Starting phenix.real_space_refine on Wed Apr 17 05:02:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfk_10493/04_2024/6tfk_10493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfk_10493/04_2024/6tfk_10493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfk_10493/04_2024/6tfk_10493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfk_10493/04_2024/6tfk_10493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfk_10493/04_2024/6tfk_10493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tfk_10493/04_2024/6tfk_10493.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 56 5.16 5 C 13760 2.51 5 N 3532 2.21 5 O 4344 1.98 5 H 21544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 761": "OE1" <-> "OE2" Residue "C PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 350": "OE1" <-> "OE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 390": "OE1" <-> "OE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 720": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 761": "OE1" <-> "OE2" Residue "D PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 43237 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "C" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "D" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.25, per 1000 atoms: 0.42 Number of scatterers: 43237 At special positions: 0 Unit cell: (150.865, 150.865, 155.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 Mg 1 11.99 O 4344 8.00 N 3532 7.00 C 13760 6.00 H 21544 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.10 Conformation dependent library (CDL) restraints added in 4.7 seconds 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 27.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 95 through 182 Proline residue: A 119 - end of helix Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 267 through 296 Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'B' and resid 95 through 182 Proline residue: B 119 - end of helix Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 267 through 296 Processing helix chain 'B' and resid 304 through 321 Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'C' and resid 95 through 182 Proline residue: C 119 - end of helix Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.504A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 267 through 296 Processing helix chain 'C' and resid 304 through 321 Processing helix chain 'C' and resid 396 through 399 No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 511 through 518 Processing helix chain 'D' and resid 95 through 182 Proline residue: D 119 - end of helix Proline residue: D 171 - end of helix Processing helix chain 'D' and resid 204 through 219 Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 267 through 296 Processing helix chain 'D' and resid 304 through 321 Processing helix chain 'D' and resid 396 through 399 No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 511 through 518 Processing sheet with id= A, first strand: chain 'A' and resid 329 through 331 Processing sheet with id= B, first strand: chain 'A' and resid 334 through 338 Processing sheet with id= C, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.667A pdb=" N THR A 439 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 425 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A 437 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A 427 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 435 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN A 453 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 479 through 482 removed outlier: 5.570A pdb=" N LEU A 357 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA A 375 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 359 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 407 through 409 Processing sheet with id= F, first strand: chain 'A' and resid 573 through 575 Processing sheet with id= G, first strand: chain 'A' and resid 581 through 584 removed outlier: 4.059A pdb=" N TYR A 619 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASP A 611 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 617 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 596 through 598 Processing sheet with id= I, first strand: chain 'A' and resid 685 through 687 Processing sheet with id= J, first strand: chain 'A' and resid 690 through 693 Processing sheet with id= K, first strand: chain 'B' and resid 329 through 331 Processing sheet with id= L, first strand: chain 'B' and resid 334 through 338 Processing sheet with id= M, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.666A pdb=" N THR B 439 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 425 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B 437 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B 427 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 435 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASN B 453 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 479 through 482 removed outlier: 5.578A pdb=" N LEU B 357 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 375 