Starting phenix.real_space_refine on Wed Aug 7 00:55:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/08_2024/8qa6_18300_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/08_2024/8qa6_18300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/08_2024/8qa6_18300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/08_2024/8qa6_18300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/08_2024/8qa6_18300_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/08_2024/8qa6_18300_trim.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 5826 2.51 5 N 1518 2.21 5 O 1696 1.98 5 H 8720 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 92": "OD1" <-> "OD2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B GLU 458": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17808 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8797 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 31, 'TRANS': 521} Chain breaks: 2 Chain: "B" Number of atoms: 8797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8797 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 31, 'TRANS': 521} Chain breaks: 2 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'FAD': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'FAD': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {None: 2} Time building chain proxies: 9.45, per 1000 atoms: 0.53 Number of scatterers: 17808 At special positions: 0 Unit cell: (106.19, 116.522, 78.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 4 15.00 O 1696 8.00 N 1518 7.00 C 5826 6.00 H 8720 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 51.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 69 through 85 removed outlier: 3.971A pdb=" N ALA A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.626A pdb=" N ASP A 100 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.811A pdb=" N LEU A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.834A pdb=" N PHE A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.652A pdb=" N LEU A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.746A pdb=" N LYS A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 290 through 313 removed outlier: 3.891A pdb=" N SER A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.524A pdb=" N THR A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 removed outlier: 5.626A pdb=" N TYR A 404 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.990A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 467 through 477 Processing helix chain 'A' and resid 518 through 530 removed outlier: 3.767A pdb=" N LYS A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 533 No H-bonds generated for 'chain 'A' and resid 531 through 533' Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.531A pdb=" N PHE A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 631 through 644 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 69 through 85 removed outlier: 3.970A pdb=" N ALA B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.625A pdb=" N ASP B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.906A pdb=" N LEU B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.836A pdb=" N PHE B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.649A pdb=" N LEU B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.768A pdb=" N LYS B 281 " --> pdb=" O PRO B 277 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 290 through 313 removed outlier: 3.870A pdb=" N SER B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 4.515A pdb=" N THR B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 5.626A pdb=" N TYR B 404 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 407 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 427 through 441 removed outlier: 3.943A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 518 through 530 removed outlier: 3.762A pdb=" N LYS B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 533 No H-bonds generated for 'chain 'B' and resid 531 through 533' Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.534A pdb=" N PHE B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 599 Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 631 through 644 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 64 removed outlier: 3.585A pdb=" N HIS A 127 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 124 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N MET A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 126 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS A 193 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 195 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 224 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 225 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY A 255 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 227 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A 317 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP A 59 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N PHE A 320 " --> pdb=" O TRP A 59 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 61 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 485 removed outlier: 6.505A pdb=" N GLU A 514 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 484 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR A 512 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.614A pdb=" N THR A 573 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP A 561 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 571 " --> pdb=" O TRP A 561 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 64 removed outlier: 3.585A pdb=" N HIS B 127 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR B 124 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET B 154 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B 126 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B 193 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA B 195 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 224 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 225 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY B 255 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 227 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY B 317 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP B 59 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE B 320 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER B 61 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 480 through 485 removed outlier: 6.504A pdb=" N GLU B 514 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER B 484 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR B 512 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 506 through 509 removed outlier: 6.614A pdb=" N THR B 573 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP B 561 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN B 571 " --> pdb=" O TRP B 561 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1179 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: 6.64 Time building geometry restraints manager: 14.