Starting phenix.real_space_refine on Thu Mar 14 16:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0z_32930/03_2024/7x0z_32930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0z_32930/03_2024/7x0z_32930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0z_32930/03_2024/7x0z_32930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0z_32930/03_2024/7x0z_32930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0z_32930/03_2024/7x0z_32930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0z_32930/03_2024/7x0z_32930_updated.pdb" } resolution = 2.96 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= 0.029 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 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 5946 2.51 5 N 1638 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 674": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9285 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4597 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 22, 'TRANS': 553} Chain breaks: 2 Chain: "B" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4624 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 22, 'TRANS': 557} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.25, per 1000 atoms: 0.57 Number of scatterers: 9285 At special positions: 0 Unit cell: (83.83, 78.85, 131.14, 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 6 15.00 Mg 2 11.99 O 1649 8.00 N 1638 7.00 C 5946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 4 sheets defined 62.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.540A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 123 Processing helix chain 'A' and resid 129 through 174 removed outlier: 3.929A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.040A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 235 removed outlier: 4.049A pdb=" N ASP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 242 through 261 removed outlier: 3.655A pdb=" N ILE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 288 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 299 through 334 removed outlier: 3.614A pdb=" N GLN A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 345 Processing helix chain 'A' and resid 380 through 430 removed outlier: 3.667A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.572A pdb=" N PHE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 573 through 583 removed outlier: 3.549A pdb=" N VAL A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 590 No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.832A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 661 through 666 removed outlier: 4.154A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 666 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 89 through 124 removed outlier: 3.978A pdb=" N VAL B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.507A pdb=" N ILE B 140 " --> pdb=" O GLN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 174 Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.184A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 234 removed outlier: 3.717A pdb=" N ASP B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 240 through 261 Processing helix chain 'B' and resid 265 through 288 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 299 through 334 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 379 through 430 removed outlier: 3.866A pdb=" N SER B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYS B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 removed outlier: 3.575A pdb=" N PHE B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 601 through 604 No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 661 through 666 removed outlier: 4.323A pdb=" N LYS B 665 " --> pdb=" O SER B 662 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 666 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 466 through 469 removed outlier: 5.428A pdb=" N LEU A 493 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 539 through 542 removed outlier: 6.749A pdb=" N TYR A 625 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 542 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 627 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA A 653 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 628 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A 655 " --> pdb=" O LEU A 628 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 467 through 469 removed outlier: 6.182A pdb=" N LEU B 531 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.659A pdb=" N TYR B 625 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 542 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 627 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA B 653 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU B 628 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 655 " --> pdb=" O LEU B 628 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 542 hydrogen bonds defined for protein. 