Starting phenix.real_space_refine on Wed Feb 14 05:59:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2024/7r8d_24316_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2024/7r8d_24316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2024/7r8d_24316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2024/7r8d_24316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2024/7r8d_24316_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2024/7r8d_24316_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5756 2.51 5 N 1414 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B ASP 605": "OD1" <-> "OD2" Residue "B GLU 615": "OE1" <-> "OE2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 659": "NH1" <-> "NH2" Residue "B ARG 666": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8762 At special positions: 0 Unit cell: (102.459, 72.471, 120.785, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1524 8.00 N 1414 7.00 C 5756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.7 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 53.9% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 301 through 309 removed outlier: 4.841A pdb=" N VAL A 305 " --> pdb=" O CYS A 302 " (cutoff:3.500A) Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 389 through 404 removed outlier: 3.914A pdb=" N CYS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 439 through 477 Proline residue: A 460 - end of helix Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 483 through 509 Proline residue: A 496 - end of helix Proline residue: A 502 - end of helix removed outlier: 4.006A pdb=" N ILE A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 545 Processing helix chain 'A' and resid 550 through 566 Proline residue: A 558 - end of helix Proline residue: A 563 - end of helix removed outlier: 3.655A pdb=" N LEU A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.241A pdb=" N TRP A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 624 through 628 Processing helix chain 'A' and resid 636 through 665 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 278 through 281 No H-bonds generated for 'chain 'B' and resid 278 through 281' Processing helix chain 'B' and resid 301 through 309 removed outlier: 4.842A pdb=" N VAL B 305 " --> pdb=" O CYS B 302 " (cutoff:3.500A) Proline residue: B 306 - end of helix Processing helix chain 'B' and resid 321 through 329 Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.914A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 439 through 477 Proline residue: B 460 - end of helix Proline residue: B 466 - end of helix Processing helix chain 'B' and resid 483 through 509 Proline residue: B 496 - end of helix Proline residue: B 502 - end of helix removed outlier: 4.006A pdb=" N ILE B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 545 Processing helix chain 'B' and resid 550 through 566 Proline residue: B 558 - end of helix Proline residue: B 563 - end of helix removed outlier: 3.655A pdb=" N LEU B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.242A pdb=" N TRP B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 601 Processing helix chain 'B' and resid 624 through 628 Processing helix chain 'B' and resid 636 through 665 Processing sheet with id= A, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.864A pdb=" N ARG A 80 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 142 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 114 through 118 removed outlier: 6.418A pdb=" N GLN A 286 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N MET A 117 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR A 288 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER A 291 " --> pdb=" O CYS A 295 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 159 through 162 removed outlier: 6.547A pdb=" N VAL A 237 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE A 162 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE A 239 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 268 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 240 