Starting phenix.real_space_refine on Mon Mar 11 18:12:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/03_2024/7bw7_30229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/03_2024/7bw7_30229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/03_2024/7bw7_30229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/03_2024/7bw7_30229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/03_2024/7bw7_30229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/03_2024/7bw7_30229.pdb" } resolution = 4.1 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= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5621 2.51 5 N 1509 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 12": "OD1" <-> "OD2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8824 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5224 Classifications: {'peptide': 647} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 613} Chain breaks: 5 Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3224 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 4 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.57 Number of scatterers: 8824 At special positions: 0 Unit cell: (91.79, 108.23, 153.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1638 8.00 N 1509 7.00 C 5621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 13.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.745A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.558A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.956A pdb=" N HIS A 199 " --> pdb=" O CYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.854A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.751A pdb=" N GLY A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 318' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.515A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.777A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 435 through 440 removed outlier: 4.208A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 440' Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 496 through 500 Processing helix chain 'C' and resid 692 through 710 removed outlier: 3.730A pdb=" N GLU C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.824A pdb=" N CYS D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.586A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.517A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.816A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 removed outlier: 3.736A pdb=" N VAL A 254 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 248 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.521A pdb=" N CYS A 312 " --> pdb=" O VAL A 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.560A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.948A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 566 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASP A 584 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.607A pdb=" N LYS A 614 " --> pdb=" O PRO A 601 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 321 removed outlier: 6.590A pdb=" N LYS C 319 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 340 " --> pdb=" O LYS C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 531 through 533 removed outlier: 3.542A pdb=" N VAL C 532 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 599 through 605 removed outlier: 4.858A pdb=" N ASP C 600 " --> pdb=" O LYS C 616 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 630 through 631 removed outlier: 3.651A pdb=" N GLU C 782 " --> pdb=" O PHE C 631 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2764 1.34 - 1.46: 2073 1.46 - 1.58: 4125 1.58 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 9032 Sorted by residual: bond pdb=" C VAL C 597 " pdb=" N PRO C 598 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.25e-02 6.40e+03 1.41e+01 bond pdb=" CA LEU C 696 " pdb=" C LEU C 696 " ideal model delta sigma weight residual 1.522 1.457 0.064 1.72e-02 3.38e+03 1.39e+01 bond pdb=" N VAL A 377 " pdb=" CA VAL A 377 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N GLY