Starting phenix.real_space_refine on Thu Mar 14 20:25:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/03_2024/7adj_11727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/03_2024/7adj_11727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/03_2024/7adj_11727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/03_2024/7adj_11727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/03_2024/7adj_11727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/03_2024/7adj_11727.pdb" } resolution = 2.8 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= 1.000 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: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 3078 2.51 5 N 850 2.21 5 O 989 1.98 5 H 4790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 397": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 473": "OD1" <-> "OD2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 624": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 636": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A ARG 715": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9710 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9710 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 22, 'TRANS': 590} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.46, per 1000 atoms: 0.46 Number of scatterers: 9710 At special positions: 0 Unit cell: (97.94, 97.94, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 989 8.00 N 850 7.00 C 3078 6.00 H 4790 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: 7.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 37.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.635A pdb=" N GLU A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.529A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 removed outlier: 4.335A pdb=" N LYS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.932A pdb=" N LYS A 263 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER A 264 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.779A pdb=" N TRP A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 291 No H-bonds generated for 'chain 'A' and resid 290 through 291' Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.796A pdb=" N LYS A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.814A pdb=" N SER A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 388 removed outlier: 4.354A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.523A pdb=" N TYR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.821A pdb=" N VAL A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.610A pdb=" N GLY A 588 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.747A pdb=" N GLU A 659 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 710 removed outlier: 3.668A pdb=" N LYS A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 7.351A pdb=" N GLU A 140 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL A 178 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU A 142 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 379 removed outlier: 8.627A pdb=" N SER A 448 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 417 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG A 450 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 419 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LYS A 452 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 421 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET A 454 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 516 through 517 removed outlier: 5.609A pdb=" N TYR A 517 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 554 " --> pdb=" O ASP A 610 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 609 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 641 " --> pdb=" O HIS A 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652 146 hydrogen bonds defined for protein. 