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 270 " --> pdb=" O PHE A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 106 through 108 removed outlier: 3.863A pdb=" N ARG B 80 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 142 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 114 through 118 removed outlier: 6.418A pdb=" N GLN B 286 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N MET B 117 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR B 288 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 297 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER B 291 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.546A pdb=" N VAL B 237 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 162 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 239 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER B 268 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 240 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 270 " --> pdb=" O PHE B 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 388 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2700 1.34 - 1.46: 1937 1.46 - 1.58: 4215 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 8962 Sorted by residual: bond pdb=" C ILE A 562 " pdb=" N PRO A 563 " ideal model delta sigma weight residual 1.337 1.357 -0.020 9.80e-03 1.04e+04 4.13e+00 bond pdb=" C ILE B 562 " pdb=" N PRO B 563 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.80e-03 1.04e+04 3.84e+00 bond pdb=" C3 CLR A 801 " pdb=" O1 CLR A 801 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 CLR B 703 " pdb=" O1 CLR B 703 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3 CLR B 701 " pdb=" O1 CLR B 701 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 100.82 - 107.44: 301 107.44 - 114.07: 5199 114.07 - 120.69: 3874 120.69 - 127.32: 2724 127.32 - 133.95: 64 Bond angle restraints: 12162 Sorted by residual: angle pdb=" C GLN B 620 " pdb=" N LYS B 621 " pdb=" CA LYS B 621 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.93e+00 angle pdb=" C GLN A 620 " pdb=" N LYS A 621 " pdb=" CA LYS A 621 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" N GLY A 299 " pdb=" CA GLY A 299 " pdb=" C GLY A 299 " ideal model delta sigma weight residual 110.38 114.70 -4.32 1.42e+00 4.96e-01 9.27e+00 angle pdb=" N GLY B 299 " pdb=" CA GLY B 299 " pdb=" C GLY B 299 " ideal model delta sigma weight residual 110.38 114.69 -4.31 1.42e+00 4.96e-01 9.21e+00 angle pdb=" C13 CLR B 701 " pdb=" C17 CLR B 701 " pdb=" C20 CLR B 701 " ideal model delta sigma weight residual 119.60 112.16 7.44 3.00e+00 1.11e-01 6.14e+00 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5116 17.52 - 35.04: 452 35.04 - 52.56: 116 52.56 - 70.07: 14 70.07 - 87.59: 12 Dihedral angle restraints: 5710 sinusoidal: 2564 harmonic: 3146 Sorted by residual: dihedral pdb=" CB GLU B 628 " pdb=" CG GLU B 628 " pdb=" CD GLU B 628 " pdb=" OE1 GLU B 628 " ideal model delta sinusoidal sigma weight residual 0.00 87.59 -87.59 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 628 " pdb=" CG GLU A 628 " pdb=" CD GLU A 628 " pdb=" OE1 GLU A 628 " ideal model delta sinusoidal sigma weight residual 0.00 87.55 -87.55 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" CB LEU B 636 " pdb=" CG LEU B 636 " ideal model delta sinusoidal sigma weight residual -180.00 -120.23 -59.77 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1300 0.072 - 0.144: 94 0.144 - 0.215: 3 0.215 - 0.287: 15 0.287 - 0.359: 8 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C14 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C15 CLR A 804 " pdb=" C8 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C14 CLR B 701 " pdb=" C13 CLR B 701 " pdb=" C15 CLR B 701 " pdb=" C8 CLR B 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C14 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C15 CLR B 702 " pdb=" C8 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1417 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 465 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 466 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 