Starting phenix.real_space_refine
on Mon Jan 20 08:16:26 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9fmu_50570/01_2025/9fmu_50570.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9fmu_50570/01_2025/9fmu_50570.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.46
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9fmu_50570/01_2025/9fmu_50570.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9fmu_50570/01_2025/9fmu_50570.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9fmu_50570/01_2025/9fmu_50570.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9fmu_50570/01_2025/9fmu_50570.cif"
}
resolution = 4.46
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= 0.003 sd= 0.088
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 6
Type Number sf(0) Gaussians
Ca 3 9.91 5
Fe 2 7.16 5
S 131 5.16 5
C 9192 2.51 5
N 2618 2.21 5
O 2817 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 14763
Number of models: 1
Model: ""
Number of chains: 10
Chain: "A"
Number of atoms: 1069
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 141, 1069
Classifications: {'peptide': 141}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 7, 'TRANS': 133}
Chain: "B"
Number of atoms: 1123
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 146, 1123
Classifications: {'peptide': 146}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 7, 'TRANS': 138}
Chain: "C"
Number of atoms: 1982
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 254, 1982
Classifications: {'peptide': 254}
Link IDs: {'PTRANS': 12, 'TRANS': 241}
Chain breaks: 1
Chain: "D"
Number of atoms: 5585
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 738, 5585
Classifications: {'peptide': 738}
Link IDs: {'PTRANS': 23, 'TRANS': 714}
Chain breaks: 1
Chain: "E"
Number of atoms: 4845
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 640, 4845
Classifications: {'peptide': 640}
Link IDs: {'PTRANS': 19, 'TRANS': 620}
Chain breaks: 1
Chain: "A"
Number of atoms: 43
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 43
Unusual residues: {'HEM': 1}
Classifications: {'undetermined': 1}
Chain: "B"
Number of atoms: 43
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 43
Unusual residues: {'HEM': 1}
Classifications: {'undetermined': 1}
Chain: "C"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "D"
Number of atoms: 30
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 30
Unusual residues: {' CA': 2, 'NAG': 2}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "E"
Number of atoms: 15
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 15
Unusual residues: {' CA': 1, 'NAG': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Time building chain proxies: 8.47, per 1000 atoms: 0.57
Number of scatterers: 14763
At special positions: 0
Unit cell: (92.22, 137.8, 161.12, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
Fe 2 26.01
Ca 3 19.99
S 131 16.00
O 2817 8.00
N 2618 7.00
C 9192 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=53, symmetry=0
Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 266 " distance=2.05
Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 340 " distance=2.03
Simple disulfide: pdb=" SG CYS C 351 " - pdb=" SG CYS C 381 " distance=2.05
Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03
Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03
Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03
Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.04
Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03
Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.04
Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03
Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.04
Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03
Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.05
Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.03
Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.02
Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 521 " distance=2.03
Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 567 " distance=2.04
Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.04
Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.06
Simple disulfide: pdb=" SG CYS D 592 " - pdb=" SG CYS D 626 " distance=2.02
Simple disulfide: pdb=" SG CYS D 608 " - pdb=" SG CYS D 672 " distance=2.03
Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 682 " distance=2.03
Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 662 " distance=2.03
Simple disulfide: pdb=" SG CYS D 835 " - pdb=" SG CYS D 869 " distance=2.03
Simple disulfide: pdb=" SG CYS D 864 " - pdb=" SG CYS D 925 " distance=2.02
Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.05
Simple disulfide: pdb=" SG CYS D 938 " - pdb=" SG CYS D 972 " distance=2.02
Simple disulfide: pdb=" SG CYS D 954 " - pdb=" SG CYS D1018 " distance=2.04
Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.04
Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " distance=2.03
Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 309 " distance=2.03
Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 355 " distance=2.04
Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 365 " distance=2.03
Simple disulfide: pdb=" SG CYS E 335 " - pdb=" SG CYS E 345 " distance=2.03
Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 416 " distance=2.03
Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 462 " distance=2.02
Simple disulfide: pdb=" SG CYS E 411 " - pdb=" SG CYS E 472 " distance=2.03
Simple disulfide: pdb=" SG CYS E 442 " - pdb=" SG CYS E 452 " distance=2.04
Simple disulfide: pdb=" SG CYS E 487 " - pdb=" SG CYS E 521 " distance=2.03
Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 567 " distance=2.03
Simple disulfide: pdb=" SG CYS E 516 " - pdb=" SG CYS E 577 " distance=2.02
Simple disulfide: pdb=" SG CYS E 547 " - pdb=" SG CYS E 557 " distance=2.05
Simple disulfide: pdb=" SG CYS E 592 " - pdb=" SG CYS E 626 " distance=2.03
Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 672 " distance=2.03
Simple disulfide: pdb=" SG CYS E 621 " - pdb=" SG CYS E 682 " distance=2.03
Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 662 " distance=2.03
Simple disulfide: pdb=" SG CYS E 728 " - pdb=" SG CYS E 762 " distance=2.03
Simple disulfide: pdb=" SG CYS E 744 " - pdb=" SG CYS E 808 " distance=2.03
Simple disulfide: pdb=" SG CYS E 757 " - pdb=" SG CYS E 818 " distance=2.04
Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 798 " distance=2.03
Simple disulfide: pdb=" SG CYS E 835 " - pdb=" SG CYS E 869 " distance=2.03
Simple disulfide: pdb=" SG CYS E 864 " - pdb=" SG CYS E 925 " distance=2.03
Simple disulfide: pdb=" SG CYS E 895 " - pdb=" SG CYS E 905 " distance=2.05
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 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=5, symmetry=0
Links applied
NAG-ASN
" NAG C1001 " - " ASN C 184 "
" NAG C1002 " - " ASN C 241 "
" NAG D2003 " - " ASN D 320 "
" NAG D2004 " - " ASN D1027 "
" NAG E1102 " - " ASN E 767 "
Number of additional bonds: simple=5, symmetry=0
Coordination:
Other bonds:
Time building additional restraints: 4.20
Conformation dependent library (CDL) restraints added in 2.1 seconds
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 3428
Finding SS restraints...
Secondary structure from input PDB file:
61 helices and 33 sheets defined
29.3% alpha, 28.1% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 2.18
Creating SS restraints...