1599 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: 2.54 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3022 1.34 - 1.46: 1449 1.46 - 1.57: 4935 1.57 - 1.69: 13 1.69 - 1.81: 74 Bond restraints: 9493 Sorted by residual: bond pdb=" C3' ATP A 802 " pdb=" C4' ATP A 802 " ideal model delta sigma weight residual 1.526 1.306 0.220 1.10e-02 8.26e+03 3.99e+02 bond pdb=" C3' ATP B 802 " pdb=" C4' ATP B 802 " ideal model delta sigma weight residual 1.526 1.309 0.217 1.10e-02 8.26e+03 3.89e+02 bond pdb=" C1' ATP A 802 " pdb=" C2' ATP A 802 " ideal model delta sigma weight residual 1.531 1.335 0.196 1.20e-02 6.94e+03 2.68e+02 bond pdb=" C1' ATP B 802 " pdb=" C2' ATP B 802 " ideal model delta sigma weight residual 1.531 1.336 0.195 1.20e-02 6.94e+03 2.63e+02 bond pdb=" C4' ATP B 802 " pdb=" O4' ATP B 802 " ideal model delta sigma weight residual 1.444 1.577 -0.133 1.10e-02 8.26e+03 1.46e+02 ... (remaining 9488 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.61: 268 106.61 - 113.91: 5380 113.91 - 121.20: 5035 121.20 - 128.50: 2100 128.50 - 135.80: 89 Bond angle restraints: 12872 Sorted by residual: angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 116.47 20.36 1.00e+00 1.00e+00 4.15e+02 angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 124.27 15.60 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 125.96 13.91 1.00e+00 1.00e+00 1.93e+02 angle pdb=" PA ATP B 802 " pdb=" O3A ATP B 802 " pdb=" PB ATP B 802 " ideal model delta sigma weight residual 136.83 125.53 11.30 1.00e+00 1.00e+00 1.28e+02 angle pdb=" C5 ATP B 802 " pdb=" C4 ATP B 802 " pdb=" N3 ATP B 802 " ideal model delta sigma weight residual 126.80 118.06 8.74 1.00e+00 1.00e+00 7.65e+01 ... (remaining 12867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5094 17.99 - 35.98: 491 35.98 - 53.97: 79 53.97 - 71.96: 14 71.96 - 89.95: 14 Dihedral angle restraints: 5692 sinusoidal: 2338 harmonic: 3354 Sorted by residual: dihedral pdb=" CA ILE B 558 " pdb=" C ILE B 558 " pdb=" N TYR B 559 " pdb=" CA TYR B 559 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE A 558 " pdb=" C ILE A 558 " pdb=" N TYR A 559 " pdb=" CA TYR A 559 " ideal model delta harmonic sigma weight residual 180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA HIS A 669 " pdb=" C HIS A 669 " pdb=" N LEU A 670 " pdb=" CA LEU A 670 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1114 0.047 - 0.094: 250 0.094 - 0.141: 61 0.141 - 0.188: 3 0.188 - 0.235: 3 Chirality restraints: 1431 Sorted by residual: chirality pdb=" C2' ATP A 802 " pdb=" C1' ATP A 802 " pdb=" C3' ATP A 802 " pdb=" O2' ATP A 802 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C3' ATP A 802 " pdb=" C2' ATP A 802 " pdb=" C4' ATP A 802 " pdb=" O3' ATP A 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 505 " pdb=" CA ILE A 505 " pdb=" CG1 ILE A 505 " pdb=" CG2 ILE A 505 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 1428 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 535 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO A 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 508 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 106 " 0.014 2.00e-02 2.50e+03 1.13e-02 2.23e+00 pdb=" CG PHE A 106 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 106 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 106 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 106 " 0.005 2.00e-02 2.50e+03 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 56 2.56 - 3.14: 7349 3.14 - 3.73: 14958 3.73 - 4.31: 20616 4.31 - 4.90: 34946 Nonbonded interactions: 77925 Sorted by model distance: nonbonded pdb=" OG SER A 514 " pdb="MG MG A 801 " model vdw 1.974 2.170 nonbonded pdb=" OG SER B 514 " pdb="MG MG B 801 " model vdw 2.050 2.170 nonbonded pdb=" OE1 GLN B 544 " pdb="MG MG B 801 " model vdw 2.074 2.170 nonbonded pdb=" O MET A 548 " pdb=" NH2 ARG B 285 " model vdw 2.180 2.520 nonbonded pdb=" O THR B 632 " pdb=" NH1 ARG B 660 " model vdw 2.190 2.520 ... (remaining 77920 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' and (resid 64 through 351 or resid 379 through 685 or resid 801 throu \ gh 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 13.640 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.280 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.007 0.220 9493 Z= 0.476 Angle : 0.792 20.362 12872 Z= 0.533 Chirality : 0.042 0.235 1431 Planarity : 0.004 0.083 1622 Dihedral : 14.783 89.948 3536 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1144 helix: 1.50 (0.19), residues: 737 sheet: -0.80 (0.70), residues: 60 loop : -2.21 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 326 HIS 0.008 0.001 HIS B 210 PHE 0.025 0.001 PHE A 106 TYR 0.025 0.002 TYR A 110 ARG 0.003 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.972 Fit side-chains REVERT: A 72 LEU cc_start: 0.8671 (tp) cc_final: 0.8471 (tp) REVERT: A 89 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6940 (ttt180) REVERT: A 598 MET cc_start: 0.7980 (mtt) cc_final: 0.7734 (mtp) REVERT: B 421 GLU cc_start: 0.7681 (tp30) cc_final: 