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY B 359 " --> pdb=" O TYR B 373 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 407 through 409 Processing sheet with id= P, first strand: chain 'B' and resid 573 through 575 Processing sheet with id= Q, first strand: chain 'B' and resid 581 through 584 removed outlier: 4.065A pdb=" N TYR B 619 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP B 611 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 617 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 596 through 598 Processing sheet with id= S, first strand: chain 'B' and resid 685 through 687 Processing sheet with id= T, first strand: chain 'B' and resid 690 through 693 Processing sheet with id= U, first strand: chain 'C' and resid 329 through 331 Processing sheet with id= V, first strand: chain 'C' and resid 334 through 338 Processing sheet with id= W, first strand: chain 'C' and resid 346 through 350 removed outlier: 6.687A pdb=" N THR C 439 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 425 " --> pdb=" O GLU C 437 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU C 437 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE C 427 " --> pdb=" O ARG C 435 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG C 435 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN C 453 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 479 through 482 removed outlier: 5.596A pdb=" N LEU C 357 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA C 375 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY C 359 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 407 through 409 Processing sheet with id= Z, first strand: chain 'C' and resid 573 through 575 Processing sheet with id= AA, first strand: chain 'C' and resid 581 through 584 removed outlier: 4.056A pdb=" N TYR C 619 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP C 611 " --> pdb=" O ILE C 617 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 617 " --> pdb=" O ASP C 611 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 596 through 598 Processing sheet with id= AC, first strand: chain 'C' and resid 685 through 687 Processing sheet with id= AD, first strand: chain 'C' and resid 690 through 693 Processing sheet with id= AE, first strand: chain 'D' and resid 329 through 331 Processing sheet with id= AF, first strand: chain 'D' and resid 334 through 338 Processing sheet with id= AG, first strand: chain 'D' and resid 346 through 350 removed outlier: 6.682A pdb=" N THR D 439 " --> pdb=" O THR D 423 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE D 425 " --> pdb=" O GLU D 437 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU D 437 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D 427 " --> pdb=" O ARG D 435 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG D 435 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN D 453 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 479 through 482 removed outlier: 5.588A pdb=" N LEU D 357 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA D 375 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY D 359 " --> pdb=" O TYR D 373 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 407 through 409 Processing sheet with id= AJ, first strand: chain 'D' and resid 573 through 575 Processing sheet with id= AK, first strand: chain 'D' and resid 581 through 584 removed outlier: 4.050A pdb=" N TYR D 619 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASP D 611 " --> pdb=" O ILE D 617 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE D 617 " --> pdb=" O ASP D 611 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 596 through 598 Processing sheet with id= AM, first strand: chain 'D' and resid 685 through 687 Processing sheet with id= AN, first strand: chain 'D' and resid 690 through 693 1071 hydrogen bonds defined for protein. 2961 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: 18.67 Time building geometry restraints manager: 39.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21532 1.03 - 1.23: 14 1.23 - 1.42: 9114 1.42 - 1.62: 12840 1.62 - 1.81: 100 Bond restraints: 43600 Sorted by residual: bond pdb=" C GLN D 404 " pdb=" N SER D 405 " ideal model delta sigma weight residual 1.328 1.346 -0.018 1.25e-02 6.40e+03 2.03e+00 bond pdb=" N ASP C 403 " pdb=" CA ASP C 403 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.46e+00 bond pdb=" N MET A 746 " pdb=" CA MET A 746 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" N MET B 746 " pdb=" CA MET B 746 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" CA MET B 746 " pdb=" CB MET B 746 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.69e-02 3.50e+03 8.35e-01 ... (remaining 43595 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 531 106.95 - 113.71: 52944 113.71 - 120.47: 13607 120.47 - 127.23: 11646 127.23 - 133.99: 124 Bond angle restraints: 78852 Sorted by residual: angle pdb=" C ASP C 403 " pdb=" CA ASP C 403 " pdb=" CB ASP C 403 " ideal model delta sigma weight residual 110.42 116.68 -6.26 1.99e+00 2.53e-01 9.91e+00 angle pdb=" N SER D 405 " pdb=" CA SER D 405 " pdb=" C SER D 405 " ideal model delta sigma weight residual 108.54 112.48 -3.94 1.41e+00 5.03e-01 7.81e+00 angle pdb=" C ASP D 403 " pdb=" CA ASP D 403 " pdb=" CB ASP D 403 " ideal model delta sigma weight residual 110.42 115.89 -5.47 1.99e+00 2.53e-01 7.55e+00 angle pdb=" N ILE C 358 " pdb=" CA ILE C 358 " pdb=" C ILE C 358 " ideal model delta sigma weight residual 113.71 111.37 2.34 9.50e-01 1.11e+00 6.07e+00 angle pdb=" N ILE A 358 " pdb=" CA ILE A 358 " pdb=" C ILE A 358 " ideal model delta sigma weight residual 113.71 111.39 2.32 9.50e-01 1.11e+00 5.96e+00 ... (remaining 78847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 18778 13.77 - 27.54: 1221 27.54 - 41.31: 272 41.31 - 55.07: 154 55.07 - 68.84: 51 Dihedral angle restraints: 20476 sinusoidal: 11216 harmonic: 9260 Sorted by residual: dihedral pdb=" CA GLN D 404 " pdb=" C GLN D 404 " pdb=" N SER D 405 " pdb=" CA SER D 405 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA SER B 405 " pdb=" C SER B 405 " pdb=" N GLU B 406 " pdb=" CA GLU B 406 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLN C 404 " pdb=" C GLN C 404 " pdb=" N SER C 405 " pdb=" CA SER C 405 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2262 0.031 - 0.062: 796 0.062 - 0.094: 178 0.094 - 0.125: 167 0.125 - 0.156: 33 Chirality restraints: 3436 Sorted by residual: chirality pdb=" CA ILE B 788 " pdb=" N ILE B 788 " pdb=" C ILE B 788 " pdb=" CB ILE B 788 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE A 733 " pdb=" N ILE A 733 " pdb=" C ILE A 733 " pdb=" CB ILE A 733 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE C 733 " pdb=" N ILE C 733 " pdb=" C ILE C 733 " pdb=" CB ILE C 733 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 3433 not shown) Planarity restraints: 6484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS D 401 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO D 402 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 402 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 402 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 675 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO B 676 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 676 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 676 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 675 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 676 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " 0.015 5.00e-02 4.00e+02 ... (remaining 6481 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1696 2.17 - 2.78: 90255 2.78 - 3.39: 118702 3.39 - 3.99: 155600 3.99 - 4.60: 247341 Nonbonded interactions: 613594 Sorted by model distance: nonbonded pdb=" H ASN C 490 " pdb=" O LYS C 508 " model vdw 1.569 1.850 nonbonded pdb=" H ASN A 490 " pdb=" O LYS A 508 " model vdw 1.569 1.850 nonbonded pdb=" H ASN B 490 " pdb=" O LYS B 508 " model vdw 1.570 1.850 nonbonded pdb=" H ASN D 490 " pdb=" O LYS D 508 " model vdw 1.572 1.850 nonbonded pdb=" HG1 THR D 685 " pdb=" O LYS D 708 " model vdw 1.625 1.850 ... (remaining 613589 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 95 through 789) 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 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: 3.090 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: 1.020 Extract box with map and model: 6.030 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 141.850 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.002 0.035 22056 Z= 0.141 Angle : 0.469 6.264 29856 Z= 0.264 Chirality : 0.041 0.156 3436 Planarity : 0.002 0.031 3836 Dihedral : 9.645 68.843 8216 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.15), residues: 2708 helix: 0.49 (0.17), residues: 804 sheet: -1.88 (0.17), residues: 720 loop : -3.08 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 552 HIS 0.003 0.001 HIS B 235 PHE 0.007 0.001 PHE C 765 TYR 0.008 0.001 TYR C 475 ARG 0.002 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 349 time to evaluate : 3.400 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: 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 257 THR cc_start: 0.8624 (m) cc_final: 0.8407 (m) REVERT: A 679 ILE cc_start: 0.2914 (OUTLIER) cc_final: 0.2491 (pp) REVERT: A 756 PHE cc_start: 0.7794 (p90) cc_final: 0.7559 (p90) REVERT: B 635 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7958 (mtp180) REVERT: B 756 PHE cc_start: 0.7794 (p90) cc_final: 0.7514 (p90) REVERT: C 679 ILE cc_start: 0.2863 (OUTLIER) cc_final: 0.2516 (mt) REVERT: C 756 PHE cc_start: 0.7855 (p90) cc_final: 0.7644 (p90) REVERT: D 598 GLN cc_start: 0.8104 (tt0) cc_final: 0.7822 (tt0) outliers start: 6 outliers final: 2 residues processed: 355 average time/residue: 2.5658 time to fit residues: 1064.8390 Evaluate side-chains 194 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 247 optimal weight: 0.5980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN C 691 ASN ** D 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22056 Z= 0.299 Angle : 0.558 5.976 29856 Z= 0.297 Chirality : 0.042 0.147 3436 Planarity : 0.004 0.066 3836 Dihedral : 4.784 43.293 2932 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.79 % Favored : 92.13 % Rotamer: Outliers : 2.07 % Allowed : 8.41 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2708 helix: 1.40 (0.17), residues: 804 sheet: -1.47 (0.17), residues: 816 loop : -2.96 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 552 HIS 0.003 0.001 HIS A 235 PHE 0.012 0.001 PHE D 636 TYR 0.013 0.001 TYR C 410 ARG 0.005 0.000 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 3.503 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.7680 (ttm) cc_final: 0.7389 (ttm) REVERT: A 458 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: A 562 ASP cc_start: 0.5399 (OUTLIER) cc_final: 0.4693 (p0) REVERT: A 635 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7631 (mtp180) REVERT: A 679 ILE cc_start: 0.2644 (OUTLIER) cc_final: 0.2319 (mt) REVERT: B 562 ASP cc_start: 0.5547 (OUTLIER) cc_final: 0.4977 (p0) REVERT: B 756 PHE cc_start: 0.7812 (p90) cc_final: 0.7568 (p90) REVERT: C 562 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.4860 (p0) REVERT: C 679 ILE cc_start: 0.2459 (OUTLIER) cc_final: 0.2168 (mt) REVERT: D 137 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8615 (mp) REVERT: D 347 MET cc_start: 0.7688 (ttm) cc_final: 0.7370 (ttm) REVERT: D 535 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8384 (mp) REVERT: D 562 ASP cc_start: 0.5142 (OUTLIER) cc_final: 0.4395 (p0) REVERT: D 679 ILE cc_start: 0.2755 (OUTLIER) cc_final: 0.2277 (mt) outliers start: 51 outliers final: 21 residues processed: 216 average time/residue: 2.2294 time to fit residues: 575.3539 Evaluate side-chains 183 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN B 691 ASN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22056 Z= 0.283 Angle : 0.530 5.878 29856 Z= 0.284 Chirality : 0.042 0.160 3436 Planarity : 0.004 0.040 3836 Dihedral : 4.818 43.222 2930 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.57 % Favored : 91.36 % Rotamer: Outliers : 2.64 % Allowed : 9.51 % Favored : 87.85 % 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: -1.40 (0.16), residues: 2708 helix: 1.75 (0.17), residues: 804 sheet: -1.29 (0.17), residues: 820 loop : -2.78 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 552 HIS 0.003 0.001 HIS A 235 PHE 0.009 0.001 PHE D 636 TYR 0.011 0.001 TYR B 410 ARG 0.005 0.000 ARG D 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 170 time to evaluate : 3.716 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: 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 144 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7778 (mttt) REVERT: A 347 MET cc_start: 0.7674 (ttm) cc_final: 0.7412 (ttm) REVERT: A 562 ASP cc_start: 0.5276 (OUTLIER) cc_final: 0.4627 (p0) REVERT: A 635 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7623 (mtp180) REVERT: B 129 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7870 (mmt) REVERT: B 144 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7742 (mttt) REVERT: B 465 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7067 (mtm180) REVERT: B 562 ASP cc_start: 0.5451 (OUTLIER) cc_final: 0.4884 (p0) REVERT: B 735 ASN cc_start: 0.6155 (t0) cc_final: 0.5927 (t0) REVERT: B 756 PHE cc_start: 0.7740 (p90) cc_final: 0.7500 (p90) REVERT: C 562 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.4832 (p0) REVERT: C 635 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7698 (mtp180) REVERT: C 679 ILE cc_start: 0.2380 (OUTLIER) cc_final: 0.2104 (mt) REVERT: D 129 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7907 (mmt) REVERT: D 137 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8555 (mp) REVERT: D 347 MET cc_start: 0.7658 (ttm) cc_final: 0.7338 (ttm) REVERT: D 562 ASP cc_start: 0.5014 (OUTLIER) cc_final: 0.4320 (p0) REVERT: D 679 ILE cc_start: 0.2266 (OUTLIER) cc_final: 0.1990 (mt) outliers start: 65 outliers final: 26 residues processed: 219 average time/residue: 2.2668 time to fit residues: 592.3861 Evaluate side-chains 189 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 715 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 262 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22056 Z= 0.308 Angle : 0.535 5.914 29856 Z= 0.289 Chirality : 0.043 0.139 3436 Planarity : 0.004 0.037 3836 Dihedral : 4.818 43.286 2928 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.90 % Favored : 91.99 % Rotamer: Outliers : 2.93 % Allowed : 9.80 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2708 helix: 1.86 (0.17), residues: 804 sheet: -1.18 (0.17), residues: 820 loop : -2.70 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 552 HIS 0.003 0.001 HIS D 235 PHE 0.007 0.001 PHE D 636 TYR 0.012 0.001 TYR B 410 ARG 0.003 0.000 ARG D 435 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 160 time to evaluate : 4.011 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8437 (mmm) cc_final: 0.7930 (mmt) REVERT: A 144 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7786 (mttt) REVERT: A 347 MET cc_start: 0.7683 (ttm) cc_final: 0.7425 (ttm) REVERT: A 361 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 458 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: A 504 