Starting phenix.real_space_refine on Fri Mar 15 02:34:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klv_22919/03_2024/7klv_22919_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klv_22919/03_2024/7klv_22919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klv_22919/03_2024/7klv_22919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klv_22919/03_2024/7klv_22919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klv_22919/03_2024/7klv_22919_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klv_22919/03_2024/7klv_22919_updated.pdb" } resolution = 3.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 522 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 6233 2.51 5 N 1715 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 521": "OD1" <-> "OD2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 658": "NH1" <-> "NH2" Residue "B ASP 670": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.95, per 1000 atoms: 0.60 Number of scatterers: 9871 At special positions: 0 Unit cell: (121.378, 129.018, 90.8216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 44 16.00 P 6 15.00 Mg 2 11.99 O 1869 8.00 N 1715 7.00 C 6233 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 8 sheets defined 40.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 110 through 134 removed outlier: 3.507A pdb=" N ILE A 113 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.505A pdb=" N SER A 207 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 409 through 432 Processing helix chain 'A' and resid 434 through 454 removed outlier: 3.545A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 removed outlier: 3.604A pdb=" N LYS A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.698A pdb=" N ALA A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 550 through 556 removed outlier: 3.940A pdb=" N VAL A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 589 removed outlier: 4.313A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.714A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 3.885A pdb=" N LEU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 removed outlier: 3.543A pdb=" N VAL A 690 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY A 691 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 692 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 700 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 179 through 187 removed outlier: 3.634A pdb=" N LEU B 187 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.557A pdb=" N SER B 207 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 352 through 355 No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 409 through 432 removed outlier: 3.648A pdb=" N ASP B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 removed outlier: 6.252A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.559A pdb=" N LYS B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 512 through 517 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.733A pdb=" N VAL B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 589 Processing helix chain 'B' and resid 616 through 624 removed outlier: 3.760A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET B 624 " --> pdb=" O HIS B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 649 through 660 removed outlier: 3.653A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 680 removed outlier: 3.553A pdb=" N ASP B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 700 removed outlier: 3.537A pdb=" N MET B 689 " --> pdb=" O PRO B 686 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 690 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 691 " --> pdb=" O ALA B 688 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 699 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 700 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 285 through 287 removed outlier: 7.080A pdb=" N ILE A 143 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 233 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 327 through 333 removed outlier: 3.915A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 546 through 549 Processing sheet with id= D, first strand: chain 'A' and resid 596 through 599 Processing sheet with id= E, first strand: chain 'B' and resid 284 through 287 removed outlier: 3.509A pdb=" N GLY B 250 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 242 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 327 through 333 removed outlier: 3.750A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 546 through 549 Processing sheet with id= H, first strand: chain 'B' and resid 597 through 599 removed outlier: 7.102A pdb=" N LEU B 642 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 609 " --> pdb=" O GLU B 643 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3260 1.34 - 1.46: 2185 1.46 - 1.58: 4512 1.58 - 1.70: 6 1.70 - 1.82: 80 Bond restraints: 10043 Sorted by residual: bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O5' ANP A 901 " pdb=" PA ANP A 901 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 10038 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.20: 147 105.20 - 112.40: 5141 112.40 - 119.59: 3298 119.59 - 126.79: 4857 126.79 - 133.98: 110 Bond angle restraints: 13553 Sorted by residual: angle pdb=" PB ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 126.95 110.29 16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 111.18 15.77 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O2B