C 580 " pdb=" CA GLY C 580 " ideal model delta sigma weight residual 1.446 1.485 -0.039 1.13e-02 7.83e+03 1.19e+01 bond pdb=" N THR C 578 " pdb=" CA THR C 578 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.02e+01 ... (remaining 9027 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.57: 191 105.57 - 112.71: 4644 112.71 - 119.86: 3111 119.86 - 127.01: 4176 127.01 - 134.15: 111 Bond angle restraints: 12233 Sorted by residual: angle pdb=" C TYR C 579 " pdb=" CA TYR C 579 " pdb=" CB TYR C 579 " ideal model delta sigma weight residual 110.04 100.28 9.76 1.51e+00 4.39e-01 4.18e+01 angle pdb=" N PRO C 621 " pdb=" CA PRO C 621 " pdb=" C PRO C 621 " ideal model delta sigma weight residual 113.86 106.93 6.93 1.25e+00 6.40e-01 3.07e+01 angle pdb=" N PRO A 432 " pdb=" CA PRO A 432 " pdb=" C PRO A 432 " ideal model delta sigma weight residual 113.40 120.78 -7.38 1.34e+00 5.57e-01 3.04e+01 angle pdb=" C VAL C 597 " pdb=" N PRO C 598 " pdb=" CA PRO C 598 " ideal model delta sigma weight residual 120.21 125.30 -5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" N VAL A 324 " pdb=" CA VAL A 324 " pdb=" C VAL A 324 " ideal model delta sigma weight residual 111.89 104.50 7.39 1.44e+00 4.82e-01 2.64e+01 ... (remaining 12228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4697 17.95 - 35.90: 610 35.90 - 53.85: 129 53.85 - 71.80: 14 71.80 - 89.75: 9 Dihedral angle restraints: 5459 sinusoidal: 2267 harmonic: 3192 Sorted by residual: dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 75 " pdb=" CB CYS D 75 " ideal model delta sinusoidal sigma weight residual -86.00 -151.20 65.20 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual -86.00 -145.19 59.19 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA CYS A 207 " pdb=" C CYS A 207 " pdb=" N CYS A 208 " pdb=" CA CYS A 208 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1020 0.067 - 0.133: 274 0.133 - 0.200: 39 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CA PRO A 432 " pdb=" N PRO A 432 " pdb=" C PRO A 432 " pdb=" CB PRO A 432 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CG LEU C 434 " pdb=" CB LEU C 434 " pdb=" CD1 LEU C 434 " pdb=" CD2 LEU C 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE C 457 " pdb=" N ILE C 457 " pdb=" C ILE C 457 " pdb=" CB ILE C 457 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1334 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 577 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ARG C 577 " 0.078 2.00e-02 2.50e+03 pdb=" O ARG C 577 " -0.029 2.00e-02 2.50e+03 pdb=" N THR C 578 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 494 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO C 495 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 591 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ASP C 591 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP C 591 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA C 592 " 0.015 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 245 2.62 - 3.19: 8823 3.19 - 3.76: 13629 3.76 - 4.33: 18090 4.33 - 4.90: 27791 Nonbonded interactions: 68578 Sorted by model distance: nonbonded pdb=" OG SER C 437 " pdb=" O GLU C 517 " model vdw 2.050 2.440 nonbonded pdb=" OG SER A 116 " pdb=" OD1 ASN A 143 " model vdw 2.118 2.440 nonbonded pdb=" OG SER A 198 " pdb=" NE ARG A 229 " model vdw 2.122 2.520 nonbonded pdb=" OH TYR A 628 " pdb=" OE2 GLU A 766 " model vdw 2.136 2.440 nonbonded pdb=" OG SER D 67 " pdb=" OE1 GLN D 70 " model vdw 2.141 2.440 ... (remaining 68573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.150 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: 0.000 Extract box with map and model: 1.360 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.580 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 : 0.008 0.078 9032 Z= 0.508 Angle : 1.056 9.759 12233 Z= 0.606 Chirality : 0.060 0.333 1337 Planarity : 0.006 0.066 1568 Dihedral : 16.200 89.747 3340 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 40.