0.7280 (pt0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 1.4369 time to fit residues: 195.0254 Evaluate side-chains 105 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9493 Z= 0.302 Angle : 0.595 12.409 12872 Z= 0.298 Chirality : 0.042 0.152 1431 Planarity : 0.004 0.067 1622 Dihedral : 8.822 82.766 1358 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.06 % Allowed : 8.63 % Favored : 89.31 % 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: 0.55 (0.25), residues: 1144 helix: 1.60 (0.19), residues: 734 sheet: -0.88 (0.70), residues: 60 loop : -2.18 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 326 HIS 0.008 0.002 HIS A 659 PHE 0.017 0.001 PHE A 106 TYR 0.017 0.002 TYR B 310 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.998 Fit side-chains REVERT: A 72 LEU cc_start: 0.8719 (tp) cc_final: 0.8513 (tp) REVERT: A 335 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8071 (mtt) REVERT: A 574 GLN cc_start: 0.7083 (tp40) cc_final: 0.6797 (mm110) REVERT: A 598 MET cc_start: 0.8008 (mtt) cc_final: 0.7705 (mtp) REVERT: B 421 GLU cc_start: 0.7678 (tp30) cc_final: 0.7301 (pt0) REVERT: B 487 GLU cc_start: 0.6401 (tt0) cc_final: 0.5857 (tt0) outliers start: 20 outliers final: 9 residues processed: 124 average time/residue: 1.5001 time to fit residues: 196.9995 Evaluate side-chains 117 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 672 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 28 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 210 HIS B 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9493 Z= 0.192 Angle : 0.517 9.927 12872 Z= 0.259 Chirality : 0.039 0.146 1431 Planarity : 0.004 0.057 1622 Dihedral : 8.445 88.694 1358 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.44 % Allowed : 11.51 % Favored : 87.05 % 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: 0.85 (0.25), residues: 1144 helix: 1.91 (0.19), residues: 733 sheet: -1.73 (0.57), residues: 80 loop : -2.00 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 PHE 0.013 0.001 PHE A 106 TYR 0.014 0.001 TYR B 310 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.036 Fit side-chains REVERT: A 69 ARG cc_start: 0.7120 (ttm170) cc_final: 0.6916 (tpp80) REVERT: A 72 LEU cc_start: 0.8656 (tp) cc_final: 0.8452 (tp) REVERT: A 155 GLU cc_start: 0.7696 (tt0) cc_final: 0.7413 (tt0) REVERT: A 272 GLU cc_start: 0.7895 (tt0) cc_final: 0.7608 (tt0) REVERT: A 598 MET cc_start: 0.8016 (mtt) cc_final: 0.7728 (mtp) REVERT: A 659 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7362 (p90) REVERT: B 421 GLU cc_start: 0.7672 (tp30) cc_final: 0.7278 (pt0) outliers start: 14 outliers final: 5 residues processed: 119 average time/residue: 1.4467 time to fit residues: 182.5346 Evaluate side-chains 111 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9493 Z= 0.199 Angle : 0.516 11.083 12872 Z= 0.258 Chirality : 0.039 0.146 1431 Planarity : 0.004 0.054 1622 Dihedral : 8.048 88.002 1358 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.06 % Allowed : 12.74 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1144 helix: 2.01 (0.19), residues: 736 sheet: -1.72 (0.58), residues: 80 loop : -1.95 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 PHE 0.010 0.001 PHE A 106 TYR 0.015 0.001 TYR B 310 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.101 Fit side-chains REVERT: A 155 GLU cc_start: 0.7713 (tt0) cc_final: 0.7419 (tt0) REVERT: A 272 GLU cc_start: 0.7929 (tt0) cc_final: 0.7634 (tt0) REVERT: A 335 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: A 403 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8037 (mtt) REVERT: A 598 MET cc_start: 0.8039 (mtt) cc_final: 0.7735 (mtp) REVERT: B 421 GLU cc_start: 0.7689 (tp30) cc_final: 0.7262 (pt0) outliers start: 20 outliers final: 8 residues processed: 123 average time/residue: 1.3278 time to fit residues: 174.0389 Evaluate side-chains 116 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.0060 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9493 Z= 0.264 Angle : 0.552 11.994 12872 Z= 0.275 Chirality : 0.040 0.149 1431 Planarity : 0.004 0.053 1622 Dihedral : 7.937 86.233 1358 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.98 % Allowed : 13.36 % Favored : 83.66 % 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: 0.89 (0.26), residues: 1144 helix: 1.92 (0.19), residues: 738 sheet: -1.72 (0.58), residues: 80 loop : -1.98 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 PHE 0.009 0.001 PHE A 252 TYR 0.015 0.001 TYR B 310 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.043 Fit side-chains REVERT: A 155 GLU cc_start: 0.7793 (tt0) cc_final: 0.7481 (tt0) REVERT: A 272 GLU cc_start: 0.8023 (tt0) cc_final: 0.7673 (tt0) REVERT: A 311 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6502 (tp40) REVERT: A 335 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7574 (mtt) REVERT: A 598 MET cc_start: 0.8012 (mtt) cc_final: 0.7704 (mtp) REVERT: A 659 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.6989 (p-80) REVERT: B 421 GLU cc_start: 0.7703 (tp30) cc_final: 0.7303 (pt0) REVERT: B 580 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7748 (mp) REVERT: B 602 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8217 (ptmm) REVERT: B 659 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6744 (p90) REVERT: B 672 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7995 (tp40) outliers start: 29 outliers final: 11 residues processed: 129 average time/residue: 1.3868 time to fit residues: 190.0757 Evaluate side-chains 122 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 672 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 0.0370 chunk 92 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 210 HIS ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9493 Z= 0.199 Angle : 0.516 10.804 12872 Z= 0.258 Chirality : 0.039 0.149 1431 Planarity : 0.004 0.050 1622 Dihedral : 7.520 87.136 1358 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.77 % Allowed : 15.01 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1144 helix: 2.05 (0.19), residues: 738 sheet: -1.93 (0.61), residues: 69 loop : -1.95 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 PHE 0.009 0.001 PHE A 252 TYR 0.014 0.001 TYR B 310 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.027 Fit side-chains REVERT: A 155 GLU cc_start: 0.7765 (tt0) cc_final: 0.7446 (tt0) REVERT: A 272 GLU cc_start: 0.8013 (tt0) cc_final: 0.7697 (tt0) REVERT: A 311 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6498 (tp40) REVERT: A 312 ASP cc_start: 0.7727 (m-30) cc_final: 0.7245 (m-30) REVERT: A 335 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7482 (mtt) REVERT: A 501 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7745 (ttm) REVERT: A 598 MET cc_start: 0.8013 (mtt) cc_final: 0.7693 (mtp) REVERT: A 684 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7295 (tp) REVERT: B 421 GLU cc_start: 0.7706 (tp30) cc_final: 0.7290 (pt0) REVERT: B 487 GLU cc_start: 0.6223 (tt0) cc_final: 0.5915 (tt0) REVERT: B 602 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8233 (ptmm) outliers start: 27 outliers final: 12 residues processed: 130 average time/residue: 1.3665 time to fit residues: 188.9522 Evaluate side-chains 119 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 602 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 169 HIS A 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9493 Z= 0.179 Angle : 0.505 11.526 12872 Z= 0.251 Chirality : 0.039 0.160 1431 Planarity : 0.004 0.050 1622 Dihedral : 7.276 87.955 1358 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.57 % Allowed : 15.72 % Favored : 81.71 % 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: 1144 helix: 2.06 (0.18), residues: 744 sheet: -1.73 (0.59), residues: 80 loop : -1.96 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 PHE 0.006 0.001 PHE A 106 TYR 0.014 0.001 TYR B 310 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.033 Fit side-chains REVERT: A 152 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6666 (mtm-85) REVERT: A 155 GLU cc_start: 0.7691 (tt0) cc_final: 0.7402 (tt0) REVERT: A 272 GLU cc_start: 0.8003 (tt0) cc_final: 0.7675 (tt0) REVERT: A 311 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6478 (tp40) REVERT: A 312 ASP cc_start: 0.7734 (m-30) cc_final: 0.7264 (m-30) REVERT: A 598 MET cc_start: 0.7991 (mtt) cc_final: 0.7671 (mtp) REVERT: A 684 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7305 (tp) REVERT: B 421 GLU cc_start: 0.7702 (tp30) cc_final: 0.7265 (pt0) REVERT: B 487 GLU cc_start: 0.6004 (tt0) cc_final: 0.5723 (tt0) REVERT: B 602 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8163 (ptmm) REVERT: B 659 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.6797 (p90) outliers start: 25 outliers final: 12 residues processed: 127 average time/residue: 1.3285 time to fit residues: 179.8419 Evaluate side-chains 120 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 659 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9493 Z= 0.243 Angle : 0.557 12.871 12872 Z= 0.274 Chirality : 0.041 0.232 1431 Planarity : 0.004 0.051 1622 Dihedral : 7.531 86.590 1358 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.88 % Allowed : 16.03 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1144 helix: 2.01 (0.18), residues: 738 sheet: -1.88 (0.62), residues: 69 loop : -1.95 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 PHE 0.007 0.001 PHE A 540 TYR 0.015 0.001 TYR A 310 ARG 0.004 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.101 Fit side-chains REVERT: A 155 GLU cc_start: 0.7756 (tt0) cc_final: 0.7444 (tt0) REVERT: A 272 GLU cc_start: 0.8032 (tt0) cc_final: 0.7679 (tt0) REVERT: A 311 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6482 (tp40) REVERT: A 427 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7653 (mp0) REVERT: A 498 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 659 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.6734 (p90) REVERT: A 684 