT: A 568 MET cc_start: 0.8565 (mmt) cc_final: 0.8218 (mmt) REVERT: A 581 MET cc_start: 0.6980 (ptt) cc_final: 0.6574 (ttp) REVERT: A 598 LEU cc_start: 0.9309 (tt) cc_final: 0.9102 (tt) REVERT: A 709 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 300 ASP cc_start: 0.7787 (m-30) cc_final: 0.7300 (p0) REVERT: C 414 LEU cc_start: 0.8629 (mt) cc_final: 0.8357 (mm) REVERT: C 436 PHE cc_start: 0.9137 (t80) cc_final: 0.8862 (t80) REVERT: C 473 PHE cc_start: 0.8282 (m-10) cc_final: 0.7852 (m-10) REVERT: C 499 ARG cc_start: 0.8355 (mmp80) cc_final: 0.8073 (tpp-160) REVERT: C 504 LYS cc_start: 0.7925 (tttt) cc_final: 0.7257 (tptm) REVERT: C 551 ASN cc_start: 0.8569 (m110) cc_final: 0.8140 (m110) REVERT: C 674 LEU cc_start: 0.9118 (tp) cc_final: 0.8729 (mp) REVERT: C 677 MET cc_start: 0.7344 (ttt) cc_final: 0.6702 (mtt) REVERT: C 709 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 300 ASP cc_start: 0.7664 (m-30) cc_final: 0.7068 (p0) REVERT: D 311 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8717 (mm-30) REVERT: D 318 LYS cc_start: 0.8166 (mttm) cc_final: 0.7729 (mmmt) REVERT: D 487 TYR cc_start: 0.9077 (t80) cc_final: 0.7375 (t80) REVERT: D 499 ARG cc_start: 0.8683 (mmp80) cc_final: 0.8419 (mmm160) REVERT: D 504 LYS cc_start: 0.7860 (tttt) cc_final: 0.7295 (mmtp) REVERT: D 551 ASN cc_start: 0.8592 (m110) cc_final: 0.8171 (m110) REVERT: D 568 MET cc_start: 0.7691 (mtm) cc_final: 0.7478 (mtm) REVERT: D 581 MET cc_start: 0.6901 (ptt) cc_final: 0.6633 (ttp) REVERT: D 674 LEU cc_start: 0.9095 (tp) cc_final: 0.8709 (mp) REVERT: B 300 ASP cc_start: 0.7787 (m-30) cc_final: 0.7233 (p0) REVERT: B 473 PHE cc_start: 0.8277 (m-10) cc_final: 0.8001 (m-10) REVERT: B 498 GLN cc_start: 0.8052 (mm110) cc_final: 0.7584 (mm-40) REVERT: B 499 ARG cc_start: 0.8528 (mmp80) cc_final: 0.8229 (mmm-85) REVERT: B 504 LYS cc_start: 0.7775 (tttt) cc_final: 0.7179 (tptm) REVERT: B 536 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: B 551 ASN cc_start: 0.8592 (m110) cc_final: 0.8162 (m110) REVERT: B 571 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8608 (tmtt) REVERT: B 575 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7355 (ttm-80) REVERT: B 581 MET cc_start: 0.7474 (mmm) cc_final: 0.7251 (ttp) REVERT: B 674 LEU cc_start: 0.8996 (tp) cc_final: 0.8612 (mp) outliers start: 44 outliers final: 39 residues processed: 453 average time/residue: 0.2708 time to fit residues: 181.6688 Evaluate side-chains 455 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 415 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 126 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 93 optimal weight: 0.0070 chunk 120 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16204 Z= 0.153 Angle : 0.606 12.193 21984 Z= 0.304 Chirality : 0.040 0.215 2476 Planarity : 0.004 0.094 2692 Dihedral : 4.975 59.498 2488 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.22 % Allowed : 21.90 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.52 (0.20), residues: 1904 helix: 1.70 (0.15), residues: 1160 sheet: -2.10 (0.69), residues: 60 loop : -1.91 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 697 HIS 0.001 0.000 HIS D 410 PHE 0.026 0.001 PHE D 742 TYR 0.025 0.001 TYR C 444 ARG 0.010 0.000 ARG B 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 451 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9123 (t80) cc_final: 0.8800 (t80) REVERT: A 311 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 436 PHE cc_start: 0.9104 (t80) cc_final: 0.8828 (t80) REVERT: A 504 LYS cc_start: 0.7871 (tttt) cc_final: 0.7175 (mmtp) REVERT: A 533 GLN cc_start: 0.8094 (tt0) cc_final: 0.7345 (tm-30) REVERT: A 551 ASN cc_start: 0.8322 (m110) cc_final: 0.7888 (m110) REVERT: A 568 MET cc_start: 0.8595 (mmt) cc_final: 0.8179 (mmt) REVERT: A 571 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8343 (tmtt) REVERT: A 572 MET cc_start: 0.7423 (mtm) cc_final: 0.7141 (mtt) REVERT: A 584 TYR cc_start: 0.9003 (t80) cc_final: 0.8695 (t80) REVERT: A 598 LEU cc_start: 0.9269 (tt) cc_final: 0.9044 (tt) REVERT: A 709 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8164 (tm-30) REVERT: C 300 ASP cc_start: 0.7729 (m-30) cc_final: 0.7259 (p0) REVERT: C 414 LEU cc_start: 0.8630 (mt) cc_final: 0.8347 (mm) REVERT: C 436 PHE cc_start: 0.9100 (t80) cc_final: 0.8828 (t80) REVERT: C 491 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8222 (tpp80) REVERT: C 499 ARG cc_start: 0.8313 (mmp80) cc_final: 0.8038 (tpp-160) REVERT: C 504 LYS cc_start: 0.7880 (tttt) cc_final: 0.7262 (tptm) REVERT: C 551 ASN cc_start: 0.8523 (m110) cc_final: 0.8063 (m110) REVERT: C 571 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8623 (tmtt) REVERT: C 575 ARG cc_start: 0.6716 (mmt-90) cc_final: 0.6225 (ttm-80) REVERT: C 674 LEU cc_start: 0.9073 (tp) cc_final: 0.8734 (mp) REVERT: C 709 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8144 (tm-30) REVERT: D 300 ASP cc_start: 0.7689 (m-30) cc_final: 0.7113 (p0) REVERT: D 318 LYS cc_start: 0.8106 (mttm) cc_final: 0.7726 (mmmt) REVERT: D 397 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7963 (pt0) REVERT: D 504 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7312 (mmtp) REVERT: D 511 TYR cc_start: 0.7987 (t80) cc_final: 0.7730 (t80) REVERT: D 551 ASN cc_start: 0.8336 (m110) cc_final: 0.7874 (m110) REVERT: D 581 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6498 (ttp) REVERT: D 674 LEU cc_start: 0.9050 (tp) cc_final: 0.8695 (mp) REVERT: B 300 ASP cc_start: 0.7792 (m-30) cc_final: 0.7234 (p0) REVERT: B 487 TYR cc_start: 0.9009 (t80) cc_final: 0.7889 (t80) REVERT: B 498 GLN cc_start: 0.8082 (mm110) cc_final: 0.7584 (mm-40) REVERT: B 499 ARG cc_start: 0.8559 (mmp80) cc_final: 0.8148 (mmm-85) REVERT: B 504 LYS cc_start: 0.7679 (tttt) cc_final: 0.7110 (tptm) REVERT: B 511 TYR cc_start: 0.7665 (t80) cc_final: 0.7415 (t80) REVERT: B 536 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: B 551 ASN cc_start: 0.8273 (m110) cc_final: 0.7799 (m110) REVERT: B 571 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8558 (tmtt) REVERT: B 575 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.7289 (ttm-80) REVERT: B 581 MET cc_start: 0.7584 (mmm) cc_final: 0.7233 (ttp) REVERT: B 674 LEU cc_start: 0.9021 (tp) cc_final: 0.8651 (mp) outliers start: 38 outliers final: 33 residues processed: 462 average time/residue: 0.2867 time to fit residues: 198.3356 Evaluate side-chains 467 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 431 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 704 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.202397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128464 restraints weight = 22557.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132746 restraints weight = 11308.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135324 restraints weight = 7919.972| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.267 16204 Z= 0.331 Angle : 0.819 59.191 21984 Z= 0.453 Chirality : 0.045 0.902 2476 Planarity : 0.004 0.086 2692 Dihedral : 4.973 59.357 2488 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.39 % Allowed : 22.25 % Favored : 75.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.69 % 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: 0.49 (0.20), residues: 1904 helix: 1.70 (0.15), residues: 1156 sheet: -2.08 (0.69), residues: 60 loop : -1.94 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 697 HIS 0.009 0.001 HIS B 320 PHE 0.055 0.001 PHE B 473 TYR 0.016 0.001 TYR B 554 ARG 0.008 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3936.62 seconds wall clock time: 71 minutes 46.15 seconds (4306.15 seconds total)