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8001 (p) REVERT: A 526 LYS cc_start: 0.7638 (tptm) cc_final: 0.7375 (ptmm) REVERT: A 562 ASP cc_start: 0.5294 (OUTLIER) cc_final: 0.4637 (p0) REVERT: A 635 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7639 (ttp80) REVERT: B 129 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7911 (mmt) REVERT: B 144 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7758 (mttt) REVERT: B 361 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: B 465 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7032 (mtm180) REVERT: B 504 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8004 (p) REVERT: B 525 THR cc_start: 0.8181 (p) cc_final: 0.7636 (p) REVERT: B 562 ASP cc_start: 0.5456 (OUTLIER) cc_final: 0.4928 (p0) REVERT: B 635 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7642 (ttp80) REVERT: B 756 PHE cc_start: 0.7680 (p90) cc_final: 0.7403 (p90) REVERT: C 129 MET cc_start: 0.8527 (mmm) cc_final: 0.8023 (mmt) REVERT: C 465 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6976 (mtm180) REVERT: C 504 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8002 (p) REVERT: C 525 THR cc_start: 0.8129 (p) cc_final: 0.7576 (p) REVERT: C 562 ASP cc_start: 0.5446 (OUTLIER) cc_final: 0.4859 (p0) REVERT: C 635 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7706 (ttp80) REVERT: C 679 ILE cc_start: 0.2260 (OUTLIER) cc_final: 0.2005 (mt) REVERT: D 129 MET cc_start: 0.8484 (mmm) cc_final: 0.7905 (mmt) REVERT: D 137 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8543 (mp) REVERT: D 347 MET cc_start: 0.7647 (ttm) cc_final: 0.7340 (ttm) REVERT: D 361 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: D 465 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6815 (mtm180) REVERT: D 504 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7984 (p) REVERT: D 525 THR cc_start: 0.8167 (p) cc_final: 0.7622 (p) REVERT: D 562 ASP cc_start: 0.5089 (OUTLIER) cc_final: 0.4438 (p0) REVERT: D 679 ILE cc_start: 0.2167 (OUTLIER) cc_final: 0.1893 (mt) outliers start: 72 outliers final: 26 residues processed: 217 average time/residue: 2.3291 time to fit residues: 598.0548 Evaluate side-chains 200 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 ASN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22056 Z= 0.260 Angle : 0.518 6.100 29856 Z= 0.278 Chirality : 0.042 0.142 3436 Planarity : 0.003 0.034 3836 Dihedral : 4.754 42.036 2928 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 2.68 % Allowed : 10.93 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2708 helix: 2.03 (0.17), residues: 804 sheet: -1.09 (0.18), residues: 788 loop : -2.71 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 552 HIS 0.003 0.001 HIS D 235 PHE 0.011 0.001 PHE A 760 TYR 0.014 0.001 TYR B 410 ARG 0.003 0.000 ARG D 435 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 157 time to evaluate : 3.604 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8401 (mmm) cc_final: 0.7889 (mmt) REVERT: A 144 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7782 (mttt) REVERT: A 347 MET cc_start: 0.7705 (ttm) cc_final: 0.7400 (ttm) REVERT: A 361 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: A 458 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: A 465 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6874 (mtm180) REVERT: A 504 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7973 (p) REVERT: A 562 ASP cc_start: 0.5289 (OUTLIER) cc_final: 0.4633 (p0) REVERT: A 635 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7619 (ttp80) REVERT: B 129 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7917 (mmt) REVERT: B 144 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7808 (mttt) REVERT: B 465 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6912 (mtm180) REVERT: B 504 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8036 (p) REVERT: B 562 ASP cc_start: 0.5460 (OUTLIER) cc_final: 0.4944 (p0) REVERT: B 756 PHE cc_start: 0.7657 (p90) cc_final: 0.7411 (p90) REVERT: C 129 MET cc_start: 0.8465 (mmm) cc_final: 0.7961 (mmt) REVERT: C 465 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6860 (mtm180) REVERT: C 504 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8044 (p) REVERT: C 562 ASP cc_start: 0.5458 (OUTLIER) cc_final: 0.4882 (p0) REVERT: C 634 LYS cc_start: 0.7150 (mmtp) cc_final: 0.6477 (mtpm) REVERT: C 635 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7696 (ttp80) REVERT: C 679 ILE cc_start: 0.1967 (OUTLIER) cc_final: 0.1660 (mt) REVERT: D 129 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7921 (mmt) REVERT: D 137 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8517 (mp) REVERT: D 347 MET cc_start: 0.7645 (ttm) cc_final: 0.7351 (ttm) REVERT: D 361 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: D 465 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6809 (mtm180) REVERT: D 504 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8041 (p) REVERT: D 635 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7597 (ttp80) REVERT: D 679 ILE cc_start: 0.2349 (OUTLIER) cc_final: 0.2082 (mt) outliers start: 66 outliers final: 29 