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8702 1.03 - 1.22: 18 1.22 - 1.42: 3990 1.42 - 1.62: 5266 1.62 - 1.81: 80 Bond restraints: 18056 Sorted by residual: bond pdb=" C2' SAM B 701 " pdb=" C3' SAM B 701 " ideal model delta sigma weight residual 1.532 1.247 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' SAM A 701 " pdb=" C3' SAM A 701 " ideal model delta sigma weight residual 1.532 1.247 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' SAM B 703 " pdb=" C3' SAM B 703 " ideal model delta sigma weight residual 1.532 1.251 0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C2' SAM A 703 " pdb=" C3' SAM A 703 " ideal model delta sigma weight residual 1.532 1.251 0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C6 SAM A 703 " pdb=" N6 SAM A 703 " ideal model delta sigma weight residual 1.333 1.456 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 18051 not shown) Histogram of bond angle deviations from ideal: 96.41 - 108.47: 5726 108.47 - 120.53: 21889 120.53 - 132.59: 4939 132.59 - 144.65: 30 144.65 - 156.71: 4 Bond angle restraints: 32588 Sorted by residual: angle pdb=" C1' SAM B 703 " pdb=" N9 SAM B 703 " pdb=" C8 SAM B 703 " ideal model delta sigma weight residual 123.85 96.41 27.44 3.00e+00 1.11e-01 8.37e+01 angle pdb=" C1' SAM A 703 " pdb=" N9 SAM A 703 " pdb=" C8 SAM A 703 " ideal model delta sigma weight residual 123.85 96.45 27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C1' SAM B 703 " pdb=" N9 SAM B 703 " pdb=" C4 SAM B 703 " ideal model delta sigma weight residual 130.15 156.71 -26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" C1' SAM A 703 " pdb=" N9 SAM A 703 " pdb=" C4 SAM A 703 " ideal model delta sigma weight residual 130.15 156.60 -26.45 3.00e+00 1.11e-01 7.78e+01 angle pdb=" C1' SAM B 701 " pdb=" N9 SAM B 701 " pdb=" C8 SAM B 701 " ideal model delta sigma weight residual 123.85 98.83 25.02 3.00e+00 1.11e-01 6.96e+01 ... (remaining 32583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 8233 34.91 - 69.81: 373 69.81 - 104.72: 34 104.72 - 139.62: 0 139.62 - 174.53: 2 Dihedral angle restraints: 8642 sinusoidal: 4752 harmonic: 3890 Sorted by residual: dihedral pdb=" O5' FAD A 702 " pdb=" O3P FAD A 702 " pdb=" P FAD A 702 " pdb=" PA FAD A 702 " ideal model delta sinusoidal sigma weight residual -61.77 112.76 -174.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5' FAD B 702 " pdb=" O3P FAD B 702 " pdb=" P FAD B 702 " pdb=" PA FAD B 702 " ideal model delta sinusoidal sigma weight residual -61.77 112.71 -174.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA ILE B 192 " pdb=" C ILE B 192 " pdb=" N CYS B 193 " pdb=" CA CYS B 193 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 8639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.323: 1360 0.323 - 0.646: 4 0.646 - 0.969: 0 0.969 - 1.292: 0 1.292 - 1.616: 4 Chirality restraints: 1368 Sorted by residual: chirality pdb=" SD SAM B 701 " pdb=" CG SAM B 701 " pdb=" CE SAM B 701 " pdb=" C5' SAM B 701 " both_signs ideal model delta sigma weight residual False 5.50 3.89 1.62 2.00e-01 2.50e+01 6.52e+01 chirality pdb=" SD SAM A 701 " pdb=" CG SAM A 701 " pdb=" CE SAM A 701 " pdb=" C5' SAM A 701 " both_signs ideal model delta sigma weight residual False 5.50 3.89 1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" SD SAM A 703 " pdb=" CG SAM A 703 " pdb=" CE SAM A 703 " pdb=" C5' SAM A 703 " both_signs ideal model delta sigma weight residual False 5.50 3.94 1.57 2.00e-01 2.50e+01 6.14e+01 ... (remaining 1365 not shown) Planarity restraints: 2646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 152 " 0.056 2.00e-02 2.50e+03 6.90e-02 7.14e+01 pdb=" CG ASN B 152 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 152 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 152 " -0.108 2.00e-02 2.50e+03 pdb="HD21 ASN B 152 " -0.006 2.00e-02 2.50e+03 pdb="HD22 ASN B 152 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 152 " -0.055 2.00e-02 2.50e+03 6.87e-02 7.08e+01 pdb=" CG ASN A 152 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 152 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 152 " 0.108 2.00e-02 2.50e+03 pdb="HD21 ASN A 152 " 0.006 2.00e-02 2.50e+03 pdb="HD22 ASN A 152 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 118 " -0.038 2.00e-02 2.50e+03 4.61e-02 3.19e+01 pdb=" CG ASN A 118 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 118 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 118 " 0.073 2.00e-02 2.50e+03 pdb="HD21 ASN A 118 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN A 118 " -0.071 2.00e-02 2.50e+03 ... (remaining 2643 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 912 2.17 - 2.78: 34656 2.78 - 3.39: 51387 3.39 - 3.99: 66352 3.99 - 4.60: 103216 Nonbonded interactions: 256523 Sorted by model distance: nonbonded pdb=" OE1 GLU A 568 " pdb="HE22 GLN B 571 " model vdw 1.565 2.450 nonbonded pdb="HE22 GLN A 571 " pdb=" OE1 GLU B 568 " model vdw 1.566 2.450 nonbonded pdb="HE21 GLN A 555 " pdb=" H GLU B 568 " model vdw 1.605 2.100 nonbonded pdb=" HZ3 LYS B 584 " pdb=" OD1 ASP B 585 " model vdw 1.669 2.450 nonbonded pdb=" O VAL B 240 " pdb=" HG1 THR B 244 " model vdw 1.670 2.450 ... (remaining 256518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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=0.00 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: 5.640 