Processing helix chain 'A' and resid 3 through 16
removed outlier: 3.517A pdb=" N LYS A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A)
Processing helix chain 'A' and resid 17 through 19
No H-bonds generated for 'chain 'A' and resid 17 through 19'
Processing helix chain 'A' and resid 20 through 36
Processing helix chain 'A' and resid 37 through 43
Processing helix chain 'A' and resid 52 through 72
Processing helix chain 'A' and resid 75 through 89
removed outlier: 4.180A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A)
removed outlier: 5.057A pdb=" N ALA A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A)
removed outlier: 5.497A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A)
Processing helix chain 'A' and resid 95 through 113
removed outlier: 3.955A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A)
Processing helix chain 'A' and resid 114 through 117
Processing helix chain 'A' and resid 118 through 138
Processing helix chain 'B' and resid 4 through 18
Processing helix chain 'B' and resid 22 through 35
Processing helix chain 'B' and resid 38 through 43
removed outlier: 3.739A pdb=" N PHE B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A)
Processing helix chain 'B' and resid 50 through 57
Processing helix chain 'B' and resid 57 through 77
removed outlier: 3.800A pdb=" N LYS B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A)
Processing helix chain 'B' and resid 80 through 95
removed outlier: 4.188A pdb=" N THR B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A)
removed outlier: 4.761A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A)
removed outlier: 5.294A pdb=" N LEU B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A)
Processing helix chain 'B' and resid 100 through 119
removed outlier: 3.829A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A)
Processing helix chain 'B' and resid 120 through 122
No H-bonds generated for 'chain 'B' and resid 120 through 122'
Processing helix chain 'B' and resid 123 through 142
Processing helix chain 'C' and resid 200 through 205
Processing helix chain 'C' and resid 213 through 218
Processing helix chain 'C' and resid 219 through 221
No H-bonds generated for 'chain 'C' and resid 219 through 221'
Processing helix chain 'C' and resid 305 through 314
Processing helix chain 'C' and resid 318 through 322
Processing helix chain 'C' and resid 395 through 405
Processing helix chain 'D' and resid 189 through 200
Processing helix chain 'D' and resid 210 through 215
removed outlier: 4.370A pdb=" N PHE D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A)
Processing helix chain 'D' and resid 234 through 238
Processing helix chain 'D' and resid 249 through 253
removed outlier: 3.521A pdb=" N ASP D 253 " --> pdb=" O HIS D 250 " (cutoff:3.500A)
Processing helix chain 'D' and resid 259 through 263
Processing helix chain 'D' and resid 296 through 308
Processing helix chain 'D' and resid 341 through 345
Processing helix chain 'D' and resid 403 through 414
Processing helix chain 'D' and resid 448 through 452
Processing helix chain 'D' and resid 504 through 507
removed outlier: 4.120A pdb=" N PHE D 507 " --> pdb=" O ASP D 504 " (cutoff:3.500A)
No H-bonds generated for 'chain 'D' and resid 504 through 507'
Processing helix chain 'D' and resid 508 through 519
Processing helix chain 'D' and resid 553 through 557
Processing helix chain 'D' and resid 568 through 572
Processing helix chain 'D' and resid 613 through 624
Processing helix chain 'D' and resid 658 through 662
Processing helix chain 'D' and resid 856 through 867
Processing helix chain 'D' and resid 901 through 905
Processing helix chain 'D' and resid 959 through 970
Processing helix chain 'D' and resid 1004 through 1008
Processing helix chain 'D' and resid 1019 through 1023
Processing helix chain 'E' and resid 296 through 307
Processing helix chain 'E' and resid 341 through 345
Processing helix chain 'E' and resid 356 through 360
removed outlier: 3.884A pdb=" N ASP E 360 " --> pdb=" O HIS E 357 " (cutoff:3.500A)
Processing helix chain 'E' and resid 403 through 414
Processing helix chain 'E' and resid 448 through 452
Processing helix chain 'E' and resid 503 through 507
removed outlier: 3.917A pdb=" N PHE E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A)
Processing helix chain 'E' and resid 508 through 519
Processing helix chain 'E' and resid 553 through 557
Processing helix chain 'E' and resid 568 through 572
Processing helix chain 'E' and resid 613 through 624
Processing helix chain 'E' and resid 658 through 662
Processing helix chain 'E' and resid 749 through 760
Processing helix chain 'E' and resid 794 through 798
Processing helix chain 'E' and resid 809 through 813
Processing helix chain 'E' and resid 856 through 867
Processing helix chain 'E' and resid 901 through 905
Processing helix chain 'E' and resid 916 through 920
Processing sheet with id=AA1, first strand: chain 'C' and resid 229 through 230
Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 302
removed outlier: 8.320A pdb=" N VAL C 278 " --> pdb=" O HIS C 362 " (cutoff:3.500A)
removed outlier: 5.663A pdb=" N HIS C 362 " --> pdb=" O VAL C 278 " (cutoff:3.500A)
removed outlier: 4.470A pdb=" N SER C 282 " --> pdb=" O ALA C 358 " (cutoff:3.500A)
removed outlier: 5.088A pdb=" N ALA C 358 " --> pdb=" O SER C 282 " (cutoff:3.500A)
removed outlier: 3.616A pdb=" N GLY C 373 " --> pdb=" O PHE C 359 " (cutoff:3.500A)
removed outlier: 6.904A pdb=" N VAL C 361 " --> pdb=" O ALA C 371 " (cutoff:3.500A)
removed outlier: 5.693A pdb=" N ALA C 371 " --> pdb=" O VAL C 361 " (cutoff:3.500A)
removed outlier: 6.730A pdb=" N ASP C 363 " --> pdb=" O TRP C 369 " (cutoff:3.500A)
removed outlier: 5.699A pdb=" N TRP C 369 " --> pdb=" O ASP C 363 " (cutoff:3.500A)
removed outlier: 7.396A pdb=" N VAL C 388 " --> pdb=" O SER C 376 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'D' and resid 157 through 166
removed outlier: 4.701A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'D' and resid 157 through 166
removed outlier: 4.701A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'D' and resid 264 through 269
Processing sheet with id=AA6, first strand: chain 'D' and resid 264 through 269
removed outlier: 6.755A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A)
removed outlier: 4.154A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A)
removed outlier: 7.840A pdb=" N TRP D 329 " --> pdb=" O TRP D 287 " (cutoff:3.500A)
removed outlier: 8.447A pdb=" N THR D 289 " --> pdb=" O TRP D 329 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'D' and resid 372 through 380
removed outlier: 4.922A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'D' and resid 372 through 380
removed outlier: 4.922A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A)
removed outlier: 6.790A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A)
removed outlier: 3.879A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A)
removed outlier: 8.517A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A)
removed outlier: 6.973A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'D' and resid 476 through 482