residues processed: 214 average time/residue: 2.2758 time to fit residues: 581.0003 Evaluate side-chains 198 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 148 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 715 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22056 Z= 0.244 Angle : 0.511 8.409 29856 Z= 0.274 Chirality : 0.042 0.167 3436 Planarity : 0.003 0.031 3836 Dihedral : 4.712 39.528 2928 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 2.56 % Allowed : 11.50 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2708 helix: 2.20 (0.17), residues: 804 sheet: -1.07 (0.18), residues: 788 loop : -2.67 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 552 HIS 0.003 0.001 HIS D 235 PHE 0.008 0.001 PHE A 783 TYR 0.013 0.001 TYR C 410 ARG 0.003 0.000 ARG D 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 148 time to evaluate : 3.774 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7907 (mmt) REVERT: A 144 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7789 (mttt) REVERT: A 347 MET cc_start: 0.7717 (ttm) cc_final: 0.7420 (ttm) REVERT: A 361 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: A 458 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: A 465 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6806 (mtm180) REVERT: A 504 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 562 ASP cc_start: 0.5408 (OUTLIER) cc_final: 0.4759 (p0) REVERT: A 635 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7585 (ttp80) REVERT: B 129 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7895 (mmt) REVERT: B 144 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7780 (mttt) REVERT: B 504 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8040 (p) REVERT: B 562 ASP cc_start: 0.5467 (OUTLIER) cc_final: 0.4970 (p0) REVERT: B 635 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7866 (ttp80) REVERT: B 756 PHE cc_start: 0.7671 (p90) cc_final: 0.7437 (p90) REVERT: C 129 MET cc_start: 0.8468 (mmm) cc_final: 0.7954 (mmt) REVERT: C 435 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7750 (ttm-80) REVERT: C 465 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6815 (mtm180) REVERT: C 504 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8037 (p) REVERT: C 562 ASP cc_start: 0.5583 (OUTLIER) cc_final: 0.5003 (p0) REVERT: C 634 LYS cc_start: 0.7159 (mmtp) cc_final: 0.6472 (mtpm) REVERT: C 635 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7670 (ttp80) REVERT: C 679 ILE cc_start: 0.1633 (OUTLIER) cc_final: 0.1413 (mt) REVERT: D 124 MET cc_start: 0.7344 (mmm) cc_final: 0.7131 (mtp) REVERT: D 129 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7969 (mmt) REVERT: D 137 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8504 (mp) REVERT: D 347 MET cc_start: 0.7655 (ttm) cc_final: 0.7394 (ttm) REVERT: D 361 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: D 465 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6881 (mtm180) REVERT: D 504 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8034 (p) REVERT: D 635 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7529 (ttp80) REVERT: D 679 ILE cc_start: 0.2637 (OUTLIER) cc_final: 0.2371 (mt) outliers start: 63 outliers final: 31 residues processed: 201 average time/residue: 2.3409 time to fit residues: 558.1457 Evaluate side-chains 199 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 146 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 262 optimal weight: 20.0000 chunk 164 optimal weight: 0.0970 chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22056 Z= 0.159 Angle : 0.487 10.051 29856 Z= 0.260 Chirality : 0.041 0.164 3436 Planarity : 0.003 0.029 3836 Dihedral : 4.582 37.826 2928 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 1.99 % Allowed : 12.07 % Favored : 85.93 % 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: -0.83 (0.16), residues: 2708 helix: 2.40 (0.18), residues: 804 sheet: -0.90 (0.19), residues: 756 loop : -2.57 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 658 HIS 0.002 0.001 HIS D 235 PHE 0.023 0.001 PHE C 636 TYR 0.011 0.001 TYR B 410 ARG 0.002 0.000 ARG D 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 159 time to evaluate : 3.477 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8390 (mmm) cc_final: 0.7912 (mmt) REVERT: A 144 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7771 (mttt) REVERT: A 347 MET cc_start: 0.7713 (ttm) cc_final: 0.7452 (ttm) REVERT: A 458 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: A 465 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6802 (mtm180) REVERT: A 504 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 129 MET cc_start: 0.8488 (mmm) cc_final: 0.7996 (mmt) REVERT: B 144 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7774 (mttt) REVERT: B 168 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 465 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6902 (mtm180) REVERT: B 562 ASP cc_start: 0.5474 (OUTLIER) cc_final: 0.4969 (p0) REVERT: B 756 PHE cc_start: 0.7663 (p90) cc_final: 0.7436 (p90) REVERT: C 129 MET cc_start: 0.8439 (mmm) cc_final: 0.7930 (mmt) REVERT: C 