369 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: 3.27 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.08: 1784 1.08 - 1.26: 3876 1.26 - 1.44: 1312 1.44 - 1.62: 2826 1.62 - 1.80: 6 Bond restraints: 9804 Sorted by residual: bond pdb=" ND2 ASN A 389 " pdb="HD22 ASN A 389 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" NH1 ARG A 316 " pdb="HH11 ARG A 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CD2 PHE A 390 " pdb=" HD2 PHE A 390 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N TYR A 578 " pdb=" H TYR A 578 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG A 636 " pdb="HH12 ARG A 636 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 9799 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.36: 567 106.36 - 113.51: 10411 113.51 - 120.67: 4792 120.67 - 127.82: 1864 127.82 - 134.97: 39 Bond angle restraints: 17673 Sorted by residual: angle pdb=" C TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta sigma weight residual 109.95 125.18 -15.23 1.99e+00 2.53e-01 5.85e+01 angle pdb=" CA ASP A 420 " pdb=" CB ASP A 420 " pdb=" CG ASP A 420 " ideal model delta sigma weight residual 112.60 119.91 -7.31 1.00e+00 1.00e+00 5.35e+01 angle pdb=" CA ASP A 627 " pdb=" CB ASP A 627 " pdb=" CG ASP A 627 " ideal model delta sigma weight residual 112.60 119.40 -6.80 1.00e+00 1.00e+00 4.63e+01 angle pdb=" OD1 ASN A 207 " pdb=" CG ASN A 207 " pdb=" ND2 ASN A 207 " ideal model delta sigma weight residual 122.60 116.15 6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " pdb=" CG TYR A 284 " ideal model delta sigma weight residual 113.90 125.29 -11.39 1.80e+00 3.09e-01 4.00e+01 ... (remaining 17668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4135 17.69 - 35.38: 346 35.38 - 53.06: 91 53.06 - 70.75: 40 70.75 - 88.44: 6 Dihedral angle restraints: 4618 sinusoidal: 2535 harmonic: 2083 Sorted by residual: dihedral pdb=" C TYR A 284 " pdb=" N TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta harmonic sigma weight residual -122.60 -142.68 20.08 0 2.50e+00 1.60e-01 6.45e+01 dihedral pdb=" CA LYS A 497 " pdb=" C LYS A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 147.49 32.51 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA SER A 687 " pdb=" C SER A 687 " pdb=" N ILE A 688 " pdb=" CA ILE A 688 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 4615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 556 0.130 - 0.260: 140 0.260 - 0.390: 17 0.390 - 0.520: 1 0.520 - 0.650: 1 Chirality restraints: 715 Sorted by residual: chirality pdb=" CA TYR A 284 " pdb=" N TYR A 284 " pdb=" C TYR A 284 " pdb=" CB TYR A 284 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA THR A 486 " pdb=" N THR A 486 " pdb=" C THR A 486 " pdb=" CB THR A 486 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA ASN A 256 " pdb=" N ASN A 256 " pdb=" C ASN A 256 " pdb=" CB ASN A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 712 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.232 2.00e-02 2.50e+03 1.14e-01 5.19e+02 pdb=" CG TRP A 286 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " 0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.058 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " 0.116 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TRP A 286 " -0.134 2.00e-02 2.50e+03 pdb=" HE1 TRP A 286 " -0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP A 286 " -0.110 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 286 " 0.114 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 286 " -0.193 2.00e-02 2.50e+03 pdb=" HH2 TRP A 286 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.257 2.00e-02 2.50e+03 1.10e-01 3.60e+02 pdb=" CG TYR A 284 " -0.214 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.123 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR A 284 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR A 284 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR A 284 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 TYR A 284 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 515 " -0.195 2.00e-02 2.50e+03 8.84e-02 3.12e+02 pdb=" CG TRP A 515 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP A 515 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 515 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 515 " 0.082 2.00e-02 2.50e+03 pdb=" CE2 TRP A 515 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 515 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 515 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 515 " 0.052 2.00e-02 2.50e+03 pdb=" CH2 TRP A 515 