Processing sheet with id=AB1, first strand: chain 'D' and resid 476 through 482
removed outlier: 6.793A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A)
removed outlier: 3.977A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A)
removed outlier: 3.631A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A)
removed outlier: 6.994A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A)
removed outlier: 6.889A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'D' and resid 543 through 545
Processing sheet with id=AB3, first strand: chain 'D' and resid 583 through 586
Processing sheet with id=AB4, first strand: chain 'D' and resid 583 through 586
removed outlier: 6.108A pdb=" N VAL D 596 " --> pdb=" O LEU D 607 " (cutoff:3.500A)
removed outlier: 7.002A pdb=" N TRP D 646 " --> pdb=" O TRP D 604 " (cutoff:3.500A)
removed outlier: 5.916A pdb=" N SER D 606 " --> pdb=" O TRP D 646 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'D' and resid 649 through 650
Processing sheet with id=AB6, first strand: chain 'D' and resid 823 through 827
Processing sheet with id=AB7, first strand: chain 'D' and resid 823 through 827
removed outlier: 4.501A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'D' and resid 887 through 888
Processing sheet with id=AB9, first strand: chain 'D' and resid 929 through 932
Processing sheet with id=AC1, first strand: chain 'D' and resid 929 through 932
removed outlier: 6.664A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A)
removed outlier: 3.919A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A)
removed outlier: 10.608A pdb=" N TRP D 950 " --> pdb=" O ILE D 991 " (cutoff:3.500A)
removed outlier: 9.420A pdb=" N LEU D 993 " --> pdb=" O TRP D 950 " (cutoff:3.500A)
removed outlier: 6.971A pdb=" N THR D 952 " --> pdb=" O LEU D 993 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'E' and resid 264 through 269
Processing sheet with id=AC3, first strand: chain 'E' and resid 264 through 269
Processing sheet with id=AC4, first strand: chain 'E' and resid 372 through 380
removed outlier: 5.065A pdb=" N ALA E 383 " --> pdb=" O GLY E 378 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'E' and resid 372 through 380
removed outlier: 5.065A pdb=" N ALA E 383 " --> pdb=" O GLY E 378 " (cutoff:3.500A)
removed outlier: 5.944A pdb=" N VAL E 386 " --> pdb=" O VAL E 397 " (cutoff:3.500A)
removed outlier: 8.217A pdb=" N LEU E 437 " --> pdb=" O LEU E 394 " (cutoff:3.500A)
removed outlier: 6.782A pdb=" N LYS E 396 " --> pdb=" O LEU E 437 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'E' and resid 476 through 482
removed outlier: 6.673A pdb=" N GLY E 574 " --> pdb=" O ILE E 527 " (cutoff:3.500A)
removed outlier: 4.580A pdb=" N ILE E 527 " --> pdb=" O GLY E 574 " (cutoff:3.500A)
removed outlier: 6.556A pdb=" N VAL E 576 " --> pdb=" O VAL E 525 " (cutoff:3.500A)
Processing sheet with id=AC7, first strand: chain 'E' and resid 476 through 482
removed outlier: 3.624A pdb=" N THR E 498 " --> pdb=" O HIS E 495 " (cutoff:3.500A)
removed outlier: 4.622A pdb=" N GLN E 539 " --> pdb=" O TRP E 499 " (cutoff:3.500A)
Processing sheet with id=AC8, first strand: chain 'E' and resid 543 through 545
Processing sheet with id=AC9, first strand: chain 'E' and resid 583 through 586
removed outlier: 6.655A pdb=" N ILE E 681 " --> pdb=" O LEU E 630 " (cutoff:3.500A)
Processing sheet with id=AD1, first strand: chain 'E' and resid 583 through 586
removed outlier: 6.388A pdb=" N VAL E 596 " --> pdb=" O LEU E 607 " (cutoff:3.500A)
removed outlier: 7.350A pdb=" N TRP E 646 " --> pdb=" O TRP E 604 " (cutoff:3.500A)
removed outlier: 6.184A pdb=" N SER E 606 " --> pdb=" O TRP E 646 " (cutoff:3.500A)
Processing sheet with id=AD2, first strand: chain 'E' and resid 649 through 650
Processing sheet with id=AD3, first strand: chain 'E' and resid 719 through 726
removed outlier: 4.829A pdb=" N ALA E 729 " --> pdb=" O GLY E 724 " (cutoff:3.500A)
Processing sheet with id=AD4, first strand: chain 'E' and resid 719 through 726
removed outlier: 4.829A pdb=" N ALA E 729 " --> pdb=" O GLY E 724 " (cutoff:3.500A)
removed outlier: 7.007A pdb=" N VAL E 732 " --> pdb=" O ILE E 743 " (cutoff:3.500A)
removed outlier: 4.206A pdb=" N ILE E 743 " --> pdb=" O VAL E 732 " (cutoff:3.500A)
removed outlier: 7.425A pdb=" N TRP E 782 " --> pdb=" O TRP E 740 " (cutoff:3.500A)
removed outlier: 8.107A pdb=" N THR E 742 " --> pdb=" O TRP E 782 " (cutoff:3.500A)
Processing sheet with id=AD5, first strand: chain 'E' and resid 823 through 827
removed outlier: 4.591A pdb=" N TRP E 922 " --> pdb=" O ASN E 876 " (cutoff:3.500A)
Processing sheet with id=AD6, first strand: chain 'E' and resid 823 through 827
removed outlier: 6.227A pdb=" N LEU E 839 " --> pdb=" O VAL E 850 " (cutoff:3.500A)
651 hydrogen bonds defined for protein.
1704 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 6.30
Time building geometry restraints manager: 4.68 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.21 - 1.39: 6026
1.39 - 1.56: 8929
1.56 - 1.73: 7
1.73 - 1.90: 148
1.90 - 2.07: 8
Bond restraints: 15118
Sorted by residual:
bond pdb=" CB CYS D 577 "
pdb=" SG CYS D 577 "
ideal model delta sigma weight residual
1.808 1.701 0.107 3.30e-02 9.18e+02 1.04e+01
bond pdb=" CB CYS D 228 "
pdb=" SG CYS D 228 "
ideal model delta sigma weight residual
1.808 1.714 0.094 3.30e-02 9.18e+02 8.07e+00
bond pdb=" CB CYS D 516 "
pdb=" SG CYS D 516 "
ideal model delta sigma weight residual
1.808 1.716 0.092 3.30e-02 9.18e+02 7.81e+00
bond pdb=" CB CYS D 895 "
pdb=" SG CYS D 895 "
ideal model delta sigma weight residual
1.808 1.723 0.085 3.30e-02 9.18e+02 6.65e+00
bond pdb=" CB CYS E 547 "
pdb=" SG CYS E 547 "
ideal model delta sigma weight residual
1.808 1.726 0.082 3.30e-02 9.18e+02 6.15e+00
... (remaining 15113 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 4.22: 20295
4.22 - 8.45: 196
8.45 - 12.67: 27
12.67 - 16.89: 7
16.89 - 21.11: 3
Bond angle restraints: 20528
Sorted by residual:
angle pdb=" CA CYS D 557 "
pdb=" CB CYS D 557 "
pdb=" SG CYS D 557 "
ideal model delta sigma weight residual
114.40 135.51 -21.11 2.30e+00 1.89e-01 8.43e+01
angle pdb=" CA CYS E 547 "
pdb=" CB CYS E 547 "
pdb=" SG CYS E 547 "
ideal model delta sigma weight residual
114.40 132.19 -17.79 2.30e+00 1.89e-01 5.98e+01
angle pdb=" CA CYS D 547 "
pdb=" CB CYS D 547 "
pdb=" SG CYS D 547 "
ideal model delta sigma weight residual
114.40 131.94 -17.54 2.30e+00 1.89e-01 5.81e+01
angle pdb=" CA CYS D 516 "
pdb=" CB CYS D 516 "
pdb=" SG CYS D 516 "
ideal model delta sigma weight residual
114.40 129.79 -15.39 2.30e+00 1.89e-01 4.48e+01
angle pdb=" C CYS D 547 "
pdb=" CA CYS D 547 "
pdb=" CB CYS D 547 "
ideal model delta sigma weight residual
109.54 120.92 -11.38 1.84e+00 2.95e-01 3.83e+01
... (remaining 20523 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.77: 8260
17.77 - 35.54: 581
35.54 - 53.30: 112
53.30 - 71.07: 32
71.07 - 88.84: 17
Dihedral angle restraints: 9002
sinusoidal: 3631
harmonic: 5371
Sorted by residual:
dihedral pdb=" CB CYS D 835 "
pdb=" SG CYS D 835 "
pdb=" SG CYS D 869 "
pdb=" CB CYS D 869 "
ideal model delta sinusoidal sigma weight residual