168 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7817 (mt-10) REVERT: C 188 PHE cc_start: 0.6756 (t80) cc_final: 0.6537 (t80) REVERT: C 465 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6831 (mtm180) REVERT: C 504 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8030 (p) REVERT: C 634 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6433 (mtpm) REVERT: C 679 ILE cc_start: 0.1581 (OUTLIER) cc_final: 0.1359 (mt) REVERT: D 113 MET cc_start: 0.6303 (ppp) cc_final: 0.5932 (ppp) REVERT: D 129 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7954 (mmt) REVERT: D 137 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8491 (mp) REVERT: D 168 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7823 (mt-10) REVERT: D 347 MET cc_start: 0.7655 (ttm) cc_final: 0.7344 (ttm) REVERT: D 465 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6795 (mtm180) REVERT: D 679 ILE cc_start: 0.2589 (OUTLIER) cc_final: 0.2333 (mt) outliers start: 49 outliers final: 26 residues processed: 201 average time/residue: 2.4024 time to fit residues: 573.6164 Evaluate side-chains 187 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22056 Z= 0.290 Angle : 0.527 8.371 29856 Z= 0.283 Chirality : 0.042 0.153 3436 Planarity : 0.003 0.029 3836 Dihedral : 4.707 37.139 2928 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.57 % Favored : 91.29 % Rotamer: Outliers : 2.15 % Allowed : 12.44 % Favored : 85.41 % 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: -1.03 (0.16), residues: 2708 helix: 2.19 (0.17), residues: 804 sheet: -1.06 (0.18), residues: 788 loop : -2.65 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 684 HIS 0.003 0.001 HIS D 235 PHE 0.020 0.001 PHE C 636 TYR 0.014 0.001 TYR A 410 ARG 0.003 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 146 time to evaluate : 3.335 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 129 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7922 (mmt) REVERT: A 144 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7797 (mttt) REVERT: A 347 MET cc_start: 0.7723 (ttm) cc_final: 0.7437 (ttm) REVERT: A 458 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: A 465 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6797 (mtm180) REVERT: A 504 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7957 (p) REVERT: A 526 LYS cc_start: 0.7521 (tptm) cc_final: 0.7317 (ptmt) REVERT: B 129 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7944 (mmt) REVERT: B 144 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7795 (mttt) REVERT: B 465 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6928 (mtm180) REVERT: B 504 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8025 (p) REVERT: B 562 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5118 (p0) REVERT: B 756 PHE cc_start: 0.7661 (p90) cc_final: 0.7432 (p90) REVERT: C 129 MET cc_start: 0.8437 (mmm) cc_final: 0.7973 (mmt) REVERT: C 504 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7973 (p) REVERT: C 562 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.5016 (p0) REVERT: C 679 ILE cc_start: 0.1629 (OUTLIER) cc_final: 0.1413 (mt) REVERT: C 746 MET cc_start: 0.5307 (ttm) cc_final: 0.5105 (tpp) REVERT: D 113 MET cc_start: 0.6283 (ppp) cc_final: 0.5976 (ppp) REVERT: D 129 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7959 (mmt) REVERT: D 137 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8455 (mp) REVERT: D 347 MET cc_start: 0.7667 (ttm) cc_final: 0.7418 (ttm) REVERT: D 465 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6844 (mtm180) REVERT: D 504 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7963 (p) REVERT: D 562 ASP cc_start: 0.5178 (OUTLIER) cc_final: 0.4514 (p0) REVERT: D 635 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8187 (ttp80) REVERT: D 679 ILE cc_start: 0.2611 (OUTLIER) cc_final: 0.2330 (mt) REVERT: D 746 MET cc_start: 0.5430 (ttm) cc_final: 0.5144 (tpp) outliers start: 53 outliers final: 26 residues processed: 191 average time/residue: 2.2141 time to fit residues: 507.0325 Evaluate side-chains 188 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 635 ARG Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 715 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 220 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22056 Z= 0.205 Angle : 0.509 10.419 29856 Z= 0.272 Chirality : 0.041 0.155 3436 Planarity : 0.003 0.029 3836 Dihedral : 4.639 36.086 2928 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.17 % Rotamer: Outliers : 2.03 % Allowed : 12.76 % Favored : 85.20 % 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: -0.93 (0.16), residues: 2708 helix: 2.34 (0.17), residues: 804 sheet: -1.09 (0.18), residues: 796 loop : -2.59 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 684 HIS 0.003 0.001 HIS D 235 PHE 0.019 0.001 PHE C 636 TYR 0.048 0.001 TYR C 766 ARG 0.016 0.000 ARG C 734 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 4.091 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: A 129 MET cc_start: 0.8385 (mmm) cc_final: 0.7874 (mmt) REVERT: A 144 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7784 (mttt) REVERT: A 347 MET cc_start: 0.7719 (ttm) cc_final: 0.7456 (ttm) REVERT: A 458 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: A 504 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8028 (p) REVERT: A 562 ASP cc_start: 0.5421 (OUTLIER) cc_final: 0.4770 (p0) REVERT: B 124 MET cc_start: 0.7364 (mmm) cc_final: 0.7137 (mtp) REVERT: B 129 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7929 (mmt) REVERT: B 144 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7782 (mttt) REVERT: B 168 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 504 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8036 (p) REVERT: B 562 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5128 (p0) REVERT: B 756 PHE cc_start: 0.7664 (p90) cc_final: 0.7449 (p90) REVERT: C 129 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7953 (mmt) REVERT: C 504 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8043 (p) REVERT: C 746 MET cc_start: 0.5299 (ttm) cc_final: 0.4951 (tpp) REVERT: D 113 MET cc_start: 0.6285 (ppp) cc_final: 0.5962 (ppp) REVERT: D 129 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7982 (mmt) REVERT: D 168 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 347 MET cc_start: 0.7665 (ttm) cc_final: 0.7358 (ttm) REVERT: D 465 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6757 (mtm180) REVERT: D 504 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8033 (p) REVERT: D 562 ASP cc_start: 0.5167 (OUTLIER) cc_final: 0.4456 (p0) REVERT: D 746 MET cc_start: 0.5400 (ttm) cc_final: 0.5120 (tpp) outliers start: 50 outliers final: 26 residues processed: 191 average time/residue: 2.2196 time to fit residues: 512.5444 Evaluate side-chains 183 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 715 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 0.8980 chunk 258 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 270 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22056 Z= 0.236 Angle : 0.512 10.420 29856 Z= 0.274 Chirality : 0.042 0.149 3436 Planarity : 0.003 0.033 3836 Dihedral : 4.543 19.208 2924 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.12 % Favored : 91.73 % Rotamer: Outliers : 1.95 % Allowed : 13.05 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2708 helix: 2.30 (0.17), residues: 804 sheet: -1.13 (0.18), residues: 796 loop : -2.60 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 684 HIS 0.003 0.001 HIS C 235 PHE 0.019 0.001 PHE C 636 TYR 0.015 0.001 TYR D 410 ARG 0.006 0.000 ARG C 734 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 146 time to evaluate : 3.401 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: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7921 (mmt) REVERT: A 144 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7775 (mttt) REVERT: A 347 MET cc_start: 0.7720 (ttm) cc_final: 0.7459 (ttm) REVERT: A 458 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: A 562 ASP cc_start: 0.5429 (OUTLIER) cc_final: 0.4768 (p0) REVERT: B 129 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7940 (mmt) REVERT: B 144 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7786 (mttt) REVERT: B 504 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 562 ASP cc_start: 0.5593 (OUTLIER) cc_final: 0.5122 (p0) REVERT: B 635 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7961 (ttp80) REVERT: B 756 PHE cc_start: 0.7655 (p90) cc_final: 0.7444 (p90) REVERT: C 129 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7959 (mmt) REVERT: C 504 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7966 (p) REVERT: C 562 ASP cc_start: 0.5485 (OUTLIER) cc_final: 0.4913 (p0) REVERT: C 746 MET cc_start: 0.5186 (ttm) cc_final: 0.4855 (tpp) REVERT: D 129 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7995 (mmt) REVERT: D 347 MET cc_start: 0.7672 (ttm) cc_final: 0.7364 (ttm) REVERT: D 562 ASP cc_start: 0.5198 (OUTLIER) cc_final: 0.4484 (p0) outliers start: 48 outliers final: 30 residues processed: 188 average time/residue: 2.0953 time to fit residues: 477.4943 Evaluate side-chains 187 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 715 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.206501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128996 restraints weight = 76860.480| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.30 r_work: 0.3355 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22056 Z= 0.158 Angle : 0.483 8.866 29856 Z= 0.257 Chirality : 0.041 0.147 3436 Planarity : 0.003 0.035 3836 Dihedral : 4.397 18.232 2924 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.68 % Favored : 93.17 % Rotamer: Outliers : 1.87 % Allowed : 13.25 % Favored : 84.88 % 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: -0.77 (0.16), residues: 2708 helix: 2.54 (0.18), residues: 804 sheet: -1.01 (0.19), residues: 732 loop : -2.48 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 658 HIS 0.003 0.001 HIS A 235 PHE 0.019 0.001 PHE C 636 TYR 0.013 0.001 TYR A 410 ARG 0.006 0.000 ARG D 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12602.62 seconds wall clock time: 228 minutes 39.94 seconds (13719.94 seconds total)