ANP B 901 " ideal model delta sigma weight residual 120.08 109.03 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O2B ANP A 901 " ideal model delta sigma weight residual 120.08 109.20 10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " pdb=" O2G ANP A 901 " ideal model delta sigma weight residual 101.05 109.65 -8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 13548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5491 17.90 - 35.80: 554 35.80 - 53.70: 93 53.70 - 71.59: 30 71.59 - 89.49: 13 Dihedral angle restraints: 6181 sinusoidal: 2583 harmonic: 3598 Sorted by residual: dihedral pdb=" CA LEU A 539 " pdb=" C LEU A 539 " pdb=" N ARG A 540 " pdb=" CA ARG A 540 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 658 " pdb=" CD ARG A 658 " pdb=" NE ARG A 658 " pdb=" CZ ARG A 658 " ideal model delta sinusoidal sigma weight residual 90.00 134.96 -44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA GLU B 633 " pdb=" C GLU B 633 " pdb=" N ARG B 634 " pdb=" CA ARG B 634 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1280 0.056 - 0.111: 228 0.111 - 0.167: 18 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1525 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 639 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO B 640 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 640 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 640 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 585 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP B 585 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 585 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 585 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 585 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 585 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 621 " 0.008 2.00e-02 2.50e+03 9.18e-03 1.47e+00 pdb=" CG PHE A 621 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 621 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 621 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 621 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 621 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 621 " 0.001 2.00e-02 2.50e+03 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.61: 90 2.61 - 3.24: 9470 3.24 - 3.87: 18293 3.87 - 4.51: 24672 4.51 - 5.14: 40188 Nonbonded interactions: 92713 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 902 " model vdw 1.974 2.170 nonbonded pdb=" O3G ANP B 901 " pdb="MG MG B 902 " model vdw 2.000 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 902 " model vdw 2.025 2.170 nonbonded pdb=" O3G ANP A 901 " pdb="MG MG A 902 " model vdw 2.038 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.050 2.170 ... (remaining 92708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 704 or resid 901 through 903)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 7.290 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.320 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.004 0.143 10043 Z= 0.246 Angle : 0.654 16.661 13553 Z= 0.320 Chirality : 0.042 0.279 1528 Planarity : 0.003 0.054 1720 Dihedral : 15.235 89.492 3843 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1210 helix: 1.04 (0.24), residues: 510 sheet: 0.36 (0.39), residues: 189 loop : -1.42 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 PHE 0.021 0.001 PHE A 621 TYR 0.008 0.001 TYR B 206 ARG 0.012 0.001 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.239 Fit side-chains REVERT: A 181 LYS cc_start: 0.8593 (mmmt) cc_final: 0.7953 (mtpp) REVERT: A 210 MET cc_start: 0.8400 (ttp) cc_final: 0.8127 (ptm) REVERT: A 309 TRP cc_start: 0.7420 (t-100) cc_final: 0.7109 (t-100) REVERT: A 490 MET cc_start: 0.8229 (ptp) cc_final: 0.7940 (ptp) REVERT: A 624 MET cc_start: 0.0541 (mtt) cc_final: 0.0311 (tpp) REVERT: A 689 MET cc_start: 0.8639 (ppp) cc_final: 0.7765 (ppp) REVERT: B 93 GLU cc_start: 0.8126 (tp30) cc_final: 0.7861 (tt0) REVERT: B 333 THR cc_start: 0.7945 (m) cc_final: 0.7616 (p) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2562 time to fit residues: 44.7153 Evaluate side-chains 88 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 288 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 479 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10043 Z= 0.266 Angle : 0.561 9.005 13553 Z= 0.293 Chirality : 0.043 0.174 1528 Planarity : 0.004 0.032 1720 Dihedral : 6.802 57.831 1402 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.31 % Allowed : 7.47 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1210 helix: 0.76 (0.23), residues: 521 sheet: 0.34 (0.38), residues: 193 loop : -1.51 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 585 HIS 0.005 0.001 HIS B 129 PHE 0.013 0.001 PHE A 264 TYR 0.013 0.001 TYR B 437 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.238 Fit side-chains REVERT: A 181 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7929 (mtpp) REVERT: A 309 TRP cc_start: 0.7495 (t-100) cc_final: 0.7189 (t-100) REVERT: A 553 ASP cc_start: 0.8787 (t70) cc_final: 0.8391 (t0) REVERT: A 585 TRP cc_start: 0.7813 (t60) cc_final: 0.7598 (t60) REVERT: B 93 GLU cc_start: 0.8164 (tp30) cc_final: 0.7728 (tp30) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.2488 time to fit residues: 35.3921 Evaluate side-chains 95 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10043 Z= 0.358 Angle : 0.599 8.659 13553 Z= 0.313 Chirality : 0.045 0.159 1528 