465 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 466 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 466 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 466 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 416 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C THR B 416 " -0.018 2.00e-02 2.50e+03 pdb=" O THR B 416 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 417 " 0.006 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 690 2.74 - 3.28: 8798 3.28 - 3.82: 14580 3.82 - 4.36: 17017 4.36 - 4.90: 30064 Nonbonded interactions: 71149 Sorted by model distance: nonbonded pdb=" O ILE A 404 " pdb=" OG1 THR A 411 " model vdw 2.202 2.440 nonbonded pdb=" O ILE B 404 " pdb=" OG1 THR B 411 " model vdw 2.202 2.440 nonbonded pdb=" OE1 GLN B 164 " pdb=" OE1 GLN B 242 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN A 164 " pdb=" OE1 GLN A 242 " model vdw 2.225 3.040 nonbonded pdb=" O SER A 386 " pdb=" OG SER A 386 " model vdw 2.243 2.440 ... (remaining 71144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.030 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 0.021 8962 Z= 0.145 Angle : 0.655 7.436 12162 Z= 0.339 Chirality : 0.052 0.359 1420 Planarity : 0.003 0.037 1474 Dihedral : 14.260 87.593 3688 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.93 % Allowed : 11.16 % Favored : 86.91 % 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: -1.18 (0.24), residues: 1078 helix: 0.39 (0.20), residues: 620 sheet: -0.65 (0.53), residues: 78 loop : -2.83 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 480 HIS 0.001 0.000 HIS B 618 PHE 0.006 0.001 PHE A 570 TYR 0.005 0.001 TYR A 510 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 0.990 Fit side-chains REVERT: A 166 ASP cc_start: 0.7231 (m-30) cc_final: 0.6919 (m-30) REVERT: A 198 LYS cc_start: 0.8073 (tttp) cc_final: 0.7721 (ttpt) REVERT: A 618 HIS cc_start: 0.7980 (t70) cc_final: 0.7528 (t-170) REVERT: A 659 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6703 (ttm170) REVERT: B 166 ASP cc_start: 0.7197 (m-30) cc_final: 0.6914 (m-30) REVERT: B 198 LYS cc_start: 0.8046 (tttp) cc_final: 0.7744 (ttpt) REVERT: B 618 HIS cc_start: 0.7984 (t70) cc_final: 0.7497 (t-170) REVERT: B 659 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.6700 (ttm170) outliers start: 18 outliers final: 14 residues processed: 204 average time/residue: 0.2229 time to fit residues: 61.3521 Evaluate side-chains 158 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 636 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 337 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 515 GLN A 620 GLN B 336 GLN B 337 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 515 GLN B 620 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8962 Z= 0.272 Angle : 0.579 5.417 12162 Z= 0.277 Chirality : 0.042 0.136 1420 Planarity : 0.004 0.045 1474 Dihedral : 7.242 59.868 1728 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.26 % Allowed : 13.84 % Favored : 80.90 % 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: -0.28 (0.26), residues: 1078 helix: 0.94 (0.21), residues: 646 sheet: -0.33 (0.53), residues: 78 loop : -2.29 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 511 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.002 PHE A 570 TYR 0.013 0.001 TYR A 592 ARG 0.003 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7327 (m-30) cc_final: 0.7004 (m-30) REVERT: A 198 LYS cc_start: 0.8184 (tttp) cc_final: 0.7717 (ttpt) REVERT: A 568 SER cc_start: 0.8775 (t) cc_final: 0.8538 (t) REVERT: A 659 ARG cc_start: 0.7063 (ttt-90) cc_final: 0.6749 (ttm170) REVERT: B 166 ASP cc_start: 0.7334 (m-30) cc_final: 0.6999 (m-30) REVERT: B 198 LYS cc_start: 0.8182 (tttp) cc_final: 0.7772 (ttpt) REVERT: B 568 SER cc_start: 0.8781 (t) cc_final: 0.8541 (t) REVERT: B 584 MET cc_start: 0.7613 (mtt) cc_final: 0.7349 (mtt) REVERT: B 659 ARG cc_start: 0.7110 (ttt-90) cc_final: 0.6749 (ttm170) outliers start: 49 outliers final: 35 residues processed: 168 average time/residue: 0.2021 time to fit residues: 47.5656 