Starting phenix.real_space_refine (version: dev) on Sun Feb 19 08:37:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/02_2023/7adj_11727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/02_2023/7adj_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_11727/02_2023/7adj_11727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/02_2023/7adj_11727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/02_2023/7adj_11727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adj_11727/02_2023/7adj_11727.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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-4877/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: 4.92, per 1000 atoms: 0.51 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: 8.16 Conformation dependent library (CDL) restraints added in 849.5 milliseconds 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: 0.43 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: 3.61 Time building geometry restraints manager: 8.45 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: 3558 17.69 - 35.38: 300 35.38 - 53.06: 53 53.06 - 70.75: 31 70.75 - 88.44: 6 Dihedral angle restraints: 3948 sinusoidal: 1865 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 3945 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 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. 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: 0.960 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: 0.130 Extract box with map and model: 4.310 Check model and map are aligned: 0.130 Process input model: 35.300 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 % 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 *********************** 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 : 0.857 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 outliers start: 1 outliers final: 1 residues processed: 119 average time/residue: 2.7049 time to fit residues: 333.9475 Evaluate side-chains 76 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2404 time to fit residues: 1.3228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 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: 0.7030 moved from start: 0.3348 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= 0.199 Angle : 0.640 7.942 6760 Z= 0.351 Chirality : 0.044 0.211 715 Planarity : 0.004 0.034 896 Dihedral : 6.792 31.632 670 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 3.31 % 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 (0.33), residues: 611 helix: -1.75 (0.33), residues: 174 sheet: 0.13 (0.60), residues: 70 loop : -1.01 (0.33), residues: 367 *********************** 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 104 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 91 average time/residue: 2.8837 time to fit residues: 271.9018 Evaluate side-chains 69 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1713 time to fit residues: 1.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.0470 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 445 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5014 Z= 0.225 Angle : 0.595 7.885 6760 Z= 0.323 Chirality : 0.043 0.209 715 Planarity : 0.004 0.025 896 Dihedral : 6.118 29.838 670 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.33), residues: 611 helix: -1.10 (0.37), residues: 174 sheet: 0.65 (0.65), residues: 63 loop : -1.22 (0.32), residues: 374 *********************** 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 95 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 83 average time/residue: 2.4362 time to fit residues: 211.3875 Evaluate side-chains 65 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 1.1380 time to fit residues: 6.0639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN A 563 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 5014 Z= 0.402 Angle : 0.705 8.686 6760 Z= 0.385 Chirality : 0.046 0.239 715 Planarity : 0.005 0.039 896 Dihedral : 6.590 33.119 670 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 5.88 % 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: -1.99 (0.31), residues: 611 helix: -1.28 (0.36), residues: 175 sheet: 0.80 (0.65), residues: 58 loop : -1.75 (0.29), residues: 378 *********************** 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 101 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 0.860 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 89 average time/residue: 2.3740 time to fit residues: 221.3388 Evaluate side-chains 80 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 7 average time/residue: 0.7464 time to fit residues: 6.9172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 0.026 5014 Z= 0.169 Angle : 0.548 9.948 6760 Z= 0.293 Chirality : 0.041 0.208 715 Planarity : 0.003 0.033 896 Dihedral : 5.710 29.439 670 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 4.41 % 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: -1.56 (0.32), residues: 611 helix: -0.69 (0.38), residues: 176 sheet: 1.08 (0.67), residues: 58 loop : -1.62 (0.31), residues: 377 *********************** 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 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 0.845 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 82 average time/residue: 2.2067 time to fit residues: 189.8048 Evaluate side-chains 80 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 5 average time/residue: 1.0038 time to fit residues: 6.6172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 59 optimal weight: 3.9990 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: 3.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN A 563 ASN A 590 HIS A 645 ASN A 684 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 5014 Z= 0.326 Angle : 0.628 9.128 6760 Z= 0.340 Chirality : 0.044 0.216 715 Planarity : 0.004 0.038 896 Dihedral : 6.058 30.750 670 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer Outliers : 4.78 % 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 (0.32), residues: 611 helix: -0.87 (0.37), residues: 175 sheet: 1.01 (0.66), residues: 58 loop : -1.81 (0.30), residues: 378 *********************** 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 92 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 0.902 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 83 average time/residue: 2.1207 time to fit residues: 184.7548 Evaluate side-chains 79 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 6 average time/residue: 0.4642 time to fit residues: 4.2895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 440 GLN A 563 ASN A 590 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5014 Z= 0.234 Angle : 0.583 10.116 6760 Z= 0.311 Chirality : 0.042 0.203 715 Planarity : 0.003 0.036 896 Dihedral : 5.740 27.276 670 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.32), residues: 611 helix: -0.65 (0.38), residues: 176 sheet: 1.15 (0.67), residues: 58 loop : -1.81 (0.30), residues: 377 *********************** 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 86 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.836 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 2.1543 time to fit residues: 178.7370 Evaluate side-chains 73 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 4 average time/residue: 0.7322 time to fit residues: 4.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 440 GLN A 563 ASN A 590 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5014 Z= 0.209 Angle : 0.555 9.534 6760 Z= 0.297 Chirality : 0.041 0.171 715 Planarity : 0.003 0.031 896 Dihedral : 5.537 26.058 670 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 3.49 % 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: -1.59 (0.33), residues: 611 helix: -0.51 (0.39), residues: 176 sheet: 1.22 (0.68), residues: 58 loop : -1.79 (0.30), residues: 377 *********************** 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 85 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.916 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 79 average time/residue: 2.2056 time to fit residues: 182.9764 Evaluate side-chains 77 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 5 average time/residue: 1.0242 time to fit residues: 6.9140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 440 GLN A 563 ASN A 590 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5014 Z= 0.210 Angle : 0.557 10.198 6760 Z= 0.297 Chirality : 0.041 0.163 715 Planarity : 0.003 0.029 896 Dihedral : 5.474 25.545 670 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer Outliers : 3.12 % 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: -1.49 (0.33), residues: 611 helix: -0.45 (0.40), residues: 176 sheet: 1.31 (0.70), residues: 58 loop : -1.72 (0.30), residues: 377 *********************** 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 83 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.801 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 2.1300 time to fit residues: 172.5159 Evaluate side-chains 75 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 1.1204 time to fit residues: 6.0566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 563 ASN A 590 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5014 Z= 0.173 Angle : 0.539 10.727 6760 Z= 0.284 Chirality : 0.041 0.149 715 Planarity : 0.003 0.027 896 Dihedral : 5.256 24.610 670 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 2.21 % 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: -1.34 (0.33), residues: 611 helix: -0.32 (0.40), residues: 176 sheet: 1.34 (0.71), residues: 58 loop : -1.61 (0.31), residues: 377 ********************** 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 79 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.636 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 2.1376 time to fit residues: 170.7138 Evaluate side-chains 71 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 1 average time/residue: 0.2693 time to fit residues: 1.4353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 440 GLN A 563 ASN A 590 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.205603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181834 restraints weight = 15364.340| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.82 r_work: 0.4039 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5014 Z= 0.165 Angle : 0.524 8.137 6760 Z= 0.279 Chirality : 0.040 0.142 715 Planarity : 0.003 0.025 896 Dihedral : 5.139 24.832 670 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 2.57 % 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: -1.24 (0.34), residues: 611 helix: -0.22 (0.41), residues: 176 sheet: 1.42 (0.72), residues: 58 loop : -1.57 (0.31), residues: 377 =============================================================================== Job complete usr+sys time: 4697.25 seconds wall clock time: 83 minutes 13.78 seconds (4993.78 seconds total)