93.00 169.99 -76.99 1 1.00e+01 1.00e-02 7.44e+01
dihedral pdb=" CB CYS D 335 "
pdb=" SG CYS D 335 "
pdb=" SG CYS D 345 "
pdb=" CB CYS D 345 "
ideal model delta sinusoidal sigma weight residual
93.00 23.89 69.11 1 1.00e+01 1.00e-02 6.18e+01
dihedral pdb=" CB CYS D 184 "
pdb=" SG CYS D 184 "
pdb=" SG CYS D 248 "
pdb=" CB CYS D 248 "
ideal model delta sinusoidal sigma weight residual
93.00 25.60 67.40 1 1.00e+01 1.00e-02 5.91e+01
... (remaining 8999 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.103: 2000
0.103 - 0.207: 177
0.207 - 0.310: 19
0.310 - 0.413: 7
0.413 - 0.516: 2
Chirality restraints: 2205
Sorted by residual:
chirality pdb=" CA CYS D 547 "
pdb=" N CYS D 547 "
pdb=" C CYS D 547 "
pdb=" CB CYS D 547 "
both_signs ideal model delta sigma weight residual
False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.66e+00
chirality pdb=" CA CYS E 547 "
pdb=" N CYS E 547 "
pdb=" C CYS E 547 "
pdb=" CB CYS E 547 "
both_signs ideal model delta sigma weight residual
False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00
chirality pdb=" CA CYS D 228 "
pdb=" N CYS D 228 "
pdb=" C CYS D 228 "
pdb=" CB CYS D 228 "
both_signs ideal model delta sigma weight residual
False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00
... (remaining 2202 not shown)
Planarity restraints: 2661
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA ASN B 102 " -0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01
pdb=" C ASN B 102 " 0.094 2.00e-02 2.50e+03
pdb=" O ASN B 102 " -0.035 2.00e-02 2.50e+03
pdb=" N PHE B 103 " -0.032 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA ARG B 40 " 0.027 2.00e-02 2.50e+03 5.42e-02 2.94e+01
pdb=" C ARG B 40 " -0.094 2.00e-02 2.50e+03
pdb=" O ARG B 40 " 0.035 2.00e-02 2.50e+03
pdb=" N PHE B 41 " 0.032 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA GLY A 25 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01
pdb=" C GLY A 25 " -0.077 2.00e-02 2.50e+03
pdb=" O GLY A 25 " 0.029 2.00e-02 2.50e+03
pdb=" N ALA A 26 " 0.026 2.00e-02 2.50e+03
... (remaining 2658 not shown)
Histogram of nonbonded interaction distances:
1.96 - 2.55: 160
2.55 - 3.14: 12275
3.14 - 3.72: 23995
3.72 - 4.31: 32449
4.31 - 4.90: 51821
Nonbonded interactions: 120700
Sorted by model distance:
nonbonded pdb=" OD2 ASP D 225 "
pdb="CA CA D2001 "
model vdw
1.959 2.510
nonbonded pdb=" OH TYR D 424 "
pdb=" O GLU D 467 "
model vdw
1.979 3.040
nonbonded pdb=" OG SER E 879 "
pdb=" OD1 ASP E 881 "
model vdw
1.993 3.040
nonbonded pdb=" O GLY D 294 "
pdb="CA CA D2002 "
model vdw
2.104 2.510
nonbonded pdb=" OD1 ASP C 349 "
pdb=" N THR C 350 "
model vdw
2.124 3.120
... (remaining 120695 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 2.100
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 0.590
Check model and map are aligned: 0.110
Set scattering table: 0.140
Process input model: 36.240
Find NCS groups from input model: 0.270
Set up NCS constraints: 0.060
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.770
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 42.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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 : 0.005 0.107 15118 Z= 0.361
Angle : 1.182 21.112 20528 Z= 0.655
Chirality : 0.065 0.516 2205
Planarity : 0.009 0.100 2656
Dihedral : 13.083 88.839 5415
Min Nonbonded Distance : 1.959
Molprobity Statistics.
All-atom Clashscore : 20.15
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 4.31 %
Favored : 95.38 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.59 %
Favored : 98.41 %
Cbeta Deviations : 0.23 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.05 %
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: -1.25 (0.17), residues: 1903
helix: -1.81 (0.20), residues: 415
sheet: -0.55 (0.32), residues: 237
loop : -0.47 (0.16), residues: 1251
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.039 0.003 TRP E 796
HIS 0.011 0.001 HIS C 337
PHE 0.037 0.002 PHE E 438
TYR 0.038 0.003 TYR D 465
ARG 0.022 0.003 ARG D 198
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
200 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 200
time to evaluate : 1.659
Fit side-chains
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8523 (pt0) cc_final: 0.8121 (tm-30)
REVERT: A 104 CYS cc_start: 0.9389 (m) cc_final: 0.8699 (p)
REVERT: B 19 ASN cc_start: 0.8830 (m-40) cc_final: 0.8450 (t0)
REVERT: B 47 ASP cc_start: 0.8030 (p0) cc_final: 0.7752 (m-30)
REVERT: B 65 LYS cc_start: 0.9749 (pptt) cc_final: 0.9102 (mmpt)
REVERT: C 175 TRP cc_start: 0.8692 (p90) cc_final: 0.7991 (p90)
REVERT: C 191 LEU cc_start: 0.8435 (tp) cc_final: 0.8116 (mm)
REVERT: C 230 LEU cc_start: 0.9394 (tp) cc_final: 0.9075 (tt)
REVERT: C 263 MET cc_start: 0.8262 (tmm) cc_final: 0.8026 (tmm)
REVERT: C 343 MET cc_start: 0.7348 (ppp) cc_final: 0.6937 (ppp)
REVERT: C 378 ASP cc_start: 0.8510 (p0) cc_final: 0.8203 (p0)
REVERT: D 330 LEU cc_start: 0.8635 (mm) cc_final: 0.8394 (mt)
REVERT: D 339 GLU cc_start: 0.6642 (mp0) cc_final: 0.6415 (mp0)
REVERT: D 884 MET cc_start: 0.0288 (ppp) cc_final: -0.0857 (tmm)
REVERT: D 903 TRP cc_start: 0.8887 (m-90) cc_final: 0.8656 (m-90)
REVERT: D 931 LEU cc_start: 0.7079 (mm) cc_final: 0.6845 (mm)
REVERT: E 298 TYR cc_start: 0.8847 (m-10) cc_final: 0.8623 (m-80)
REVERT: E 466 GLU cc_start: 0.4802 (mt-10) cc_final: 0.4413 (mm-30)
REVERT: E 507 PHE cc_start: 0.8840 (t80) cc_final: 0.8562 (t80)
REVERT: E 659 MET cc_start: 0.7215 (mpp) cc_final: 0.6928 (mmm)
outliers start: 0
outliers final: 0
residues processed: 200
average time/residue: 0.2671
time to fit residues: 79.7324
Evaluate side-chains
104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 104
time to evaluate : 1.604
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 160 optimal weight: 10.0000
chunk 144 optimal weight: 6.9990
chunk 79 optimal weight: 10.0000
chunk 49 optimal weight: 3.9990
chunk 97 optimal weight: 5.9990
chunk 76 optimal weight: 3.9990
chunk 148 optimal weight: 9.9990
chunk 57 optimal weight: 4.9990
chunk 90 optimal weight: 3.9990
chunk 110 optimal weight: 9.9990
chunk 172 optimal weight: 9.9990
overall best weight: 4.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 72 HIS
** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 ASN
C 337 HIS
C 362 HIS
** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 284 GLN
** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 532 HIS
** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 986 GLN
E 754 HIS
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.067065 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.049107 restraints weight = 93521.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.050957 restraints weight = 52226.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.052212 restraints weight = 34275.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start: 0.3442
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.115 15118 Z= 0.442
Angle : 0.843 13.416 20528 Z= 0.444
Chirality : 0.050 0.227 2205
Planarity : 0.006 0.062 2656
Dihedral : 7.248 86.861 2143
Min Nonbonded Distance : 2.095
Molprobity Statistics.