Evaluate side-chains 163 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8962 Z= 0.195 Angle : 0.511 5.263 12162 Z= 0.246 Chirality : 0.039 0.137 1420 Planarity : 0.003 0.044 1474 Dihedral : 6.817 59.223 1722 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.15 % Allowed : 14.81 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 1078 helix: 1.18 (0.22), residues: 650 sheet: -0.29 (0.53), residues: 88 loop : -2.05 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 583 HIS 0.001 0.000 HIS A 183 PHE 0.012 0.001 PHE A 570 TYR 0.009 0.001 TYR B 592 ARG 0.002 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 128 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7306 (m-30) cc_final: 0.7001 (m-30) REVERT: A 198 LYS cc_start: 0.8187 (tttp) cc_final: 0.7721 (ttpt) REVERT: A 568 SER cc_start: 0.8692 (t) cc_final: 0.8444 (t) REVERT: A 659 ARG cc_start: 0.7076 (ttt-90) cc_final: 0.6739 (ttm170) REVERT: B 166 ASP cc_start: 0.7292 (m-30) cc_final: 0.7000 (m-30) REVERT: B 198 LYS cc_start: 0.8186 (tttp) cc_final: 0.7768 (ttpt) REVERT: B 500 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6631 (tpp) REVERT: B 568 SER cc_start: 0.8723 (t) cc_final: 0.8467 (t) REVERT: B 659 ARG cc_start: 0.7091 (ttt-90) cc_final: 0.6756 (ttm170) outliers start: 48 outliers final: 33 residues processed: 162 average time/residue: 0.1901 time to fit residues: 43.9527 Evaluate side-chains 155 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 500 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8962 Z= 0.404 Angle : 0.629 5.537 12162 Z= 0.302 Chirality : 0.044 0.145 1420 Planarity : 0.004 0.046 1474 Dihedral : 6.831 59.497 1719 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.22 % Allowed : 15.34 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 1078 helix: 0.91 (0.21), residues: 650 sheet: -0.08 (0.58), residues: 78 loop : -1.92 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 480 HIS 0.003 0.001 HIS A 183 PHE 0.017 0.002 PHE A 570 TYR 0.013 0.002 TYR B 592 ARG 0.002 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 119 time to evaluate : 0.988 Fit side-chains REVERT: A 166 ASP cc_start: 0.7347 (m-30) cc_final: 0.7035 (m-30) REVERT: A 198 LYS cc_start: 0.8143 (tttp) cc_final: 0.7659 (ttpt) REVERT: A 659 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6837 (ttm170) REVERT: B 166 ASP cc_start: 0.7358 (m-30) cc_final: 0.7040 (m-30) REVERT: B 198 LYS cc_start: 0.8114 (tttp) cc_final: 0.7653 (ttpt) REVERT: B 500 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6865 (tpp) REVERT: B 659 ARG cc_start: 0.7185 (ttt-90) cc_final: 0.6835 (ttm170) outliers start: 58 outliers final: 37 residues processed: 160 average time/residue: 0.1787 time to fit residues: 41.6198 Evaluate side-chains 153 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 115 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8962 Z= 0.329 Angle : 0.591 7.329 12162 Z= 0.284 Chirality : 0.043 0.139 1420 Planarity : 0.004 0.046 1474 Dihedral : 6.663 57.139 1719 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.76 % Allowed : 15.99 % Favored : 77.25 % 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: -0.03 (0.27), residues: 1078 helix: 0.97 (0.21), residues: 650 sheet: -0.20 (0.58), residues: 78 loop : -1.85 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 480 HIS 0.002 0.001 HIS B 183 PHE 0.015 0.001 PHE B 570 TYR 0.012 0.001 TYR B 510 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 114 time to evaluate : 0.998 Fit side-chains REVERT: A 82 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 166 ASP cc_start: 0.7426 (m-30) cc_final: 0.7028 (m-30) REVERT: A 198 LYS cc_start: 0.8119 (tttp) cc_final: 0.7646 (ttpt) REVERT: A 659 ARG cc_start: 0.7174 (ttt-90) cc_final: 0.6836 (ttm170) REVERT: B 82 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7767 (tt) REVERT: B 166 ASP cc_start: 0.7426 (m-30) cc_final: 0.7023 (m-30) REVERT: B 198 LYS cc_start: 0.8125 (tttp) cc_final: 0.7655 (ttpt) REVERT: B 500 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6859 (tpp) REVERT: B 659 ARG cc_start: 