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 TRP A 515 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 TRP A 515 " 0.139 2.00e-02 2.50e+03 pdb=" HE3 TRP A 515 " 0.088 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 515 " -0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 515 " 0.106 2.00e-02 2.50e+03 pdb=" HH2 TRP A 515 " -0.092 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 775 2.21 - 2.81: 17385 2.81 - 3.40: 26400 3.40 - 4.00: 34964 4.00 - 4.60: 50209 Nonbonded interactions: 129733 Sorted by model distance: nonbonded pdb=" OD1 ASP A 610 " pdb=" HG SER A 612 " model vdw 1.609 1.850 nonbonded pdb=" HG1 THR A 486 " pdb=" O ALA A 514 " model vdw 1.618 1.850 nonbonded pdb=" O LEU A 205 " pdb=" HH TYR A 249 " model vdw 1.637 1.850 nonbonded pdb=" HH TYR A 388 " pdb=" OD2 ASP A 442 " model vdw 1.653 1.850 nonbonded pdb=" OD1 ASP A 422 " pdb=" HG SER A 424 " model vdw 1.665 1.850 ... (remaining 129728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.800 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: 0.150 Extract box with map and model: 4.050 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.390 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:16.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 : 0.014 0.118 5014 Z= 0.893 Angle : 1.990 15.226 6760 Z= 1.350 Chirality : 0.113 0.650 715 Planarity : 0.015 0.128 896 Dihedral : 14.683 88.439 1912 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.18 % Allowed : 6.80 % Favored : 93.01 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.31), residues: 611 helix: -3.22 (0.26), residues: 155 sheet: 0.05 (0.61), residues: 62 loop : -0.92 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.033 TRP A 286 HIS 0.016 0.007 HIS A 664 PHE 0.047 0.011 PHE A 206 TYR 0.246 0.021 TYR A 284 ARG 0.008 0.002 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8037 (mttt) REVERT: A 174 LYS cc_start: 0.7867 (tptt) cc_final: 0.7108 (ttpt) REVERT: A 222 LYS cc_start: 0.7381 (mttt) cc_final: 0.6819 (mtpt) REVERT: A 276 LYS cc_start: 0.7332 (mmmm) cc_final: 0.7058 (ttpp) REVERT: A 305 LYS cc_start: 0.6252 (pttp) cc_final: 0.6043 (mtmm) REVERT: A 391 LYS cc_start: 0.7318 (mtmm) cc_final: 0.7091 (mtmm) REVERT: A 399 SER cc_start: 0.8142 (p) cc_final: 0.7743 (m) REVERT: A 472 LYS cc_start: 0.6988 (ttpt) cc_final: 0.6650 (ttmm) REVERT: A 475 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6728 (mm110) REVERT: A 523 ARG cc_start: 0.6911 (ttm-80) cc_final: 0.6591 (ttm-80) REVERT: A 634 GLU cc_start: 0.6888 (tt0) cc_final: 0.6312 (tm-30) REVERT: A 640 GLU cc_start: 0.7277 (tt0) cc_final: 0.6872 (mp0) REVERT: A 647 GLU cc_start: 0.6924 (mp0) cc_final: 0.6602 (mm-30) outliers start: 1 outliers final: 1 residues processed: 119 average time/residue: 2.5644 time to fit residues: 316.7293 Evaluate side-chains 82 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 260 ASN A 369 ASN A 458 ASN A 461 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN A 581 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 711 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5014 Z= 0.201 Angle : 0.627 7.859 6760 Z= 0.347 Chirality : 0.044 0.209 715 Planarity : 0.004 0.033 896 Dihedral : 6.963 40.197 672 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.76 % Allowed : 14.52 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.68 (0.32), residues: 611 helix: -1.76 (0.34), residues: 174 sheet: 0.15 (0.59), residues: 69 loop : -1.01 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 286 HIS 0.004 0.002 HIS A 170 PHE 0.012 0.001 PHE A 390 TYR 0.054 0.002 TYR A 284 ARG 0.002 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7797 (tptt) cc_final: 0.7113 (ttpt) REVERT: A 222 LYS cc_start: 0.7552 (mttt) cc_final: 0.6979 (mtpt) REVERT: A 232 GLU cc_start: 0.3465 (tt0) cc_final: 0.3258 (mt-10) REVERT: A 284 TYR cc_start: 0.5140 (OUTLIER) cc_final: 0.4521 (p90) REVERT: A 305 LYS cc_start: 0.6195 (pttp) cc_final: 0.5651 (mtmm) REVERT: A 309 LYS cc_start: 0.5881 (mtpt) cc_final: 0.5330 (mppt) REVERT: A 325 GLU cc_start: 0.7384 (pm20) cc_final: 0.6959 (pm20) REVERT: A 397 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5256 (mtm-85) REVERT: A 405 ASN cc_start: 