All-atom Clashscore : 20.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.73 %
Favored : 96.27 %
Rotamer:
Outliers : 0.19 %
Allowed : 6.49 %
Favored : 93.32 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.05 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.50 (0.18), residues: 1903
helix: 0.14 (0.24), residues: 412
sheet: -0.30 (0.33), residues: 225
loop : -0.46 (0.17), residues: 1266
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.036 0.003 TRP D 450
HIS 0.011 0.002 HIS B 92
PHE 0.021 0.003 PHE E 821
TYR 0.021 0.003 TYR D 354
ARG 0.008 0.001 ARG D 865
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
112 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 109
time to evaluate : 1.787
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8501 (pt0) cc_final: 0.7637 (tm-30)
REVERT: A 104 CYS cc_start: 0.9095 (m) cc_final: 0.8263 (t)
REVERT: B 19 ASN cc_start: 0.9200 (m-40) cc_final: 0.8802 (t0)
REVERT: B 65 LYS cc_start: 0.9771 (pptt) cc_final: 0.9030 (mmpt)
REVERT: C 175 TRP cc_start: 0.9009 (p90) cc_final: 0.8583 (p90)
REVERT: C 349 ASP cc_start: 0.8300 (t0) cc_final: 0.7998 (t0)
REVERT: D 449 LEU cc_start: 0.9229 (pp) cc_final: 0.8502 (tp)
REVERT: D 884 MET cc_start: 0.1010 (ppp) cc_final: 0.0080 (tmm)
REVERT: D 931 LEU cc_start: 0.7921 (mm) cc_final: 0.7617 (mt)
REVERT: E 507 PHE cc_start: 0.8639 (t80) cc_final: 0.8155 (t80)
REVERT: E 640 LYS cc_start: 0.8700 (pttt) cc_final: 0.8394 (tptp)
outliers start: 3
outliers final: 3
residues processed: 112
average time/residue: 0.2501
time to fit residues: 44.7602
Evaluate side-chains
78 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 75
time to evaluate : 1.849
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 6 optimal weight: 4.9990
chunk 34 optimal weight: 2.9990
chunk 150 optimal weight: 7.9990
chunk 138 optimal weight: 5.9990
chunk 76 optimal weight: 0.8980
chunk 130 optimal weight: 8.9990
chunk 142 optimal weight: 5.9990
chunk 61 optimal weight: 4.9990
chunk 94 optimal weight: 9.9990
chunk 180 optimal weight: 0.0670
chunk 161 optimal weight: 10.0000
overall best weight: 2.7924
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 396 GLN
D 250 HIS
** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.067426 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.049437 restraints weight = 91089.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.051338 restraints weight = 50925.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.052636 restraints weight = 33450.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start: 0.4123
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.082 15118 Z= 0.278
Angle : 0.673 11.475 20528 Z= 0.353
Chirality : 0.045 0.180 2205
Planarity : 0.005 0.058 2656
Dihedral : 6.782 79.067 2143
Min Nonbonded Distance : 2.193
Molprobity Statistics.
All-atom Clashscore : 14.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.42 %
Favored : 96.58 %
Rotamer:
Outliers : 0.00 %
Allowed : 4.90 %
Favored : 95.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.05 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.28 (0.19), residues: 1903
helix: 0.64 (0.25), residues: 415
sheet: -0.31 (0.31), residues: 239
loop : -0.41 (0.18), residues: 1249
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.032 0.002 TRP E 295
HIS 0.008 0.001 HIS D 347
PHE 0.018 0.002 PHE A 117
TYR 0.018 0.002 TYR D 427
ARG 0.010 0.001 ARG D 318
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 104
time to evaluate : 1.899
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8445 (pt0) cc_final: 0.7977 (tm-30)
REVERT: A 104 CYS cc_start: 0.9075 (m) cc_final: 0.8104 (t)
REVERT: B 19 ASN cc_start: 0.9207 (m-40) cc_final: 0.8790 (t0)
REVERT: B 141 LEU cc_start: 0.9217 (tp) cc_final: 0.8922 (tp)
REVERT: C 349 ASP cc_start: 0.7963 (t0) cc_final: 0.7550 (t0)
REVERT: D 342 ILE cc_start: 0.8898 (mp) cc_final: 0.8677 (tp)
REVERT: D 659 MET cc_start: 0.8521 (tpp) cc_final: 0.8228 (tpt)
REVERT: D 822 MET cc_start: 0.7144 (tmm) cc_final: 0.6700 (tmm)
REVERT: D 884 MET cc_start: 0.1084 (ppp) cc_final: 0.0204 (tmm)
REVERT: D 995 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9200 (mm-30)
REVERT: E 507 PHE cc_start: 0.8559 (t80) cc_final: 0.8113 (t80)
outliers start: 0
outliers final: 0
residues processed: 104
average time/residue: 0.2254
time to fit residues: 38.6299
Evaluate side-chains
68 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 68
time to evaluate : 1.784
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 181 optimal weight: 2.9990
chunk 182 optimal weight: 5.9990
chunk 9 optimal weight: 1.9990
chunk 150 optimal weight: 20.0000
chunk 132 optimal weight: 20.0000
chunk 109 optimal weight: 7.9990
chunk 170 optimal weight: 0.8980
chunk 63 optimal weight: 6.9990
chunk 142 optimal weight: 0.0980
chunk 119 optimal weight: 0.7980
chunk 138 optimal weight: 1.9990
overall best weight: 1.1584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 HIS
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 464 HIS
D 495 HIS
** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.068538 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.050705 restraints weight = 88610.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.052696 restraints weight = 49001.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.054061 restraints weight = 31888.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start: 0.4360
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.073 15118 Z= 0.179
Angle : 0.604 9.417 20528 Z= 0.312
Chirality : 0.044 0.168 2205
Planarity : 0.004 0.063 2656
Dihedral : 6.367 79.838 2143
Min Nonbonded Distance : 2.254
Molprobity Statistics.