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: 0.270 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 58.940 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.285 9336 Z= 0.620 Angle : 1.084 27.438 12696 Z= 0.428 Chirality : 0.098 1.616 1368 Planarity : 0.006 0.094 1608 Dihedral : 17.507 174.526 3576 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.52 % Allowed : 18.92 % Favored : 80.56 % 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: -0.54 (0.25), residues: 1094 helix: -0.01 (0.23), residues: 470 sheet: -0.08 (0.37), residues: 176 loop : -0.69 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 95 HIS 0.006 0.001 HIS B 181 PHE 0.021 0.001 PHE A 582 TYR 0.017 0.002 TYR B 90 ARG 0.009 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7861 (mmt) cc_final: 0.7466 (mmt) outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 1.8599 time to fit residues: 216.2211 Evaluate side-chains 106 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 TYR Chi-restraints excluded: chain B residue 119 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 477 GLN B 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9336 Z= 0.318 Angle : 0.620 5.866 12696 Z= 0.314 Chirality : 0.043 0.153 1368 Planarity : 0.005 0.039 1608 Dihedral : 11.345 176.319 1418 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 17.67 % Favored : 80.35 % 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: 0.68 (0.26), residues: 1094 helix: 1.35 (0.24), residues: 476 sheet: -0.18 (0.38), residues: 178 loop : -0.15 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 95 HIS 0.004 0.001 HIS B 539 PHE 0.025 0.002 PHE B 582 TYR 0.013 0.002 TYR A 197 ARG 0.006 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7251 (mp0) REVERT: B 137 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6503 (mm-30) REVERT: B 399 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7264 (mp0) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 1.9994 time to fit residues: 257.6241 Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.0370 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9336 Z= 0.202 Angle : 0.535 4.442 12696 Z= 0.271 Chirality : 0.040 0.147 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.717 171.597 1414 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.04 % Allowed : 18.30 % Favored : 80.67 % 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: 1.08 (0.26), residues: 1094 helix: 1.74 (0.24), residues: 476 sheet: -0.14 (0.38), residues: 178 loop : 0.05 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.006 0.001 HIS A 181 PHE 0.019 0.001 PHE A 582 TYR 0.011 0.001 TYR B 197 ARG 0.004 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7250 (mp0) REVERT: B 137 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6539 (mm-30) REVERT: B 399 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7262 (mp0) outliers start: 10 outliers final: 7 residues processed: 114 average time/residue: 2.0330 time to fit residues: 253.9379 Evaluate side-chains 109 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 477 GLN A 555 GLN B 133 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9336 Z= 0.244 Angle : 0.544 4.357 12696 Z= 0.275 Chirality : 0.041 0.143 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.697 168.301 1414 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.46 % Allowed : 18.30 % Favored : 80.25 % 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: 1.20 (0.26), residues: 1094 helix: 1.79 (0.24), residues: 476 sheet: -0.00 (0.39), residues: 174 loop : 0.16 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.004 0.001 HIS B 181 PHE 0.019 0.002 PHE A 582 TYR 0.012 0.001 TYR A 512 ARG 0.003 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7279 (mp0) REVERT: B 137 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6618 (mm-30) REVERT: B 399 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7286 (mp0) outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 2.1185 time to fit residues: 265.4105 Evaluate side-chains 111 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 555 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9336 Z= 0.168 Angle : 0.506 4.352 12696 Z= 0.255 Chirality : 0.039 0.140 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.478 171.067 1414 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.46 % Allowed : 18.71 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1094 helix: 1.96 (0.24), residues: 476 sheet: 0.06 (0.40), residues: 174 loop : 0.32 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 95 HIS 0.005 0.001 HIS B 181 PHE 0.016 0.001 PHE A 582 TYR 0.010 0.001 TYR A 512 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7298 (mp0) REVERT: A 473 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6613 (tmm160) REVERT: B 137 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 399 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7292 (mp0) REVERT: B 473 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6662 (tmm160) outliers start: 14 outliers final: 6 residues processed: 118 average time/residue: 2.1337 time to fit residues: 274.0927 Evaluate side-chains 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 473 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 555 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9336 Z= 0.338 Angle : 0.578 4.543 12696 Z= 0.294 Chirality : 0.042 0.137 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.935 165.003 1414 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.49 % Allowed : 17.78 % Favored : 79.73 % 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: 1.11 (0.26), residues: 1094 helix: 1.77 (0.23), residues: 476 sheet: -0.20 (0.39), residues: 174 loop : 0.11 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.003 0.001 HIS A 319 PHE 0.020 0.002 PHE A 582 TYR 0.015 0.002 TYR A 512 ARG 0.004 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: A 399 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7313 (mp0) REVERT: A 555 GLN cc_start: 0.8552 (tp40) cc_final: 0.7706 (tp-100) REVERT: B 106 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 128 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7967 (mmt) REVERT: B 137 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6630 (mm-30) REVERT: B 399 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7315 (mp0) REVERT: B 473 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6691 (tmm160) outliers start: 24 outliers final: 14 residues processed: 123 average time/residue: 2.1011 time to fit residues: 281.2139 Evaluate side-chains 126 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 634 GLN B 555 GLN B 634 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9336 Z= 0.169 Angle : 0.515 5.309 12696 Z= 0.261 Chirality : 0.040 0.140 1368 Planarity : 0.004 0.039 1608 Dihedral : 10.624 169.491 1414 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.77 % Allowed : 18.92 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1094 helix: 2.02 (0.24), residues: 476 sheet: -0.07 (0.40), residues: 174 loop : 0.