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.38 % Favored : 76.62 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.62 (0.21), residues: 1065 helix: -3.74 (0.35), residues: 101 sheet: -3.83 (0.34), residues: 190 loop : -4.03 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 183 HIS 0.007 0.002 HIS D 5 PHE 0.029 0.003 PHE A 400 TYR 0.027 0.003 TYR D 26 ARG 0.009 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7987 (tt) cc_final: 0.7682 (tp) REVERT: A 246 TYR cc_start: 0.7658 (m-80) cc_final: 0.7110 (m-80) REVERT: A 382 PHE cc_start: 0.8574 (m-10) cc_final: 0.8320 (m-10) REVERT: A 513 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6743 (mp10) REVERT: A 616 LYS cc_start: 0.9016 (tppt) cc_final: 0.8632 (tppt) REVERT: A 780 ARG cc_start: 0.7569 (ptt180) cc_final: 0.7125 (ptm-80) REVERT: C 355 GLU cc_start: 0.7858 (tt0) cc_final: 0.7392 (pt0) REVERT: C 382 PHE cc_start: 0.8463 (t80) cc_final: 0.7999 (t80) REVERT: C 552 LEU cc_start: 0.9076 (tp) cc_final: 0.8812 (tp) REVERT: C 780 ARG cc_start: 0.7148 (ttt-90) cc_final: 0.6133 (mtp85) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2929 time to fit residues: 59.6759 Evaluate side-chains 117 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9032 Z= 0.298 Angle : 0.845 11.517 12233 Z= 0.434 Chirality : 0.051 0.173 1337 Planarity : 0.005 0.054 1568 Dihedral : 7.731 26.273 1184 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.62 % Favored : 80.38 % Rotamer: Outliers : 0.30 % Allowed : 13.72 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.26 (0.22), residues: 1065 helix: -3.31 (0.38), residues: 101 sheet: -3.81 (0.33), residues: 202 loop : -3.70 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 632 HIS 0.007 0.001 HIS A 429 PHE 0.019 0.002 PHE A 381 TYR 0.029 0.002 TYR A 430 ARG 0.006 0.001 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.250 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: A 101 LEU cc_start: 0.7890 (tt) cc_final: 0.7616 (tp) REVERT: A 246 TYR cc_start: 0.7070 (m-80) cc_final: 0.6588 (m-80) REVERT: A 294 MET cc_start: 0.6178 (ppp) cc_final: 0.5929 (ppp) REVERT: A 425 LYS cc_start: 0.7239 (ttmt) cc_final: 0.6884 (tmtt) REVERT: A 426 LEU cc_start: 0.7423 (tt) cc_final: 0.6656 (tt) REVERT: A 472 LEU cc_start: 0.6751 (tp) cc_final: 0.6468 (pt) REVERT: A 513 GLN cc_start: 0.7405 (tp-100) cc_final: 0.6705 (mp10) REVERT: A 616 LYS cc_start: 0.8811 (tppt) cc_final: 0.8349 (tppt) REVERT: A 765 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7415 (mttm) REVERT: C 355 GLU cc_start: 0.7805 (tt0) cc_final: 0.7332 (pt0) REVERT: C 381 PHE cc_start: 0.8569 (p90) cc_final: 0.8065 (p90) REVERT: C 409 ARG cc_start: 0.6261 (mtt90) cc_final: 0.6042 (mmt90) REVERT: C 552 LEU cc_start: 0.9057 (tp) cc_final: 0.7905 (tp) REVERT: C 780 ARG cc_start: 0.7042 (ttt-90) cc_final: 0.6328 (mtp-110) outliers start: 3 outliers final: 2 residues processed: 156 average time/residue: 0.2668 time to fit residues: 54.7837 Evaluate side-chains 115 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 594 ASN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9032 Z= 0.304 Angle : 0.836 10.306 12233 Z= 0.428 Chirality : 0.051 0.180 1337 Planarity : 0.005 0.053 1568 Dihedral : 7.571 29.439 1184 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.25 % Favored : 80.75 % Rotamer: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.04 (0.22), residues: 1065 helix: -3.06 (0.40), residues: 107 sheet: -3.66 (0.33), residues: 196 loop : -3.57 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 251 HIS 0.007 0.001 HIS C 429 PHE 0.016 0.002 PHE A 381 TYR 0.025 0.002 TYR C 430 ARG 0.006 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.963 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: A 110 MET cc_start: 0.7963 (mmm) cc_final: 0.7735 (mmm) REVERT: A 246 TYR cc_start: 0.6974 (m-80) cc_final: 0.6561 (m-80) REVERT: A 427 PHE cc_start: 0.6928 (t80) cc_final: 0.6711 (t80) REVERT: A 513 GLN cc_start: 0.7354 (tp-100) cc_final: 0.6736 (mp10) REVERT: A 616 LYS cc_start: 0.8796 (tppt) cc_final: 0.8379 (tppt) REVERT: A 783 LEU cc_start: 0.9108 (tp) cc_final: 0.8594 (tp) REVERT: C 355 GLU cc_start: 0.7692 (tt0) cc_final: 0.7209 (pt0) REVERT: C 381 PHE cc_start: 0.8445 (p90) cc_final: 0.8074 (p90) REVERT: C 382 PHE cc_start: 0.8551 (t80) cc_final: 0.8022 (t80) REVERT: C 552 LEU cc_start: 0.9070 (tp) cc_final: 0.8740 (tp) REVERT: C 577 ARG cc_start: 0.6554 (tpt-90) cc_final: 0.6279 (mmt90) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2274 time to fit residues: 45.3860 Evaluate side-chains 113 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS A 148 ASN A 263 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9032 Z= 0.464 Angle : 0.937 11.810 12233 Z= 0.480 Chirality : 0.054 0.285 1337 Planarity : 0.007 0.064 1568 Dihedral : 8.054 30.881 1184 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 33.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 23.94 % Favored : 75.96 % Rotamer: Outliers : 0.20 % Allowed : 8.58 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.15 (0.22), residues: 1065 helix: -3.27 (0.37), residues: 107 sheet: -3.68 (0.35), residues: 174 loop : -3.68 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 615 HIS 0.024 0.002 HIS A 429 PHE 0.032 0.003 PHE A 381 TYR 0.034 0.003 TYR A 401 ARG 0.011 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.063 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: A 110 MET cc_start: 0.8017 (mmm) cc_final: 0.7685 (mmm) REVERT: A 246 TYR cc_start: 0.7058 (m-80) cc_final: 0.6574 (m-80) REVERT: A 425 LYS cc_start: 0.7379 (ttmt) cc_final: 0.6927 (tmtt) REVERT: A 481 SER cc_start: 0.8761 (m) cc_final: 0.8515 (p) REVERT: A 513 GLN cc_start: 0.7281 (tp-100) cc_final: 0.6571 (mp10) REVERT: A 616 LYS cc_start: 0.8975 (tttp) cc_final: 0.8692 (tppt) REVERT: A 783 LEU cc_start: 0.9102 (tp) cc_final: 0.8834 (tp) REVERT: C 409 ARG cc_start: 0.6332 (mtt90) cc_final: 0.6071 (mmt90) REVERT: C 552 LEU cc_start: 0.9190 (tp) cc_final: 0.8833 (tp) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.2466 time to fit residues: 46.9377 Evaluate side-chains 112 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 561 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9032 Z= 0.271 Angle : 0.807 10.881 12233 Z= 0.413 Chirality : 0.051 0.191 1337 Planarity : 0.005 0.051 1568 Dihedral : 7.374 29.236 1184 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.28 % Favored : 82.72 % Rotamer: Outliers : 0.30 % Allowed : 4.04 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.78 (0.23), residues: 1065 helix: -2.95 (0.41), residues: 101 sheet: -3.59 (0.35), residues: 176 loop : -3.37 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 493 HIS 0.005 0.001 HIS D 5 PHE 0.023 0.002 PHE C 475 TYR 0.024 0.002 TYR A 430 ARG 0.007 0.001 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5665 (mpp) cc_final: 0.4645 (tpt) REVERT: A 110 MET cc_start: 0.7958 (mmm) cc_final: 0.7527 (mmm) REVERT: A 246 TYR cc_start: 0.7077 (m-80) cc_final: 0.6647 (m-80) REVERT: A 360 LEU cc_start: 0.7529 (mm) cc_final: 0.6890 (tt) REVERT: A 404 ASP cc_start: 0.8566 (t0) cc_final: 0.8352 (t0) REVERT: A 425 LYS cc_start: 0.7263 (ttmt) cc_final: 0.6779 (tmtt) REVERT: A 513 GLN cc_start: 0.7340 (tp-100) cc_final: 0.6718 (mp10) REVERT: A 613 LEU cc_start: 0.9496 (mp) cc_final: 0.9277 (mm) REVERT: A 616 LYS cc_start: 0.8863 (tttp) cc_final: 0.8549 (tppt) REVERT: A 783 LEU cc_start: 0.9078 (tp) cc_final: 0.8705 (tp) REVERT: C 552 LEU cc_start: 0.9102 (tp) cc_final: 0.8758 (tp) REVERT: C 561 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7489 (tp-100) outliers start: 3 outliers final: 1 residues processed: 153 average time/residue: 0.2423 time to fit residues: 49.7321 Evaluate side-chains 110 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9032 Z= 0.259 Angle : 0.786 9.829 12233 Z= 0.399 Chirality : 0.050 0.170 1337 Planarity : 0.005 0.049 1568 Dihedral : 7.178 28.799 1184 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.58 (0.23), residues: 1065 helix: -2.81 (0.43), residues: 101 sheet: -3.40 (0.36), residues: 176 loop : -3.25 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 493 HIS 0.012 0.001 HIS A 429 PHE 0.032 0.002 PHE C 475 TYR 0.033 0.002 TYR A 430 ARG 0.004 