All-atom Clashscore : 11.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.36 %
Favored : 96.64 %
Rotamer:
Outliers : 0.00 %
Allowed : 4.14 %
Favored : 95.86 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.08 (0.19), residues: 1903
helix: 1.03 (0.26), residues: 418
sheet: -0.15 (0.32), residues: 225
loop : -0.38 (0.17), residues: 1260
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.043 0.001 TRP D 945
HIS 0.007 0.001 HIS D 347
PHE 0.015 0.001 PHE A 36
TYR 0.016 0.001 TYR D 465
ARG 0.006 0.000 ARG D 865
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
114 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 114
time to evaluate : 1.532
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8383 (pt0) cc_final: 0.7922 (tm-30)
REVERT: A 104 CYS cc_start: 0.9122 (m) cc_final: 0.8085 (t)
REVERT: B 19 ASN cc_start: 0.9248 (m-40) cc_final: 0.8856 (t0)
REVERT: B 141 LEU cc_start: 0.9139 (tp) cc_final: 0.8821 (tp)
REVERT: C 179 MET cc_start: 0.8917 (ttm) cc_final: 0.8479 (tmm)
REVERT: C 343 MET cc_start: 0.8043 (ppp) cc_final: 0.7699 (ppp)
REVERT: C 349 ASP cc_start: 0.7983 (t0) cc_final: 0.7450 (t0)
REVERT: C 370 TYR cc_start: 0.6968 (m-80) cc_final: 0.6749 (m-10)
REVERT: D 342 ILE cc_start: 0.8873 (mp) cc_final: 0.8648 (tp)
REVERT: D 659 MET cc_start: 0.8586 (tpp) cc_final: 0.8244 (tpt)
REVERT: D 884 MET cc_start: 0.1572 (ppp) cc_final: 0.1368 (ppp)
REVERT: D 888 MET cc_start: 0.3441 (tpt) cc_final: 0.3041 (tpt)
REVERT: E 507 PHE cc_start: 0.8584 (t80) cc_final: 0.7963 (t80)
outliers start: 0
outliers final: 0
residues processed: 114
average time/residue: 0.2410
time to fit residues: 44.3056
Evaluate side-chains
76 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 76
time to evaluate : 1.643
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 170 optimal weight: 9.9990
chunk 121 optimal weight: 8.9990
chunk 33 optimal weight: 5.9990
chunk 172 optimal weight: 9.9990
chunk 46 optimal weight: 5.9990
chunk 93 optimal weight: 20.0000
chunk 0 optimal weight: 7.9990
chunk 160 optimal weight: 7.9990
chunk 48 optimal weight: 1.9990
chunk 125 optimal weight: 0.0870
chunk 111 optimal weight: 0.0570
overall best weight: 2.8282
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 68 ASN
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 203 ASN
** D 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.066758 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.048776 restraints weight = 91437.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.050674 restraints weight = 51098.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.051999 restraints weight = 33598.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start: 0.4965
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.085 15118 Z= 0.286
Angle : 0.654 12.664 20528 Z= 0.340
Chirality : 0.045 0.181 2205
Planarity : 0.005 0.092 2656
Dihedral : 6.619 82.598 2143
Min Nonbonded Distance : 2.193
Molprobity Statistics.
All-atom Clashscore : 14.76
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.94 %
Favored : 96.06 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.93 %
Favored : 97.07 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.27 (0.19), residues: 1903
helix: 1.05 (0.26), residues: 415
sheet: -0.39 (0.30), residues: 242
loop : -0.54 (0.17), residues: 1246
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.032 0.002 TRP D 945
HIS 0.011 0.001 HIS D 347
PHE 0.013 0.002 PHE A 36
TYR 0.014 0.002 TYR D 427
ARG 0.006 0.001 ARG D 392
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
93 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 93
time to evaluate : 1.591
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8418 (pt0) cc_final: 0.7845 (tm-30)
REVERT: A 104 CYS cc_start: 0.9073 (m) cc_final: 0.8098 (t)
REVERT: B 19 ASN cc_start: 0.9295 (m-40) cc_final: 0.8912 (t0)
REVERT: B 106 LEU cc_start: 0.9369 (tt) cc_final: 0.8954 (pp)
REVERT: C 179 MET cc_start: 0.8969 (ttm) cc_final: 0.8441 (tmm)
REVERT: C 203 ASN cc_start: 0.7927 (m110) cc_final: 0.7623 (m-40)
REVERT: C 349 ASP cc_start: 0.8159 (t0) cc_final: 0.7850 (t0)
REVERT: C 370 TYR cc_start: 0.7307 (m-80) cc_final: 0.6989 (m-80)
REVERT: D 342 ILE cc_start: 0.8943 (mp) cc_final: 0.8727 (tp)
REVERT: D 659 MET cc_start: 0.8661 (tpp) cc_final: 0.8376 (tpt)
REVERT: D 884 MET cc_start: 0.1552 (ppp) cc_final: 0.1234 (ppp)
REVERT: E 640 LYS cc_start: 0.8629 (pttt) cc_final: 0.8264 (tmtt)
REVERT: E 786 MET cc_start: 0.8697 (pmm) cc_final: 0.8135 (pmm)
outliers start: 0
outliers final: 0
residues processed: 93
average time/residue: 0.2141
time to fit residues: 33.5171
Evaluate side-chains
68 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 68
time to evaluate : 1.597
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 126 optimal weight: 7.9990
chunk 74 optimal weight: 7.9990
chunk 46 optimal weight: 0.8980
chunk 114 optimal weight: 9.9990
chunk 158 optimal weight: 0.0270
chunk 133 optimal weight: 30.0000
chunk 116 optimal weight: 8.9990
chunk 57 optimal weight: 0.9980
chunk 143 optimal weight: 7.9990
chunk 150 optimal weight: 7.9990
chunk 43 optimal weight: 0.9980
overall best weight: 2.1840
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 464 HIS
D 618 HIS
D 946 HIS
E 391 GLN
** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.066904 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.048972 restraints weight = 91064.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.050899 restraints weight = 51125.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.052193 restraints weight = 33632.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start: 0.5286
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.073 15118 Z= 0.235
Angle : 0.619 11.712 20528 Z= 0.321
Chirality : 0.044 0.183 2205
Planarity : 0.004 0.065 2656
Dihedral : 6.505 80.649 2143
Min Nonbonded Distance : 2.206
Molprobity Statistics.