Planarity : 0.004 0.033 1720 Dihedral : 7.004 55.550 1402 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.77 % Allowed : 12.14 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1210 helix: 0.58 (0.23), residues: 514 sheet: 0.20 (0.38), residues: 194 loop : -1.59 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 585 HIS 0.005 0.001 HIS B 129 PHE 0.013 0.002 PHE A 264 TYR 0.015 0.002 TYR B 437 ARG 0.003 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.306 Fit side-chains REVERT: A 181 LYS cc_start: 0.8548 (mmmt) cc_final: 0.7977 (mtpp) REVERT: A 309 TRP cc_start: 0.7556 (t-100) cc_final: 0.7279 (t-100) REVERT: A 585 TRP cc_start: 0.7864 (t60) cc_final: 0.7648 (t60) REVERT: B 93 GLU cc_start: 0.8205 (tp30) cc_final: 0.7740 (tp30) REVERT: B 308 GLU cc_start: 0.7576 (pp20) cc_final: 0.6867 (tm-30) REVERT: B 613 LEU cc_start: 0.8215 (pt) cc_final: 0.7880 (mt) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.2363 time to fit residues: 33.8779 Evaluate side-chains 103 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 HIS B 146 GLN B 288 ASN B 320 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10043 Z= 0.154 Angle : 0.481 7.931 13553 Z= 0.253 Chirality : 0.041 0.147 1528 Planarity : 0.003 0.030 1720 Dihedral : 5.979 54.932 1402 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.05 % Allowed : 12.79 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1210 helix: 0.77 (0.24), residues: 514 sheet: 0.32 (0.38), residues: 194 loop : -1.51 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 231 HIS 0.004 0.001 HIS A 88 PHE 0.007 0.001 PHE A 183 TYR 0.010 0.001 TYR B 206 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.199 Fit side-chains REVERT: A 181 LYS cc_start: 0.8516 (mmmt) cc_final: 0.7940 (mtpp) REVERT: A 485 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: B 93 GLU cc_start: 0.8149 (tp30) cc_final: 0.7845 (tt0) REVERT: B 583 MET cc_start: 0.7724 (mmm) cc_final: 0.7472 (mmm) REVERT: B 613 LEU cc_start: 0.8173 (pt) cc_final: 0.7846 (mt) outliers start: 22 outliers final: 12 residues processed: 108 average time/residue: 0.2460 time to fit residues: 36.5227 Evaluate side-chains 100 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 29 optimal weight: 0.0870 chunk 39 optimal weight: 0.2980 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 HIS B 620 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10043 Z= 0.188 Angle : 0.491 7.484 13553 Z= 0.257 Chirality : 0.041 0.147 1528 Planarity : 0.003 0.029 1720 Dihedral : 5.945 58.665 1402 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.15 % Allowed : 13.07 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1210 helix: 0.89 (0.24), residues: 509 sheet: 0.38 (0.38), residues: 194 loop : -1.46 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 585 HIS 0.004 0.001 HIS B 129 PHE 0.013 0.001 PHE A 531 TYR 0.010 0.001 TYR B 206 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 1.206 Fit side-chains REVERT: A 181 LYS cc_start: 0.8516 (mmmt) cc_final: 0.7942 (mtpp) REVERT: B 93 GLU cc_start: 0.8147 (tp30) cc_final: 0.7859 (tt0) REVERT: B 613 LEU cc_start: 0.8179 (pt) cc_final: 0.7853 (mt) outliers start: 23 outliers final: 15 residues processed: 107 average time/residue: 0.2266 time to fit residues: 34.5921 Evaluate side-chains 106 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 288 ASN B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10043 Z= 0.359 Angle : 0.583 7.715 13553 Z= 0.304 Chirality : 0.044 0.152 1528 Planarity : 0.004 0.031 1720 Dihedral : 6.738 57.245 1402 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.80 % Allowed : 12.79 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1210 helix: 0.66 (0.24), residues: 520 sheet: 0.19 (0.38), residues: 194 loop : -1.57 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 585 HIS 0.005 0.001 HIS B 129 PHE 0.012 0.002 PHE B 239 TYR 0.016 0.002 TYR B 437 ARG 0.003 0.000 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 1.238 Fit side-chains REVERT: A 181 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7986 (mtpp) REVERT: A 485 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: B 93 GLU cc_start: 0.8210 (tp30) cc_final: 0.7926 (tt0) REVERT: B 308 GLU cc_start: 0.7513 (pp20) cc_final: 0.6860 (tm-30) REVERT: B 352 MET cc_start: 0.6346 (tpp) cc_final: 0.5800 (ttm) REVERT: B 613 LEU cc_start: 0.8201 (pt) cc_final: 0.7883 (mt) outliers start: 30 outliers final: 24 residues processed: 112 average time/residue: 0.2228 time to fit residues: 35.6686 Evaluate side-chains 115 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 661 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10043 Z= 0.205 Angle : 0.504 6.837 13553 Z= 0.264 Chirality : 0.041 0.147 1528 Planarity : 0.004 0.030 1720 Dihedral : 6.029 56.842 1402 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.52 % Allowed : 13.63 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1210 helix: 0.88 (0.24), residues: 509 sheet: 0.25 (0.38), residues: 194 loop : -1.50 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 585 HIS 0.004 0.001 HIS B 129 PHE 0.009 0.001 PHE B 239 TYR 0.010 0.001 TYR B 437 ARG 0.002 0.000 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.085 Fit side-chains REVERT: A 181 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7941 (mtpp) REVERT: A 485 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: A 583 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6947 (mpp) REVERT: B 93 GLU cc_start: 0.8165 (tp30) cc_final: 0.7896 (tt0) REVERT: B 308 GLU cc_start: 0.7452 (pp20) cc_final: 0.6700 (tm-30) REVERT: B 312 GLU cc_start: 0.8313 (pt0) cc_final: 0.7904 (pt0) REVERT: B 352 MET cc_start: 0.6153 (tpp) cc_final: 0.5738 (ttm) REVERT: B 613 LEU cc_start: 0.8232 (pt) cc_final: 0.7892 (mt) outliers start: 27 outliers final: 22 residues processed: 107 average time/residue: 0.2099 time to fit residues: 31.7061 Evaluate side-chains 116 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 661 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10043 Z= 0.142 Angle : 0.470 9.126 13553 Z= 0.244 Chirality : 0.040 0.146 1528 Planarity : 0.003 0.028 1720 Dihedral : 5.339 49.006 1402 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.71 % Allowed : 13.73 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1210 helix: 0.98 (0.24), residues: 510 sheet: 0.38 (0.38), residues: 194 loop : -1.34 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 585 HIS 0.004 0.001 HIS A 88 PHE 0.009 0.001 PHE A 531 TYR 0.008 0.001 TYR A 673 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.270 Fit side-chains REVERT: A 181 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7921 (mtpp) REVERT: A 485 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: A 583 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6994 (mpp) REVERT: B 93 GLU cc_start: 0.8138 (tp30) cc_final: 0.7916 (tt0) REVERT: B 309 TRP cc_start: 0.7645 (t60) cc_final: 0.7432 (t60) REVERT: B 352 MET cc_start: 0.6111 (tpp) cc_final: 0.5759 (ttm) REVERT: B 583 MET cc_start: 0.7707 (mmm) cc_final: 0.7470 (mmm) outliers start: 29 outliers final: 20 residues processed: 118 average time/residue: 0.2318 time to fit residues: 38.1519 Evaluate side-chains 113 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 661 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10043 Z= 0.156 Angle : 0.487 8.632 13553 Z= 0.249 Chirality : 0.040 0.149 1528 Planarity : 0.003 0.027 1720 Dihedral : 5.478 52.669 1402 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.61 % Allowed : 14.29 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1210 helix: 1.04 (0.24), residues: 509 sheet: 0.34 (0.38), residues: 195 loop : -1.28 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 585 HIS 0.003 0.001 HIS A 88 PHE 0.006 0.001 PHE B 183 TYR 0.009 0.001 TYR B 437 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 1.108 Fit side-chains REVERT: A 181 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7926 (mtpp) REVERT: A 485 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: A 583 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7016 (mpp) REVERT: B 93 GLU cc_start: 0.8152 (tp30) cc_final: 0.7935 (tt0) REVERT: B 156 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 352 MET cc_start: 0.6094 (tpp) cc_final: 0.5717 (ttm) REVERT: B 583 MET cc_start: 0.7725 (mmm) cc_final: 0.7389 (mmm) outliers start: 28 outliers final: 23 residues processed: 110 average time/residue: 0.2374 time to fit residues: 36.3113 Evaluate side-chains 117 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 661 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10043 Z= 0.173 Angle : 0.495 8.793 13553 Z= 0.254 Chirality : 0.040 0.150 1528 Planarity : 0.003 0.027 1720 Dihedral : 5.597 54.212 1402 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.61 % Allowed : 14.38 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1210 helix: 1.03 (0.24), residues: 509 sheet: 0.31 (0.38), residues: 194 loop : -1.27 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 585 HIS 0.003 0.001 HIS B 129 PHE 0.011 0.001 PHE A 531 TYR 0.009 0.001 TYR B 437 ARG 0.003 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 1.283 Fit side-chains REVERT: A 181 LYS cc_start: 0.8494 (mmmt) cc_final: 0.7928 (mtpp) REVERT: A 485 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: A 583 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: B 93 GLU cc_start: 0.8166 (tp30) cc_final: 0.7946 (tt0) REVERT: B 156 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 308 GLU cc_start: 0.7317 (pp20) cc_final: 0.6645 (tm-30) REVERT: B 352 MET cc_start: 0.6138 (tpp) cc_final: 0.5700 (ttm) REVERT: B 495 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8008 (mmp80) outliers start: 28 outliers final: 24 residues processed: 105 average time/residue: 0.2334 time to fit residues: 34.7056 Evaluate side-chains 116 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 661 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.0070 chunk 89 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.0040 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.087831 restraints weight = 17284.866| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.74 r_work: 0.3003 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10043 Z= 0.130 Angle : 0.472 8.311 13553 Z= 0.242 Chirality : 0.039 0.145 1528 Planarity : 0.003 0.028 1720 Dihedral : 5.194 48.214 1402 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.33 % Allowed : 14.57 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1210 helix: 1.12 (0.24), residues: 508 sheet: 0.36 (0.38), residues: 194 loop : -1.20 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 585 HIS 0.003 0.001 HIS A 88 PHE 0.011 0.001 PHE A 531 TYR 0.009 0.001 TYR A 673 ARG 0.004 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.69 seconds wall clock time: 39 minutes 38.43 seconds (2378.43 seconds total)