0.7185 (ttt-90) cc_final: 0.6833 (ttm170) outliers start: 63 outliers final: 45 residues processed: 162 average time/residue: 0.1765 time to fit residues: 41.7751 Evaluate side-chains 160 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 8962 Z= 0.430 Angle : 0.646 7.204 12162 Z= 0.311 Chirality : 0.045 0.161 1420 Planarity : 0.004 0.048 1474 Dihedral : 6.746 57.279 1718 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.97 % Allowed : 16.74 % Favored : 76.29 % 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: -0.31 (0.26), residues: 1078 helix: 0.74 (0.21), residues: 652 sheet: -0.48 (0.57), residues: 78 loop : -1.92 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 480 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.002 PHE A 570 TYR 0.013 0.002 TYR A 510 ARG 0.002 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 113 time to evaluate : 0.975 Fit side-chains REVERT: A 82 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 198 LYS cc_start: 0.8124 (tttp) cc_final: 0.7628 (ttpt) REVERT: A 659 ARG cc_start: 0.7213 (ttt-90) cc_final: 0.6856 (ttm170) REVERT: B 82 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7763 (tt) REVERT: B 198 LYS cc_start: 0.8139 (tttp) cc_final: 0.7717 (ttpt) REVERT: B 500 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6998 (tpp) REVERT: B 659 ARG cc_start: 0.7219 (ttt-90) cc_final: 0.6857 (ttm170) outliers start: 65 outliers final: 54 residues processed: 154 average time/residue: 0.1816 time to fit residues: 40.6219 Evaluate side-chains 167 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 110 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 MET Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8962 Z= 0.139 Angle : 0.492 7.050 12162 Z= 0.239 Chirality : 0.038 0.140 1420 Planarity : 0.003 0.045 1474 Dihedral : 6.234 58.216 1718 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.29 % Allowed : 19.21 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1078 helix: 1.34 (0.22), residues: 648 sheet: -0.41 (0.56), residues: 88 loop : -1.79 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 583 HIS 0.003 0.001 HIS B 171 PHE 0.009 0.001 PHE A 570 TYR 0.010 0.001 TYR A 510 ARG 0.002 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 1.027 Fit side-chains REVERT: A 198 LYS cc_start: 0.8104 (tttp) cc_final: 0.7620 (ttpt) REVERT: A 659 ARG cc_start: 0.7120 (ttt-90) cc_final: 0.6783 (ttm170) REVERT: B 82 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7651 (tt) REVERT: B 198 LYS cc_start: 0.8091 (tttp) cc_final: 0.7618 (ttpt) REVERT: B 500 MET cc_start: 0.7063 (tpp) cc_final: 0.6797 (tpp) REVERT: B 659 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6786 (ttm170) outliers start: 40 outliers final: 26 residues processed: 149 average time/residue: 0.1890 time to fit residues: 40.4719 Evaluate side-chains 144 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8962 Z= 0.209 Angle : 0.533 7.481 12162 Z= 0.254 Chirality : 0.040 0.140 1420 Planarity : 0.003 0.046 1474 Dihedral : 6.194 56.954 1716 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.61 % Allowed : 19.10 % Favored : 76.29 % 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: 0.41 (0.27), residues: 1078 helix: 1.36 (0.21), residues: 650 sheet: -0.12 (0.59), residues: 78 loop : -1.72 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 583 HIS 0.003 0.001 HIS A 618 PHE 0.011 0.001 PHE A 570 TYR 0.010 0.001 TYR B 510 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 114 time to evaluate : 1.510 Fit side-chains REVERT: A 198 LYS cc_start: 0.8121 (tttp) cc_final: 0.7632 (ttpt) REVERT: A 659 ARG cc_start: 0.7142 (ttt-90) cc_final: 0.6795 (ttm170) REVERT: B 198 LYS cc_start: 0.8123 (tttp) cc_final: 0.7633 (ttpt) REVERT: B 500 MET cc_start: 0.7104 (tpp) cc_final: 0.6818 (tpp) REVERT: B 659 ARG cc_start: 0.7160 (ttt-90) cc_final: 0.6791 (ttm170) outliers start: 43 outliers final: 34 residues processed: 145 average time/residue: 0.1853 time to fit residues: 39.0029 Evaluate side-chains 149 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8962 Z= 