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.046 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: A 11 MET cc_start: 0.5675 (mpp) cc_final: 0.4677 (tpt) REVERT: A 100 HIS cc_start: 0.6417 (m-70) cc_final: 0.6194 (m-70) REVERT: A 110 MET cc_start: 0.7810 (mmm) cc_final: 0.7440 (mmm) REVERT: A 246 TYR cc_start: 0.7205 (m-80) cc_final: 0.6767 (m-80) REVERT: A 360 LEU cc_start: 0.7472 (mm) cc_final: 0.6883 (tt) REVERT: A 404 ASP cc_start: 0.8589 (t0) cc_final: 0.8375 (t0) REVERT: A 513 GLN cc_start: 0.7295 (tp-100) cc_final: 0.6586 (mp10) REVERT: A 616 LYS cc_start: 0.8842 (tttp) cc_final: 0.8518 (tppt) REVERT: A 783 LEU cc_start: 0.8976 (tp) cc_final: 0.8650 (tp) REVERT: C 382 PHE cc_start: 0.8163 (t80) cc_final: 0.7833 (t80) REVERT: C 552 LEU cc_start: 0.9132 (tp) cc_final: 0.8896 (tp) REVERT: C 780 ARG cc_start: 0.6671 (ttt-90) cc_final: 0.5668 (mtp85) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2308 time to fit residues: 46.0717 Evaluate side-chains 113 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9032 Z= 0.381 Angle : 0.865 13.130 12233 Z= 0.439 Chirality : 0.051 0.221 1337 Planarity : 0.006 0.049 1568 Dihedral : 7.564 29.392 1184 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 29.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.38 % Favored : 79.62 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.82 (0.23), residues: 1065 helix: -3.16 (0.37), residues: 114 sheet: -3.36 (0.35), residues: 186 loop : -3.42 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 493 HIS 0.024 0.002 HIS A 429 PHE 0.035 0.003 PHE A 381 TYR 0.018 0.002 TYR C 587 ARG 0.008 0.001 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5788 (mpp) cc_final: 0.4768 (tpt) REVERT: A 100 HIS cc_start: 0.6787 (m-70) cc_final: 0.6397 (m-70) REVERT: A 110 MET cc_start: 0.7948 (mmm) cc_final: 0.7537 (mmm) REVERT: A 404 ASP cc_start: 0.8523 (t0) cc_final: 0.8194 (t0) REVERT: A 481 SER cc_start: 0.8754 (m) cc_final: 0.8550 (p) REVERT: A 513 GLN cc_start: 0.7226 (tp-100) cc_final: 0.6589 (mp10) REVERT: A 616 LYS cc_start: 0.8840 (tttp) cc_final: 0.8542 (tppt) REVERT: A 783 LEU cc_start: 0.9002 (tp) cc_final: 0.8680 (tp) REVERT: C 552 LEU cc_start: 0.9183 (tp) cc_final: 0.8867 (tp) REVERT: C 780 ARG cc_start: 0.6794 (ttt-90) cc_final: 0.5701 (mtp85) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2421 time to fit residues: 43.6528 Evaluate side-chains 105 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9032 Z= 0.254 Angle : 0.786 11.960 12233 Z= 0.394 Chirality : 0.050 0.168 1337 Planarity : 0.005 0.047 1568 Dihedral : 7.127 27.957 1184 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.24 % Favored : 83.76 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.35 (0.23), residues: 1065 helix: -2.77 (0.43), residues: 102 sheet: -3.16 (0.37), residues: 176 loop : -3.08 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 412 HIS 0.014 0.001 HIS A 429 PHE 0.026 0.002 PHE C 475 TYR 0.035 0.002 TYR A 374 ARG 0.005 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5643 (mpp) cc_final: 0.4800 (tpt) REVERT: A 100 HIS cc_start: 0.6549 (m-70) cc_final: 0.6236 (m-70) REVERT: A 110 MET cc_start: 0.7897 (mmm) cc_final: 0.7475 (mmm) REVERT: A 360 LEU cc_start: 0.7528 (mm) cc_final: 0.6920 (tt) REVERT: A 404 ASP cc_start: 0.8639 (t0) cc_final: 0.8360 (t0) REVERT: A 513 GLN cc_start: 0.7299 (tp-100) cc_final: 0.6614 (mp10) REVERT: A 616 LYS cc_start: 0.8788 (tttp) cc_final: 0.8424 (tppt) REVERT: A 783 LEU cc_start: 0.8995 (tp) cc_final: 0.8709 (tp) REVERT: C 552 LEU cc_start: 0.9188 (tp) cc_final: 0.8959 (tp) REVERT: C 780 ARG cc_start: 0.6626 (ttt-90) cc_final: 0.5584 (mtp85) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2246 time to fit residues: 43.6286 Evaluate side-chains 109 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9032 Z= 0.344 Angle : 0.831 11.452 12233 Z= 0.422 Chirality : 0.051 0.177 1337 Planarity : 0.005 0.053 1568 Dihedral : 7.382 28.196 1184 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.44 % Favored : 80.56 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.57 (0.23), residues: 