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7324 (tp) REVERT: B 335 MET cc_start: 0.7857 (mtt) cc_final: 0.7555 (mtt) REVERT: B 421 GLU cc_start: 0.7732 (tp30) cc_final: 0.7287 (pt0) REVERT: B 432 CYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7852 (m) REVERT: B 462 LYS cc_start: 0.7409 (tmtt) cc_final: 0.7140 (tptp) REVERT: B 487 GLU cc_start: 0.6090 (tt0) cc_final: 0.5805 (tt0) REVERT: B 602 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8072 (ptmm) REVERT: B 659 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.6950 (p90) outliers start: 28 outliers final: 10 residues processed: 126 average time/residue: 1.3960 time to fit residues: 186.7377 Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 659 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9493 Z= 0.197 Angle : 0.527 11.914 12872 Z= 0.260 Chirality : 0.040 0.229 1431 Planarity : 0.004 0.050 1622 Dihedral : 7.320 87.865 1358 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.47 % Allowed : 16.24 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1144 helix: 2.03 (0.18), residues: 744 sheet: -1.93 (0.62), residues: 70 loop : -1.94 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 PHE 0.006 0.001 PHE A 540 TYR 0.014 0.001 TYR B 310 ARG 0.006 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.981 Fit side-chains REVERT: A 155 GLU cc_start: 0.7711 (tt0) cc_final: 0.7421 (tt0) REVERT: A 272 GLU cc_start: 0.8019 (tt0) cc_final: 0.7664 (tt0) REVERT: A 311 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6483 (tp40) REVERT: A 312 ASP cc_start: 0.7627 (m-30) cc_final: 0.7270 (m-30) REVERT: A 427 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7692 (mp0) REVERT: A 498 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: A 659 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.6709 (p90) REVERT: B 335 MET cc_start: 0.7864 (mtt) cc_final: 0.7588 (mtt) REVERT: B 421 GLU cc_start: 0.7713 (tp30) cc_final: 0.7264 (pt0) REVERT: B 432 CYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7809 (m) REVERT: B 487 GLU cc_start: 0.5980 (tt0) cc_final: 0.5714 (tt0) REVERT: B 602 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8034 (ptmm) outliers start: 24 outliers final: 10 residues processed: 123 average time/residue: 1.3726 time to fit residues: 179.5049 Evaluate side-chains 120 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 602 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9493 Z= 0.218 Angle : 0.547 15.244 12872 Z= 0.268 Chirality : 0.040 0.226 1431 Planarity : 0.004 0.050 1622 Dihedral : 7.382 87.522 1358 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.95 % Allowed : 16.55 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1144 helix: 2.00 (0.18), residues: 744 sheet: -1.88 (0.63), residues: 69 loop : -1.97 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 326 HIS 0.008 0.001 HIS B 210 PHE 0.007 0.001 PHE A 333 TYR 0.015 0.001 TYR B 310 ARG 0.006 0.000 ARG B 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.105 Fit side-chains REVERT: A 155 GLU cc_start: 0.7728 (tt0) cc_final: 0.7437 (tt0) REVERT: A 272 GLU cc_start: 0.8023 (tt0) cc_final: 0.7664 (tt0) REVERT: A 311 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6499 (tp40) REVERT: A 312 ASP cc_start: 0.7643 (m-30) cc_final: 0.7269 (m-30) REVERT: A 427 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7693 (mp0) REVERT: A 498 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 659 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.6627 (p90) REVERT: B 335 MET cc_start: 0.7867 (mtt) cc_final: 0.7563 (mtt) REVERT: B 421 GLU cc_start: 0.7719 (tp30) cc_final: 0.7269 (pt0) REVERT: B 432 CYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7808 (m) REVERT: B 487 GLU cc_start: 0.6020 (tt0) cc_final: 0.5749 (tt0) REVERT: B 602 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8095 (ptmm) outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 1.3565 time to fit residues: 173.2010 Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 602 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.0470 chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS B 584 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132561 restraints weight = 9247.566| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.70 r_work: 0.3325 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9493 Z= 0.185 Angle : 0.526 14.328 12872 Z= 0.258 Chirality : 0.039 0.223 1431 Planarity : 0.004 0.049 1622 Dihedral : 7.206 88.943 1358 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.54 % Allowed : 17.27 % Favored : 81.19 % 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 (0.25), residues: 1144 helix: 2.09 (0.18), residues: 744 sheet: -1.91 (0.62), residues: 70 loop : -1.91 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 326 HIS 0.008 0.001 HIS B 210 PHE 0.006 0.001 PHE A 252 TYR 0.014 0.001 TYR B 310 ARG 0.006 0.000 ARG B 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3616.31 seconds wall clock time: 64 minutes 23.61 seconds (3863.61 seconds total)