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 59 HIS 0.004 0.001 HIS B 181 PHE 0.016 0.001 PHE A 582 TYR 0.010 0.001 TYR A 197 ARG 0.002 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7305 (mp0) REVERT: A 460 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 473 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7024 (tmm160) REVERT: B 128 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8004 (mmt) REVERT: B 137 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6591 (mm-30) REVERT: B 399 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7322 (mp0) REVERT: B 473 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6669 (tmm160) REVERT: B 594 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8257 (mm110) outliers start: 17 outliers final: 4 residues processed: 123 average time/residue: 2.0082 time to fit residues: 269.1375 Evaluate side-chains 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9336 Z= 0.260 Angle : 0.547 4.749 12696 Z= 0.277 Chirality : 0.041 0.136 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.729 166.145 1414 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.39 % Allowed : 18.61 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1094 helix: 1.99 (0.24), residues: 476 sheet: -0.15 (0.41), residues: 174 loop : 0.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.004 0.001 HIS B 181 PHE 0.018 0.002 PHE A 582 TYR 0.014 0.001 TYR A 512 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7348 (mp0) REVERT: A 460 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 473 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7056 (tmm160) REVERT: B 106 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 128 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8062 (mmt) REVERT: B 137 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6624 (mm-30) REVERT: B 399 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7343 (mp0) REVERT: B 473 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6686 (tmm160) outliers start: 23 outliers final: 10 residues processed: 125 average time/residue: 2.0675 time to fit residues: 280.8678 Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 555 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9336 Z= 0.166 Angle : 0.504 4.700 12696 Z= 0.254 Chirality : 0.039 0.137 1368 Planarity : 0.004 0.040 1608 Dihedral : 10.483 170.857 1414 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.56 % Allowed : 20.17 % Favored : 78.27 % 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: 1.71 (0.27), residues: 1094 helix: 2.20 (0.24), residues: 476 sheet: 0.12 (0.42), residues: 170 loop : 0.49 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 59 HIS 0.003 0.001 HIS B 181 PHE 0.015 0.001 PHE A 582 TYR 0.009 0.001 TYR A 197 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7334 (mp0) REVERT: A 473 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7051 (tmm160) REVERT: B 137 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6584 (mm-30) REVERT: B 399 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7344 (mp0) REVERT: B 473 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7043 (tmm160) outliers start: 15 outliers final: 5 residues processed: 121 average time/residue: 2.0688 time to fit residues: 272.4413 Evaluate side-chains 114 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 473 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9336 Z= 0.168 Angle : 0.502 4.651 12696 Z= 0.252 Chirality : 0.039 0.136 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.359 169.849 1414 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.35 % Allowed : 20.37 % Favored : 78.27 % 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: 1.78 (0.27), residues: 1094 helix: 2.27 (0.24), residues: 476 sheet: 0.13 (0.42), residues: 174 loop : 0.54 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 59 HIS 0.003 0.001 HIS B 181 PHE 0.015 0.001 PHE A 582 TYR 0.011 0.001 TYR A 512 ARG 0.003 0.000 ARG A 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7333 (mp0) REVERT: A 473 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7084 (tmm160) REVERT: B 137 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6591 (mm-30) REVERT: B 399 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7350 (mp0) REVERT: B 473 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7047 (tmm160) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 2.1355 time to fit residues: 273.7174 Evaluate side-chains 114 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124439 restraints weight = 32207.739| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.14 r_work: 0.3338 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9336 Z= 0.197 Angle : 0.511 4.656 12696 Z= 0.257 Chirality : 0.040 0.135 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.444 168.899 1414 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.46 % Allowed : 20.58 % Favored : 77.96 % 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: 1.76 (0.27), residues: 1094 helix: 2.25 (0.24), residues: 476 sheet: 0.18 (0.42), residues: 172 loop : 0.50 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 59 HIS 0.003 0.001 HIS B 181 PHE 0.016 0.001 PHE B 582 TYR 0.012 0.001 TYR B 512 ARG 0.003 0.000 ARG A 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6257.32 seconds wall clock time: 111 minutes 11.87 seconds (6671.87 seconds total)