1065 helix: -3.14 (0.37), residues: 117 sheet: -3.10 (0.37), residues: 176 loop : -3.24 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 615 HIS 0.019 0.002 HIS A 429 PHE 0.027 0.003 PHE C 475 TYR 0.025 0.002 TYR A 430 ARG 0.010 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5889 (mpp) cc_final: 0.5015 (tpt) REVERT: A 100 HIS cc_start: 0.6612 (m-70) cc_final: 0.6329 (m-70) REVERT: A 110 MET cc_start: 0.7890 (mmm) cc_final: 0.7499 (mmm) REVERT: A 404 ASP cc_start: 0.8659 (t0) cc_final: 0.8358 (t0) REVERT: A 425 LYS cc_start: 0.7324 (ttmt) cc_final: 0.6707 (tmtt) REVERT: A 428 PHE cc_start: 0.8355 (m-80) cc_final: 0.8121 (m-80) REVERT: A 513 GLN cc_start: 0.7225 (tp-100) cc_final: 0.6586 (mp10) REVERT: A 616 LYS cc_start: 0.8838 (tttp) cc_final: 0.8503 (tppt) REVERT: A 783 LEU cc_start: 0.8978 (tp) cc_final: 0.8655 (tp) REVERT: C 552 LEU cc_start: 0.9159 (tp) cc_final: 0.8858 (tp) REVERT: C 556 LEU cc_start: 0.6158 (mm) cc_final: 0.5956 (mm) REVERT: C 780 ARG cc_start: 0.6761 (ttt-90) cc_final: 0.5767 (mtp85) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2299 time to fit residues: 41.2162 Evaluate side-chains 106 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 0.0060 chunk 106 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9032 Z= 0.199 Angle : 0.748 12.239 12233 Z= 0.374 Chirality : 0.049 0.204 1337 Planarity : 0.005 0.053 1568 Dihedral : 6.629 25.676 1184 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.04 (0.24), residues: 1065 helix: -2.65 (0.43), residues: 106 sheet: -2.75 (0.40), residues: 167 loop : -2.90 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 414 HIS 0.009 0.001 HIS A 429 PHE 0.024 0.002 PHE C 475 TYR 0.019 0.002 TYR D 74 ARG 0.009 0.000 ARG A 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.041 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: A 11 MET cc_start: 0.5905 (mpp) cc_final: 0.5432 (tpt) REVERT: A 110 MET cc_start: 0.7540 (mmm) cc_final: 0.7166 (mmm) REVERT: A 246 TYR cc_start: 0.7516 (m-80) cc_final: 0.7150 (m-80) REVERT: A 360 LEU cc_start: 0.7276 (mm) cc_final: 0.6839 (tt) REVERT: A 404 ASP cc_start: 0.8474 (t0) cc_final: 0.8211 (t0) REVERT: A 428 PHE cc_start: 0.7825 (m-80) cc_final: 0.7393 (m-80) REVERT: A 493 TRP cc_start: 0.5114 (m100) cc_final: 0.4878 (m100) REVERT: A 513 GLN cc_start: 0.7295 (tp-100) cc_final: 0.6616 (mp10) REVERT: A 616 LYS cc_start: 0.8716 (tttp) cc_final: 0.8424 (tppt) REVERT: A 783 LEU cc_start: 0.9191 (tp) cc_final: 0.8928 (tp) REVERT: C 552 LEU cc_start: 0.9083 (tp) cc_final: 0.8879 (tp) REVERT: C 557 LYS cc_start: 0.6763 (mmtt) cc_final: 0.6120 (mmmt) REVERT: C 780 ARG cc_start: 0.6524 (ttt-90) cc_final: 0.5803 (mtp85) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2262 time to fit residues: 45.4775 Evaluate side-chains 115 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.2980 chunk 78 optimal weight: 0.0470 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 0.0070 chunk 35 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 overall best weight: 0.6896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** 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 = 0.4908 r_free = 0.4908 target = 0.191696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.149027 restraints weight = 19002.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.152366 restraints weight = 13026.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.154997 restraints weight = 10090.403| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9032 Z= 0.191 Angle : 0.720 11.478 12233 Z= 0.363 Chirality : 0.048 0.195 1337 Planarity : 0.005 0.053 1568 Dihedral : 6.301 24.327 1184 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -3.88 (0.24), residues: 1065 helix: -2.43 (0.44), residues: 106 sheet: -2.65 (0.39), residues: 167 loop : -2.80 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 632 HIS 0.023 0.001 HIS C 417 PHE 0.037 0.002 PHE C 475 TYR 0.016 0.001 TYR C 507 ARG 0.008 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.41 seconds wall clock time: 36 minutes 16.57 seconds (2176.57 seconds total)