0.350 Angle : 0.611 7.731 12162 Z= 0.291 Chirality : 0.043 0.144 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.439 55.064 1716 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.72 % Allowed : 19.21 % Favored : 76.07 % 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: 0.17 (0.27), residues: 1078 helix: 1.14 (0.21), residues: 650 sheet: -0.30 (0.58), residues: 78 loop : -1.76 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 480 HIS 0.004 0.001 HIS B 171 PHE 0.015 0.002 PHE A 465 TYR 0.011 0.001 TYR B 510 ARG 0.002 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 110 time to evaluate : 0.999 Fit side-chains REVERT: A 198 LYS cc_start: 0.8117 (tttp) cc_final: 0.7618 (ttpt) REVERT: A 413 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.6730 (mm) REVERT: A 416 THR cc_start: 0.9083 (t) cc_final: 0.8859 (p) REVERT: A 659 ARG cc_start: 0.7231 (ttt-90) cc_final: 0.6841 (ttm170) REVERT: B 198 LYS cc_start: 0.8123 (tttp) cc_final: 0.7692 (ttpt) REVERT: B 413 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.6738 (mm) REVERT: B 416 THR cc_start: 0.9089 (t) cc_final: 0.8865 (p) REVERT: B 500 MET cc_start: 0.7173 (tpp) cc_final: 0.6917 (tpp) REVERT: B 623 GLU cc_start: 0.8362 (tp30) cc_final: 0.7990 (tp30) REVERT: B 659 ARG cc_start: 0.7235 (ttt-90) cc_final: 0.6837 (ttm170) outliers start: 44 outliers final: 32 residues processed: 138 average time/residue: 0.1855 time to fit residues: 36.9039 Evaluate side-chains 144 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8962 Z= 0.215 Angle : 0.544 8.160 12162 Z= 0.258 Chirality : 0.040 0.141 1420 Planarity : 0.003 0.046 1474 Dihedral : 6.211 55.955 1716 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.76 % Allowed : 20.17 % Favored : 76.07 % 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: 0.40 (0.27), residues: 1078 helix: 1.33 (0.21), residues: 650 sheet: -0.12 (0.60), residues: 78 loop : -1.68 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 583 HIS 0.003 0.001 HIS A 618 PHE 0.011 0.001 PHE A 570 TYR 0.009 0.001 TYR A 510 ARG 0.001 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.023 Fit side-chains REVERT: A 198 LYS cc_start: 0.8111 (tttp) cc_final: 0.7616 (ttpt) REVERT: A 413 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.6703 (mm) REVERT: A 416 THR cc_start: 0.9103 (t) cc_final: 0.8902 (p) REVERT: A 659 ARG cc_start: 0.7203 (ttt-90) cc_final: 0.6821 (ttm170) REVERT: B 198 LYS cc_start: 0.8112 (tttp) cc_final: 0.7685 (ttpt) REVERT: B 413 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.6703 (mm) REVERT: B 416 THR cc_start: 0.9104 (t) cc_final: 0.8902 (p) REVERT: B 500 MET cc_start: 0.7134 (tpp) cc_final: 0.6847 (tpp) REVERT: B 623 GLU cc_start: 0.8348 (tp30) cc_final: 0.7996 (tp30) REVERT: B 659 ARG cc_start: 0.7203 (ttt-90) cc_final: 0.6815 (ttm170) outliers start: 35 outliers final: 29 residues processed: 139 average time/residue: 0.1902 time to fit residues: 38.3428 Evaluate side-chains 147 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** 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 = 0.3208 r_free = 0.3208 target = 0.114010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.089279 restraints weight = 10279.407| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.87 r_work: 0.2770 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8962 Z= 0.322 Angle : 0.602 8.005 12162 Z= 0.285 Chirality : 0.043 0.142 1420 Planarity : 0.004 0.046 1474 Dihedral : 6.396 54.529 1716 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.29 % Allowed : 19.74 % Favored : 75.97 % 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: 0.21 (0.27), residues: 1078 helix: 1.16 (0.21), residues: 652 sheet: -0.24 (0.59), residues: 78 loop : -1.74 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 480 HIS 0.004 0.001 HIS B 171 PHE 0.014 0.002 PHE A 465 TYR 0.011 0.001 TYR A 510 ARG 0.002 0.000 ARG B 406 =============================================================================== Job complete usr+sys time: 1963.26 seconds wall clock time: 36 minutes 21.52 seconds (2181.52 seconds total)