All-atom Clashscore : 13.79
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.10 %
Favored : 95.90 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.36 %
Favored : 97.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.25 (0.19), residues: 1903
helix: 1.17 (0.26), residues: 411
sheet: -0.64 (0.29), residues: 259
loop : -0.49 (0.18), residues: 1233
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.025 0.001 TRP D 945
HIS 0.008 0.001 HIS D 347
PHE 0.011 0.001 PHE B 118
TYR 0.013 0.002 TYR D 427
ARG 0.007 0.001 ARG D 865
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
99 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 99
time to evaluate : 2.032
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8366 (pt0) cc_final: 0.7905 (tm-30)
REVERT: A 104 CYS cc_start: 0.9104 (m) cc_final: 0.8098 (t)
REVERT: B 19 ASN cc_start: 0.9262 (m-40) cc_final: 0.8857 (t0)
REVERT: C 179 MET cc_start: 0.8966 (ttm) cc_final: 0.8467 (tmm)
REVERT: C 203 ASN cc_start: 0.7827 (m110) cc_final: 0.7498 (m-40)
REVERT: C 343 MET cc_start: 0.7600 (ptt) cc_final: 0.7131 (ptt)
REVERT: C 349 ASP cc_start: 0.8308 (t0) cc_final: 0.7991 (t0)
REVERT: D 620 LEU cc_start: 0.9704 (tp) cc_final: 0.9475 (tt)
REVERT: D 659 MET cc_start: 0.8728 (tpp) cc_final: 0.8433 (tpt)
REVERT: D 884 MET cc_start: 0.1577 (ppp) cc_final: 0.1110 (ppp)
REVERT: E 786 MET cc_start: 0.8840 (pmm) cc_final: 0.8290 (pmm)
outliers start: 0
outliers final: 0
residues processed: 99
average time/residue: 0.2147
time to fit residues: 36.4040
Evaluate side-chains
70 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 70
time to evaluate : 1.730
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 183 optimal weight: 2.9990
chunk 103 optimal weight: 4.9990
chunk 18 optimal weight: 1.9990
chunk 71 optimal weight: 0.4980
chunk 99 optimal weight: 4.9990
chunk 150 optimal weight: 6.9990
chunk 94 optimal weight: 50.0000
chunk 121 optimal weight: 9.9990
chunk 125 optimal weight: 0.9990
chunk 187 optimal weight: 6.9990
chunk 181 optimal weight: 1.9990
overall best weight: 1.6988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.067296 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.049324 restraints weight = 89965.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.051245 restraints weight = 50569.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.052554 restraints weight = 33195.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start: 0.5513
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.083 15118 Z= 0.206
Angle : 0.603 10.735 20528 Z= 0.312
Chirality : 0.044 0.185 2205
Planarity : 0.004 0.063 2656
Dihedral : 6.366 83.044 2143
Min Nonbonded Distance : 2.256
Molprobity Statistics.
All-atom Clashscore : 13.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.31 %
Favored : 95.69 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.65 %
Favored : 98.35 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.19 (0.19), residues: 1903
helix: 1.32 (0.26), residues: 411
sheet: -0.67 (0.29), residues: 249
loop : -0.49 (0.17), residues: 1243
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.001 TRP D 945
HIS 0.007 0.001 HIS D 347
PHE 0.009 0.001 PHE A 36
TYR 0.010 0.001 TYR D 427
ARG 0.003 0.000 ARG D 160
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
100 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 100
time to evaluate : 1.645
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8398 (pt0) cc_final: 0.7901 (tm-30)
REVERT: A 104 CYS cc_start: 0.9103 (m) cc_final: 0.8085 (t)
REVERT: B 19 ASN cc_start: 0.9229 (m-40) cc_final: 0.8783 (t0)
REVERT: B 52 ASP cc_start: 0.8971 (m-30) cc_final: 0.8529 (p0)
REVERT: C 179 MET cc_start: 0.8970 (ttm) cc_final: 0.8460 (tmm)
REVERT: D 620 LEU cc_start: 0.9693 (tp) cc_final: 0.9467 (tt)
REVERT: D 659 MET cc_start: 0.8749 (tpp) cc_final: 0.8423 (tpt)
REVERT: D 884 MET cc_start: 0.1618 (ppp) cc_final: 0.1116 (ppp)
REVERT: E 786 MET cc_start: 0.8835 (pmm) cc_final: 0.8290 (pmm)
REVERT: E 884 MET cc_start: 0.4269 (ppp) cc_final: 0.4015 (ppp)
outliers start: 0
outliers final: 0
residues processed: 100
average time/residue: 0.2083
time to fit residues: 35.2595
Evaluate side-chains
72 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 72
time to evaluate : 1.717
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 67 optimal weight: 0.7980
chunk 8 optimal weight: 0.9990
chunk 62 optimal weight: 5.9990
chunk 65 optimal weight: 0.9990
chunk 149 optimal weight: 9.9990
chunk 131 optimal weight: 5.9990
chunk 71 optimal weight: 0.9980
chunk 183 optimal weight: 2.9990
chunk 139 optimal weight: 0.0000
chunk 84 optimal weight: 8.9990
chunk 2 optimal weight: 1.9990
overall best weight: 0.7588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 203 ASN
D 284 GLN
D 618 HIS
** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.068612 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.050776 restraints weight = 89631.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.052722 restraints weight = 50364.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.054056 restraints weight = 33072.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start: 0.5577
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.077 15118 Z= 0.156
Angle : 0.577 8.312 20528 Z= 0.296
Chirality : 0.043 0.196 2205
Planarity : 0.004 0.065 2656
Dihedral : 6.083 83.428 2143
Min Nonbonded Distance : 2.273
Molprobity Statistics.
All-atom Clashscore : 10.91
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.31 %
Favored : 96.69 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.15 %
Favored : 98.85 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.05 (0.19), residues: 1903
helix: 1.47 (0.27), residues: 412
sheet: -0.56 (0.30), residues: 238
loop : -0.41 (0.17), residues: 1253
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.001 TRP E 295
HIS 0.005 0.001 HIS A 72
PHE 0.009 0.001 PHE E 438
TYR 0.017 0.001 TYR D 465
ARG 0.004 0.000 ARG E 865
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
108 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 108
time to evaluate : 1.630
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8427 (pt0) cc_final: 0.7913 (tm-30)
REVERT: A 104 CYS cc_start: 0.9172 (m) cc_final: 0.8117 (t)
REVERT: B 52 ASP cc_start: 0.8978 (m-30) cc_final: 0.8490 (p0)
REVERT: C 179 MET cc_start: 0.8954 (ttm) cc_final: 0.8452 (tmm)
REVERT: D 659 MET cc_start: 0.8781 (tpp) cc_final: 0.8453 (tpt)
REVERT: D 884 MET cc_start: 0.1535 (ppp) cc_final: 0.1049 (ppp)
REVERT: D 1015 HIS cc_start: 0.8760 (m90) cc_final: 0.8277 (m90)
REVERT: E 786 MET cc_start: 0.8679 (pmm) cc_final: 0.8121 (pmm)
outliers start: 0
outliers final: 0
residues processed: 108
average time/residue: 0.2096
time to fit residues: 37.6724
Evaluate side-chains
72 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 72
time to evaluate : 1.657
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 105 optimal weight: 0.4980
chunk 80 optimal weight: 0.2980
chunk 145 optimal weight: 0.9980
chunk 56 optimal weight: 0.8980
chunk 42 optimal weight: 2.9990
chunk 41 optimal weight: 1.9990
chunk 24 optimal weight: 1.9990
chunk 18 optimal weight: 1.9990
chunk 63 optimal weight: 5.9990
chunk 77 optimal weight: 10.0000
chunk 76 optimal weight: 0.8980
overall best weight: 0.7180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.069027 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.051458 restraints weight = 87828.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.053413 restraints weight = 48716.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.054757 restraints weight = 31832.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start: 0.5717
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.074 15118 Z= 0.157
Angle : 0.577 7.506 20528 Z= 0.296
Chirality : 0.043 0.186 2205
Planarity : 0.004 0.062 2656
Dihedral : 5.973 83.073 2143
Min Nonbonded Distance : 2.272
Molprobity Statistics.