0.7918 (m-40) cc_final: 0.7713 (m110) REVERT: A 440 GLN cc_start: 0.7424 (mt0) cc_final: 0.7131 (mm110) REVERT: A 441 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7057 (pttm) REVERT: A 452 LYS cc_start: 0.7355 (mtpp) cc_final: 0.7150 (mtmm) REVERT: A 472 LYS cc_start: 0.7020 (ttpt) cc_final: 0.6703 (ttmm) REVERT: A 475 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7140 (mm110) REVERT: A 617 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6938 (pp) REVERT: A 634 GLU cc_start: 0.6987 (tt0) cc_final: 0.6431 (tm-30) outliers start: 15 outliers final: 2 residues processed: 96 average time/residue: 2.8857 time to fit residues: 287.9228 Evaluate side-chains 77 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 445 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5014 Z= 0.177 Angle : 0.563 8.450 6760 Z= 0.306 Chirality : 0.042 0.205 715 Planarity : 0.004 0.034 896 Dihedral : 5.865 28.528 670 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.76 % Allowed : 18.01 % Favored : 79.23 % 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: -1.28 (0.33), residues: 611 helix: -0.96 (0.38), residues: 172 sheet: 0.61 (0.64), residues: 63 loop : -1.05 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 286 HIS 0.004 0.001 HIS A 170 PHE 0.012 0.001 PHE A 390 TYR 0.056 0.002 TYR A 284 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7688 (tptt) cc_final: 0.7041 (ttpt) REVERT: A 222 LYS cc_start: 0.7555 (mttt) cc_final: 0.6965 (mtmt) REVERT: A 268 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7175 (mtmt) REVERT: A 305 LYS cc_start: 0.6174 (pttp) cc_final: 0.5612 (mtmm) REVERT: A 309 LYS cc_start: 0.5926 (mtpt) cc_final: 0.5307 (mppt) REVERT: A 325 GLU cc_start: 0.7382 (pm20) cc_final: 0.6989 (pm20) REVERT: A 452 LYS cc_start: 0.7273 (mtpp) cc_final: 0.7058 (mtmm) REVERT: A 472 LYS cc_start: 0.7054 (ttpt) cc_final: 0.6773 (ttmm) REVERT: A 511 LEU cc_start: 0.7822 (mp) cc_final: 0.7587 (tt) REVERT: A 617 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.6979 (pp) REVERT: A 640 GLU cc_start: 0.7588 (tt0) cc_final: 0.7215 (mt-10) outliers start: 15 outliers final: 3 residues processed: 82 average time/residue: 2.5069 time to fit residues: 214.1223 Evaluate side-chains 67 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 590 HIS ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5014 Z= 0.336 Angle : 0.644 8.348 6760 Z= 0.353 Chirality : 0.045 0.220 715 Planarity : 0.005 0.041 896 Dihedral : 6.239 31.125 670 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.04 % Allowed : 17.28 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.66 (0.32), residues: 611 helix: -1.11 (0.37), residues: 174 sheet: 0.81 (0.66), residues: 58 loop : -1.46 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 515 HIS 0.006 0.002 HIS A 170 PHE 0.017 0.002 PHE A 586 TYR 0.055 0.002 TYR A 284 ARG 0.003 0.001 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7695 (tptt) cc_final: 0.7051 (ttmm) REVERT: A 222 LYS cc_start: 0.7693 (mttt) cc_final: 0.7103 (mtmt) REVERT: A 268 LYS cc_start: 0.7554 (mmmt) cc_final: 0.7212 (mtmt) REVERT: A 284 TYR cc_start: 0.5240 (OUTLIER) cc_final: 0.4869 (p90) REVERT: A 305 LYS cc_start: 0.6168 (pttp) cc_final: 0.5590 (mtmm) REVERT: A 309 LYS cc_start: 0.6124 (mtpt) cc_final: 0.5439 (mppt) REVERT: A 325 GLU cc_start: 0.7633 (pm20) cc_final: 0.7144 (pm20) REVERT: A 452 LYS cc_start: 0.7332 (mtpp) cc_final: 0.7120 (mtmm) REVERT: A 472 LYS cc_start: 0.7058 (ttpt) cc_final: 0.6606 (tppt) REVERT: A 640 GLU cc_start: 0.7607 (tt0) cc_final: 0.7103 (mp0) REVERT: A 671 ASN cc_start: 0.7920 (m-40) cc_final: 0.7513 (t0) REVERT: A 702 ARG cc_start: 0.5111 (mmp80) cc_final: 0.4367 (mtm-85) outliers start: 22 outliers final: 10 residues processed: 87 average time/residue: 2.3733 time to fit residues: 215.1799 Evaluate side-chains 87 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 695 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 590 HIS ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5014 Z= 0.312 Angle : 0.616 9.193 6760 Z= 0.336 Chirality : 0.044 0.214 715 Planarity : 0.004 0.041 896 Dihedral : 6.128 31.259 670 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.41 % Allowed : 16.18 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.81 (0.31), residues: 611 helix: -1.00 (0.37), residues: 173 sheet: 0.84 (0.65), residues: 58 loop : -1.71 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 286 HIS 0.004 0.002 HIS A 170 PHE 0.015 0.002 PHE A 586 TYR 0.058 0.002 TYR A 284 ARG 0.003 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.794 Fit side-chains REVERT: A 174 LYS cc_start: 0.7625 (tptt) cc_final: 0.7015 (ttmm) REVERT: A 222 LYS cc_start: 0.7728 (mttt) cc_final: 0.7105 (mtpt) REVERT: A 268 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7250 (mtmt) REVERT: A 283 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: A 284 TYR cc_start: 0.5225 (OUTLIER) cc_final: 0.4884 (p90) REVERT: A 305 LYS cc_start: 0.6154 (pttp) cc_final: 0.5817 (ptpp) REVERT: A 309 LYS cc_start: 0.6089 (mtpt) cc_final: 0.5416 (mppt) REVERT: A 325 GLU cc_start: 0.7644 (pm20) cc_final: 0.7163 (pm20) REVERT: A 386 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7016 (tttt) REVERT: A 420 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5024 (m-30) REVERT: A 452 LYS cc_start: 0.7352 (mtpp) cc_final: 0.7101 (mtmm) REVERT: A 472 LYS cc_start: 0.7082 (ttpt) cc_final: 0.6623 (ttmm) REVERT: A 617 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.6875 (pp) REVERT: A 624 ARG cc_start: 0.7512 (mtp180) cc_final: 0.7308 (mtp180) REVERT: A 640 GLU cc_start: 0.7656 (tt0) cc_final: 0.7096 (mp0) outliers start: 24 outliers final: 12 residues processed: 87 average time/residue: 2.4489 time to fit residues: 221.8329 Evaluate side-chains 90 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 590 HIS A 645 ASN A 684 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5014 Z= 0.284 Angle : 0.598 8.607 6760 Z= 0.324 Chirality : 0.043 0.206 715 Planarity : 0.004 0.039 896 Dihedral : 5.991 30.470 670 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.78 % Allowed : 16.73 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.32), residues: 611 helix: -0.80 (0.38), residues: 174 sheet: 0.91 (0.66), residues: 58 loop : -1.78 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 286 HIS 0.003 0.002 HIS A 590 PHE 0.013 0.002 PHE A 390 TYR 0.056 0.002 TYR A 284 ARG 0.003 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7612 (tptt) cc_final: 0.7026 (ttmm) REVERT: A 203 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7799 (m) REVERT: A 222 LYS cc_start: 0.7681 (mttt) cc_final: 0.7008 (mtpt) REVERT: A 283 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6262 (tp30) REVERT: A 284 TYR cc_start: 0.5139 (OUTLIER) cc_final: 0.4786 (p90) REVERT: A 305 LYS cc_start: 0.6114 (pttp) cc_final: 0.5757 (ptpp) REVERT: A 309 LYS cc_start: 0.6072 (mtpt) cc_final: 0.5390 (mppt) REVERT: A 325 GLU cc_start: 0.7656 (pm20) cc_final: 0.7150 (pm20) REVERT: A 386 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6995 (tttt) REVERT: A 420 ASP cc_start: 0.6101 (OUTLIER) cc_final: 0.5051 (m-30) REVERT: A 452 LYS cc_start: 0.7325 (mtpp) cc_final: 0.7045 (mtmm) REVERT: A 472 LYS cc_start: 0.7009 (ttpt) cc_final: 0.6543 (ttmm) REVERT: A 511 LEU cc_start: 0.8125 (mp) cc_final: 0.7895 (mm) REVERT: A 617 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.6898 (pp) REVERT: A 624 ARG cc_start: 0.7502 (mtp180) cc_final: 0.7271 (mtp180) REVERT: A 640 GLU cc_start: 0.7652 (tt0) cc_final: 0.7349 (mt-10) outliers start: 26 outliers final: 11 residues processed: 90 average time/residue: 2.2519 time to fit residues: 211.6486 Evaluate side-chains 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 260 ASN A 563 ASN A 590 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5014 Z= 0.254 Angle : 0.589 9.492 6760 Z= 0.316 Chirality : 0.042 0.201 715 Planarity : 0.004 0.037 896 Dihedral : 5.819 29.781 670 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.41 % Allowed : 18.38 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.32), residues: 611 helix: -0.63 (0.39), residues: 174 sheet: 1.04 (0.67), residues: 58 loop : -1.80 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.003 0.001 HIS A 590 PHE 0.012 0.001 PHE A 390 TYR 0.052 0.002 TYR A 284 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7609 (tptt) cc_final: 