Starting phenix.real_space_refine (version: dev) on Sat Feb 18 20:24:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/02_2023/7bw7_30229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/02_2023/7bw7_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_30229/02_2023/7bw7_30229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/02_2023/7bw7_30229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/02_2023/7bw7_30229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw7_30229/02_2023/7bw7_30229.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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-4877/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: 5.34, per 1000 atoms: 0.61 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: 3.52 Conformation dependent library (CDL) restraints added in 1.4 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: 0.39 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: 2.04 Time building geometry restraints manager: 3.80 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 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. 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: 0.270 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: 1.680 Check model and map are aligned: 0.140 Process input model: 25.310 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 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 % 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 *********************** 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 : 1.034 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 outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2957 time to fit residues: 60.2331 Evaluate side-chains 112 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4226 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** ** C 784 GLN ** 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: 0.6703 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 9032 Z= 0.316 Angle : 0.861 11.123 12233 Z= 0.440 Chirality : 0.051 0.170 1337 Planarity : 0.006 0.057 1568 Dihedral : 7.826 26.207 1184 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.66 % Favored : 79.34 % Rotamer Outliers : 0.30 % 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: -5.30 (0.22), residues: 1065 helix: -3.39 (0.37), residues: 101 sheet: -3.82 (0.33), residues: 202 loop : -3.74 (0.20), residues: 762 *********************** 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 154 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 153 average time/residue: 0.2586 time to fit residues: 52.1330 Evaluate side-chains 109 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1164 time to fit residues: 1.8173 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 185 HIS ** 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 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 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9032 Z= 0.254 Angle : 0.810 10.302 12233 Z= 0.414 Chirality : 0.051 0.188 1337 Planarity : 0.005 0.054 1568 Dihedral : 7.391 29.095 1184 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.37 % Favored : 82.63 % Rotamer Outliers : 0.10 % 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: -4.93 (0.22), residues: 1065 helix: -2.92 (0.42), residues: 101 sheet: -3.59 (0.33), residues: 196 loop : -3.50 (0.20), residues: 768 *********************** 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 155 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.2374 time to fit residues: 49.4574 Evaluate side-chains 108 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1108 time to fit residues: 1.5532 ------------------------------------------------------------------------------- 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: 0.0060 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 overall best weight: 3.1802 ------------------------------------------------------------------------------- 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 185 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 429 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 9032 Z= 0.340 Angle : 0.828 9.593 12233 Z= 0.424 Chirality : 0.051 0.223 1337 Planarity : 0.006 0.062 1568 Dihedral : 7.444 30.040 1184 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.91 % Favored : 80.09 % Rotamer Outliers : 0.10 % 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: -4.89 (0.22), residues: 1065 helix: -3.01 (0.38), residues: 108 sheet: -3.61 (0.34), residues: 191 loop : -3.44 (0.20), residues: 766 *********************** 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 141 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.2562 time to fit residues: 48.5908 Evaluate side-chains 103 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1190 time to fit residues: 1.7433 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** 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** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.3124 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= 0.240 Angle : 0.774 10.611 12233 Z= 0.393 Chirality : 0.050 0.164 1337 Planarity : 0.005 0.052 1568 Dihedral : 7.077 28.818 1184 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.87 % Favored : 84.13 % Rotamer Outliers : 0.10 % 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: -4.53 (0.23), residues: 1065 helix: -2.61 (0.44), residues: 98 sheet: -3.44 (0.35), residues: 181 loop : -3.20 (0.20), residues: 786 *********************** 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 148 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.2355 time to fit residues: 46.8886 Evaluate side-chains 114 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5635 ------------------------------------------------------------------------------- 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: 3.