All-atom Clashscore : 10.49
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.21 %
Favored : 96.79 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.70 %
Favored : 99.30 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.02 (0.19), residues: 1903
helix: 1.52 (0.26), residues: 412
sheet: -0.54 (0.30), residues: 228
loop : -0.42 (0.17), residues: 1263
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.037 0.001 TRP D 992
HIS 0.006 0.001 HIS D 946
PHE 0.009 0.001 PHE D 507
TYR 0.009 0.001 TYR E 580
ARG 0.003 0.000 ARG D 865
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
101 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 101
time to evaluate : 1.678
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8423 (pt0) cc_final: 0.7930 (tm-30)
REVERT: A 104 CYS cc_start: 0.9142 (m) cc_final: 0.8093 (t)
REVERT: B 52 ASP cc_start: 0.8974 (m-30) cc_final: 0.8475 (p0)
REVERT: C 179 MET cc_start: 0.8900 (ttm) cc_final: 0.8442 (tmm)
REVERT: D 659 MET cc_start: 0.8628 (tpp) cc_final: 0.8318 (tpt)
REVERT: D 884 MET cc_start: 0.1759 (ppp) cc_final: 0.1217 (ppp)
REVERT: D 1015 HIS cc_start: 0.8736 (m90) cc_final: 0.8225 (m90)
REVERT: E 786 MET cc_start: 0.8621 (pmm) cc_final: 0.8077 (pmm)
outliers start: 0
outliers final: 0
residues processed: 101
average time/residue: 0.2165
time to fit residues: 36.7362
Evaluate side-chains
73 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 73
time to evaluate : 1.769
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 80 optimal weight: 0.0270
chunk 178 optimal weight: 9.9990
chunk 174 optimal weight: 8.9990
chunk 56 optimal weight: 0.0270
chunk 50 optimal weight: 4.9990
chunk 23 optimal weight: 3.9990
chunk 152 optimal weight: 0.0470
chunk 151 optimal weight: 0.8980
chunk 141 optimal weight: 5.9990
chunk 98 optimal weight: 9.9990
chunk 103 optimal weight: 0.9990
overall best weight: 0.3996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS
** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.069492 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.051841 restraints weight = 88889.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.053806 restraints weight = 49612.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.055158 restraints weight = 32524.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start: 0.5792
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.069 15118 Z= 0.147
Angle : 0.574 7.537 20528 Z= 0.293
Chirality : 0.043 0.181 2205
Planarity : 0.004 0.064 2656
Dihedral : 5.863 82.812 2143
Min Nonbonded Distance : 2.295
Molprobity Statistics.
All-atom Clashscore : 9.87
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.15 %
Favored : 96.85 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.32 %
Favored : 99.68 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.02 (0.19), residues: 1903
helix: 1.52 (0.26), residues: 411
sheet: -0.54 (0.31), residues: 221
loop : -0.37 (0.17), residues: 1271
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.001 TRP D 992
HIS 0.004 0.001 HIS A 72
PHE 0.009 0.001 PHE E 438
TYR 0.020 0.001 TYR B 130
ARG 0.005 0.000 ARG D1012
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3806 Ramachandran restraints generated.
1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
114 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 114
time to evaluate : 1.656
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 30 GLU cc_start: 0.8395 (pt0) cc_final: 0.7870 (tm-30)
REVERT: A 104 CYS cc_start: 0.9154 (m) cc_final: 0.8548 (p)
REVERT: B 52 ASP cc_start: 0.8973 (m-30) cc_final: 0.8473 (p0)
REVERT: C 179 MET cc_start: 0.8949 (ttm) cc_final: 0.8502 (tmm)
REVERT: C 378 ASP cc_start: 0.8601 (p0) cc_final: 0.8152 (p0)
REVERT: D 659 MET cc_start: 0.8680 (tpp) cc_final: 0.8353 (tpt)
REVERT: D 884 MET cc_start: 0.1819 (ppp) cc_final: 0.1295 (ppp)
REVERT: D 1015 HIS cc_start: 0.8557 (m90) cc_final: 0.8047 (m90)
REVERT: E 786 MET cc_start: 0.8512 (pmm) cc_final: 0.7991 (pmm)
outliers start: 0
outliers final: 0
residues processed: 114
average time/residue: 0.2282
time to fit residues: 42.7561
Evaluate side-chains
83 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 83
time to evaluate : 1.619
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 190
random chunks:
chunk 145 optimal weight: 4.9990
chunk 128 optimal weight: 0.4980
chunk 0 optimal weight: 7.9990
chunk 74 optimal weight: 8.9990
chunk 116 optimal weight: 5.9990
chunk 126 optimal weight: 5.9990
chunk 68 optimal weight: 6.9990
chunk 26 optimal weight: 0.4980
chunk 3 optimal weight: 3.9990
chunk 173 optimal weight: 2.9990
chunk 132 optimal weight: 9.9990
overall best weight: 2.5986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 GLN
** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 618 HIS
D 876 ASN
E 357 HIS
** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 648 HIS
** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.066598 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.048946 restraints weight = 91024.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.050773 restraints weight = 51524.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.052016 restraints weight = 34136.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start: 0.6123
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.103 15118 Z= 0.272
Angle : 0.642 12.927 20528 Z= 0.330
Chirality : 0.045 0.273 2205
Planarity : 0.004 0.062 2656
Dihedral : 6.329 86.382 2143
Min Nonbonded Distance : 2.213
Molprobity Statistics.
All-atom Clashscore : 14.76
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.10 %
Favored : 94.90 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.25 %
Favored : 99.75 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.23 (0.19), residues: 1903
helix: 1.33 (0.26), residues: 410
sheet: -0.60 (0.29), residues: 231
loop : -0.56 (0.17), residues: 1262
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.002 TRP D 992
HIS 0.012 0.001 HIS D 347
PHE 0.013 0.002 PHE E 821
TYR 0.015 0.002 TYR E 424
ARG 0.004 0.001 ARG D 479
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 4070.32 seconds
wall clock time: 74 minutes 32.31 seconds (4472.31 seconds total)