0.7042 (ttmm) REVERT: A 203 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7827 (m) REVERT: A 222 LYS cc_start: 0.7648 (mttt) cc_final: 0.6983 (mtpt) REVERT: A 268 LYS cc_start: 0.7561 (mmmt) cc_final: 0.7212 (mtmt) REVERT: A 283 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6301 (tp30) REVERT: A 284 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.4701 (p90) REVERT: A 291 LEU cc_start: 0.7384 (mp) cc_final: 0.7176 (tp) REVERT: A 305 LYS cc_start: 0.6107 (pttp) cc_final: 0.5787 (ptpp) REVERT: A 309 LYS cc_start: 0.6061 (mtpt) cc_final: 0.5394 (mppt) REVERT: A 325 GLU cc_start: 0.7644 (pm20) cc_final: 0.7164 (pm20) REVERT: A 386 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7003 (tttt) REVERT: A 420 ASP cc_start: 0.6212 (OUTLIER) cc_final: 0.5213 (m-30) REVERT: A 452 LYS cc_start: 0.7276 (mtpp) cc_final: 0.6970 (mtmm) REVERT: A 472 LYS cc_start: 0.6990 (ttpt) cc_final: 0.6517 (ttmm) REVERT: A 498 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.6874 (t0) REVERT: A 511 LEU cc_start: 0.8146 (mp) cc_final: 0.7910 (mm) REVERT: A 617 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.6867 (pp) REVERT: A 640 GLU cc_start: 0.7644 (tt0) cc_final: 0.7272 (mt-10) outliers start: 24 outliers final: 8 residues processed: 89 average time/residue: 2.2768 time to fit residues: 211.9403 Evaluate side-chains 90 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 260 ASN A 563 ASN A 590 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5014 Z= 0.159 Angle : 0.527 10.031 6760 Z= 0.281 Chirality : 0.040 0.179 715 Planarity : 0.003 0.032 896 Dihedral : 5.322 27.502 670 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.57 % Allowed : 20.40 % Favored : 77.02 % 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: -1.30 (0.33), residues: 611 helix: -0.10 (0.41), residues: 168 sheet: 1.25 (0.69), residues: 58 loop : -1.65 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.005 0.001 HIS A 590 PHE 0.010 0.001 PHE A 390 TYR 0.045 0.001 TYR A 284 ARG 0.001 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7607 (tptt) cc_final: 0.7077 (ttmm) REVERT: A 222 LYS cc_start: 0.7622 (mttt) cc_final: 0.6965 (mtpt) REVERT: A 232 GLU cc_start: 0.3433 (mt-10) cc_final: 0.3168 (mt-10) REVERT: A 268 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7190 (mtmt) REVERT: A 283 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6328 (tp30) REVERT: A 284 TYR cc_start: 0.4637 (OUTLIER) cc_final: 0.4223 (p90) REVERT: A 305 LYS cc_start: 0.6081 (pttp) cc_final: 0.5794 (ptpp) REVERT: A 309 LYS cc_start: 0.5994 (mtpt) cc_final: 0.5344 (mppt) REVERT: A 325 GLU cc_start: 0.7536 (pm20) cc_final: 0.7140 (pm20) REVERT: A 344 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6942 (mp) REVERT: A 386 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6973 (tttt) REVERT: A 452 LYS cc_start: 0.7169 (mtpp) cc_final: 0.6855 (mtmm) REVERT: A 472 LYS cc_start: 0.6862 (ttpt) cc_final: 0.6467 (ttmm) REVERT: A 498 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.6919 (t0) REVERT: A 511 LEU cc_start: 0.8094 (mp) cc_final: 0.7853 (mm) REVERT: A 617 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.6949 (pp) REVERT: A 640 GLU cc_start: 0.7599 (tt0) cc_final: 0.7249 (mt-10) REVERT: A 671 ASN cc_start: 0.7895 (m-40) cc_final: 0.7587 (t0) outliers start: 14 outliers final: 4 residues processed: 85 average time/residue: 2.2618 time to fit residues: 201.5649 Evaluate side-chains 84 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.0010 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 260 ASN A 563 ASN A 590 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5014 Z= 0.193 Angle : 0.536 8.751 6760 Z= 0.288 Chirality : 0.041 0.185 715 Planarity : 0.004 0.030 896 Dihedral : 5.354 27.442 670 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.94 % Allowed : 20.04 % Favored : 77.02 % 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: -1.27 (0.33), residues: 611 helix: -0.10 (0.41), residues: 168 sheet: 1.24 (0.70), residues: 58 loop : -1.61 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.003 0.001 HIS A 590 PHE 0.011 0.001 PHE A 390 TYR 0.049 0.002 TYR A 284 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7607 (tptt) cc_final: 0.7082 (ttmm) REVERT: A 222 LYS cc_start: 0.7560 (mttt) cc_final: 0.6912 (mtpt) REVERT: A 268 LYS cc_start: 0.7530 (mmmt) cc_final: 0.7219 (mtmt) REVERT: A 283 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6317 (tp30) REVERT: A 284 TYR cc_start: 0.4666 (OUTLIER) cc_final: 0.4231 (p90) REVERT: A 305 LYS cc_start: 0.6083 (pttp) cc_final: 0.5493 (mtmm) REVERT: A 309 LYS cc_start: 0.5970 (mtpt) cc_final: 0.5337 (mppt) REVERT: A 325 GLU cc_start: 0.7574 (pm20) cc_final: 0.7219 (pm20) REVERT: A 386 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6978 (tttt) REVERT: A 472 LYS cc_start: 0.6746 (ttpt) cc_final: 0.6330 (ttmm) REVERT: A 498 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.6926 (t0) REVERT: A 511 LEU cc_start: 0.8100 (mp) cc_final: 0.7856 (mm) REVERT: A 617 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6824 (pp) REVERT: A 640 GLU cc_start: 0.7611 (tt0) cc_final: 0.7250 (mt-10) REVERT: A 671 ASN cc_start: 0.7908 (m-40) cc_final: 0.7603 (t0) outliers start: 16 outliers final: 6 residues processed: 83 average time/residue: 2.2868 time to fit residues: 198.2069 Evaluate side-chains 86 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 563 ASN A 590 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5014 Z= 0.160 Angle : 0.520 9.534 6760 Z= 0.277 Chirality : 0.040 0.176 715 Planarity : 0.003 0.027 896 Dihedral : 5.164 27.049 670 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.57 % Allowed : 20.77 % Favored : 76.65 % 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: -1.15 (0.33), residues: 611 helix: 0.02 (0.42), residues: 168 sheet: 1.33 (0.70), residues: 58 loop : -1.54 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.003 0.001 HIS A 590 PHE 0.010 0.001 PHE A 390 TYR 0.044 0.001 TYR A 284 ARG 0.001 0.000 ARG A 580 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7568 (tptt) cc_final: 0.7074 (ttmm) REVERT: A 222 LYS cc_start: 0.7553 (mttt) cc_final: 0.6855 (mtpt) REVERT: A 268 LYS cc_start: 0.7510 (mmmt) cc_final: 0.7190 (mtmt) REVERT: A 283 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6296 (tp30) REVERT: A 284 TYR cc_start: 0.4742 (OUTLIER) cc_final: 0.4324 (p90) REVERT: A 305 LYS cc_start: 0.6119 (pttp) cc_final: 0.5503 (mtmm) REVERT: A 309 LYS cc_start: 0.5946 (mtpt) cc_final: 0.5317 (mppt) REVERT: A 325 GLU cc_start: 0.7481 (pm20) cc_final: 0.7108 (pm20) REVERT: A 386 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6978 (tttt) REVERT: A 472 LYS cc_start: 0.6884 (ttpt) cc_final: 0.6491 (ttmm) REVERT: A 475 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6651 (mm110) REVERT: A 498 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7177 (t0) REVERT: A 511 LEU cc_start: 0.8103 (mp) cc_final: 0.7869 (mm) REVERT: A 542 HIS cc_start: 0.6338 (t70) cc_final: 0.5764 (m90) REVERT: A 617 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6924 (pp) REVERT: A 640 GLU cc_start: 0.7599 (tt0) cc_final: 0.7243 (mt-10) REVERT: A 671 ASN cc_start: 0.7890 (m-40) cc_final: 0.7593 (t0) outliers start: 14 outliers final: 6 residues processed: 86 average time/residue: 2.3754 time to fit residues: 213.6086 Evaluate side-chains 84 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.0000 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 590 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.206742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.183077 restraints weight = 15270.595| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.83 r_work: 0.4053 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5014 Z= 0.150 Angle : 0.511 10.171 6760 Z= 0.271 Chirality : 0.040 0.174 715 Planarity : 0.003 0.027 896 Dihedral : 5.012 26.703 670 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.12 % Allowed : 20.59 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.33), residues: 611 helix: 0.10 (0.42), residues: 168 sheet: 1.38 (0.72), residues: 58 loop : -1.51 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.004 0.001 HIS A 590 PHE 0.009 0.001 PHE A 390 TYR 0.043 0.001 TYR A 284 ARG 0.001 0.000 ARG A 580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4985.17 seconds wall clock time: 87 minutes 12.10 seconds (5232.10 seconds total)