Starting phenix.real_space_refine (version: dev) on Sat Feb 18 19:44:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2023/7r8d_24316_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2023/7r8d_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_2023/7r8d_24316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2023/7r8d_24316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2023/7r8d_24316_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8d_24316/02_2023/7r8d_24316_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.55, per 1000 atoms: 0.63 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: 3.69 Conformation dependent library (CDL) restraints added in 1.5 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: 1.23 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: 2.29 Time building geometry restraints manager: 3.78 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: 4712 17.52 - 35.04: 430 35.04 - 52.56: 94 52.56 - 70.07: 14 70.07 - 87.59: 12 Dihedral angle restraints: 5262 sinusoidal: 2116 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 5259 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 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. 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: 0.810 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: 4.140 Check model and map are aligned: 0.140 Process input model: 26.160 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 14.464 87.593 3240 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 % 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 *********************** 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 : 1.047 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 204 average time/residue: 0.2283 time to fit residues: 62.7755 Evaluate side-chains 154 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1198 time to fit residues: 4.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.5880 ------------------------------------------------------------------------------- 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: 0.8531 moved from start: 0.1608 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= 0.282 Angle : 0.587 5.472 12162 Z= 0.281 Chirality : 0.041 0.138 1420 Planarity : 0.004 0.045 1474 Dihedral : 4.792 56.537 1260 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 4.08 % 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: 0.91 (0.21), residues: 648 sheet: -0.34 (0.53), residues: 78 loop : -2.26 (0.33), residues: 352 *********************** 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 173 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 0.944 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 160 average time/residue: 0.1878 time to fit residues: 43.0758 Evaluate side-chains 144 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0917 time to fit residues: 5.3900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.8538 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8962 Z= 0.254 Angle : 0.540 5.300 12162 Z= 0.260 Chirality : 0.040 0.137 1420 Planarity : 0.003 0.045 1474 Dihedral : 4.904 57.386 1260 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 3.97 % 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: 0.03 (0.27), residues: 1078 helix: 1.07 (0.21), residues: 652 sheet: -0.13 (0.56), residues: 78 loop : -1.99 (0.34), residues: 348 *********************** 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 161 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.102 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 149 average time/residue: 0.1796 time to fit residues: 39.5130 Evaluate side-chains 132 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0847 time to fit residues: 4.4417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 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: 3.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8592 moved from start: 0.2277 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= 0.402 Angle : 0.632 6.089 12162 Z= 0.304 Chirality : 0.044 0.143 1420 Planarity : 0.004 0.048 1474 Dihedral : 5.307 59.307 1260 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 4.51 % 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: -0.10 (0.27), residues: 1078 helix: 0.87 (0.21), residues: 652 sheet: -0.15 (0.58), residues: 78 loop : -1.83 (0.34), residues: 348 *********************** 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 158 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 0.987 Fit side-chains outliers start: 42 outliers final: 21 residues processed: 142 average time/residue: 0.1746 time to fit residues: 37.0274 Evaluate side-chains 132 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0904 time to fit residues: 5.0261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8580 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8962 Z= 0.333 Angle : 0.588 5.881 12162 Z= 0.284 Chirality : 0.042 0.139 1420 Planarity : 0.004 0.047 1474 Dihedral : 5.308 56.828 1260 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1078 helix: 0.98 (0.21), residues: 650 sheet: -0.31 (0.58), residues: 78 loop : -1.79 (0.33), residues: 350 *********************** 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 137 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 1.000 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 131 average time/residue: 0.1775 time to fit residues: 34.7385 Evaluate side-chains 121 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0885 time to fit residues: 3.5962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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: 0.8608 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 8962 Z= 0.449 Angle : 0.667 9.803 12162 Z= 0.319 Chirality : 0.045 0.148 1420 Planarity : 0.004 0.049 1474 Dihedral : 5.528 57.323 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1078 helix: 0.75 (0.21), residues: 652 sheet: -0.64 (0.56), residues: 78 loop : -1.83 (0.33), residues: 348 *********************** 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 133 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.970 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.2001 time to fit residues: 35.7036 Evaluate side-chains 121 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0882 time to fit residues: 3.1257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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: 0.8514 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 8962 Z= 0.137 Angle : 0.499 7.062 12162 Z= 0.242 Chirality : 0.037 0.139 1420 Planarity : 0.003 0.045 1474 Dihedral : 5.161 58.414 1260 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.93 % 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: 0.40 (0.27), residues: 1078 helix: 1.39 (0.22), residues: 644 sheet: -0.55 (0.54), residues: 88 loop : -1.69 (0.34), residues: 346 *********************** 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 136 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.292 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 128 average time/residue: 0.1795 time to fit residues: 34.8199 Evaluate side-chains 126 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0799 time to fit residues: 3.1885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** A 620 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: 0.8577 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 8962 Z= 0.332 Angle : 0.605 8.645 12162 Z= 0.286 Chirality : 0.043 0.143 1420 Planarity : 0.004 0.047 1474 Dihedral : 5.284 56.547 1260 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1078 helix: 1.19 (0.21), residues: 648 sheet: -0.40 (0.57), residues: 78 loop : -1.66 (0.34), residues: 352 *********************** 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 129 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.413 Fit side-chains outliers start: 15 outliers final: 3 residues processed: 123 average time/residue: 0.1878 time to fit residues: 34.1096 Evaluate side-chains 114 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0876 time to fit residues: 2.0383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.0060 chunk 63 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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** ** A 620 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: 0.8522 moved from start: 0.2313 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= 0.150 Angle : 0.520 7.961 12162 Z= 0.246 Chirality : 0.038 0.140 1420 Planarity : 0.003 0.045 1474 Dihedral : 5.083 57.737 1260 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.54 % 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: 0.59 (0.27), residues: 1078 helix: 1.52 (0.22), residues: 644 sheet: -0.14 (0.59), residues: 78 loop : -1.62 (0.34), residues: 356 *********************** 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 116 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.963 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 115 average time/residue: 0.1814 time to fit residues: 30.8991 Evaluate side-chains 116 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0793 time to fit residues: 1.8453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8962 Z= 0.261 Angle : 0.571 8.035 12162 Z= 0.269 Chirality : 0.040 0.140 1420 Planarity : 0.004 0.046 1474 Dihedral : 5.137 57.173 1260 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1078 helix: 1.42 (0.21), residues: 646 sheet: -0.16 (0.59), residues: 78 loop : -1.66 (0.34), residues: 354 ********************** 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 121 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.040 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 119 average time/residue: 0.1883 time to fit residues: 33.0886 Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0791 time to fit residues: 1.6944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 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 = 0.3234 r_free = 0.3234 target = 0.115662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.090277 restraints weight = 10190.538| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.95 r_work: 0.2998 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8962 Z= 0.276 Angle : 0.579 8.148 12162 Z= 0.274 Chirality : 0.041 0.140 1420 Planarity : 0.004 0.046 1474 Dihedral : 5.209 56.841 1260 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.32 % 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: 1.33 (0.21), residues: 650 sheet: -0.17 (0.59), residues: 78 loop : -1.66 (0.34), residues: 350 =============================================================================== Job complete usr+sys time: 1840.00 seconds wall clock time: 34 minutes 56.94 seconds (2096.94 seconds total)