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 0.0170 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.5222 ------------------------------------------------------------------------------- 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 185 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9032 Z= 0.223 Angle : 0.754 10.574 12233 Z= 0.381 Chirality : 0.048 0.163 1337 Planarity : 0.005 0.047 1568 Dihedral : 6.785 29.346 1184 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.68 % Favored : 84.32 % Rotamer Outliers : 0.10 % 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: -4.48 (0.23), residues: 1065 helix: -2.90 (0.41), residues: 111 sheet: -3.24 (0.36), residues: 180 loop : -3.16 (0.20), residues: 774 *********************** 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 153 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.2702 time to fit residues: 55.8640 Evaluate side-chains 110 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5029 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 263 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 9032 Z= 0.422 Angle : 0.902 13.752 12233 Z= 0.459 Chirality : 0.052 0.192 1337 Planarity : 0.006 0.048 1568 Dihedral : 7.495 30.166 1184 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 20.09 % Favored : 79.81 % Rotamer Outliers : 0.00 % 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: -4.79 (0.22), residues: 1065 helix: -3.18 (0.36), residues: 117 sheet: -3.20 (0.35), residues: 198 loop : -3.42 (0.20), residues: 750 *********************** 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 140 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2473 time to fit residues: 46.6549 Evaluate side-chains 99 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4687 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN C 610 GLN ** C 622 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: 0.6507 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9032 Z= 0.212 Angle : 0.776 11.491 12233 Z= 0.392 Chirality : 0.050 0.221 1337 Planarity : 0.005 0.050 1568 Dihedral : 6.768 27.278 1184 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer Outliers : 0.00 % 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: -4.17 (0.24), residues: 1065 helix: -2.68 (0.43), residues: 104 sheet: -2.99 (0.38), residues: 173 loop : -2.95 (0.21), residues: 788 *********************** 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 145 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.178 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 outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2404 time to fit residues: 47.6691 Evaluate side-chains 110 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3856 ------------------------------------------------------------------------------- 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: 9.9990 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 chunk 101 optimal weight: 7.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 100 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9032 Z= 0.203 Angle : 0.737 11.278 12233 Z= 0.373 Chirality : 0.049 0.177 1337 Planarity : 0.005 0.050 1568 Dihedral : 6.501 26.971 1184 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer Outliers : 0.00 % 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: -4.15 (0.24), residues: 1065 helix: -2.83 (0.39), residues: 116 sheet: -2.87 (0.37), residues: 180 loop : -2.93 (0.21), residues: 769 *********************** 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 141 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.981 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 outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2364 time to fit residues: 45.3013 Evaluate side-chains 111 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5403 ------------------------------------------------------------------------------- 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: 9.9990 chunk 70 optimal weight: 0.4980 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 143 ASN ** 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 429 HIS ** C 417 HIS ** 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: 0.6479 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9032 Z= 0.197 Angle : 0.726 11.408 12233 Z= 0.365 Chirality : 0.048 0.175 1337 Planarity : 0.005 0.053 1568 Dihedral : 6.318 26.470 1184 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer Outliers : 0.00 % 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: -4.01 (0.24), residues: 1065 helix: -2.69 (0.40), residues: 117 sheet: -2.73 (0.38), residues: 175 loop : -2.85 (0.21), residues: 773 ********************** 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 139 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2354 time to fit residues: 44.3889 Evaluate side-chains 113 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4459 ------------------------------------------------------------------------------- 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: 10.0000 chunk 78 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 85 optimal weight: 0.0670 chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 0.0170 chunk 4 optimal weight: 0.0970 overall best weight: 1.0156 ------------------------------------------------------------------------------- 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 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** 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 = 0.4898 r_free = 0.4898 target = 0.190717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.160627 restraints weight = 18942.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.163632 restraints weight = 21062.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.165297 restraints weight = 16614.585| |-----------------------------------------------------------------------------| r_work (final): 0.4529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9032 Z= 0.196 Angle : 0.723 11.237 12233 Z= 0.365 Chirality : 0.048 0.175 1337 Planarity : 0.005 0.052 1568 Dihedral : 6.234 26.263 1184 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer Outliers : 0.00 % 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: -3.97 (0.24), residues: 1065 helix: -2.62 (0.40), residues: 120 sheet: -2.77 (0.37), residues: 180 loop : -2.81 (0.21), residues: 765 =============================================================================== Job complete usr+sys time: 1838.40 seconds wall clock time: 34 minutes 42.44 seconds (2082.44 seconds total)