Starting phenix.real_space_refine on Sat Dec 9 00:08:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/12_2023/7uqx_26701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/12_2023/7uqx_26701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/12_2023/7uqx_26701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/12_2023/7uqx_26701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/12_2023/7uqx_26701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/12_2023/7uqx_26701_updated.pdb" } resolution = 3.3 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 4 5.49 5 S 46 5.16 5 C 6100 2.51 5 N 1593 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "B ASP 540": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4759 Classifications: {'peptide': 583} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 555} Chain breaks: 3 Chain: "B" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4628 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 535} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.44, per 1000 atoms: 0.57 Number of scatterers: 9491 At special positions: 0 Unit cell: (102.672, 86.94, 110.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 46 16.00 P 4 15.00 O 1747 8.00 N 1593 7.00 C 6100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 802 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 13 sheets defined 33.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.786A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 432 Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.838A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 442 through 446' Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 496 through 505 removed outlier: 3.557A pdb=" N VAL A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.830A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.774A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.943A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 314' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.532A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 467 through 478 removed outlier: 3.631A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 523 removed outlier: 4.029A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 removed outlier: 3.799A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 616 through 623 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 671 through 684 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.660A pdb=" N LEU A 153 " --> pdb=" O TYR A 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 191 through 194 removed outlier: 6.740A pdb=" N MET A 215 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN A 194 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 217 " --> pdb=" O ASN A 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 264 through 267 Processing sheet with id= D, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.047A pdb=" N VAL A 356 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 336 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 358 " --> pdb=" O VAL A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 623 through 627 removed outlier: 3.818A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA A 482 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 484 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 486 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP A 517 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 671 through 673 removed outlier: 3.680A pdb=" N THR A 673 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.767A pdb=" N LEU B 152 " --> pdb=" O TYR B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.804A pdb=" N LEU B 211 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 254 through 257 removed outlier: 3.695A pdb=" N SER B 256 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 298 through 301 Processing sheet with id= K, first strand: chain 'B' and resid 317 through 320 removed outlier: 5.877A pdb=" N VAL B 340 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 320 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 342 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 598 through 601 removed outlier: 3.647A pdb=" N ALA B 598 " --> pdb=" O ALA B 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 536 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 600 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR B 457 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 537 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE B 459 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA B 458 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B 485 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL B 460 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL B 487 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR B 462 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 489 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 487 " --> pdb=" O PRO B 508 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS B 510 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TRP B 489 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 512 " --> pdb=" O TRP B 489 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.647A pdb=" N LEU B 570 " --> pdb=" O GLU B 583 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 630 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: 2.56 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3002 1.34 - 1.46: 2265 1.46 - 1.58: 4402 1.58 - 1.70: 5 1.70 - 1.82: 72 Bond restraints: 9746 Sorted by residual: bond pdb=" O1A UDP B 801 " pdb=" PA UDP B 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.91e+01 bond pdb=" N ILE B 616 " pdb=" CA ILE B 616 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.38e+00 bond pdb=" N ASP B 615 " pdb=" CA ASP B 615 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N TYR A 324 " pdb=" CA TYR A 324 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.91e+00 bond pdb=" O2A UDP B 801 " pdb=" PA UDP B 801 " ideal model delta sigma weight residual 1.527 1.481 0.046 1.80e-02 3.09e+03 6.52e+00 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.75: 354 106.75 - 113.56: 5228 113.56 - 120.37: 3536 120.37 - 127.18: 3994 127.18 - 134.00: 140 Bond angle restraints: 13252 Sorted by residual: angle pdb=" O5' UDP B 801 " pdb=" PA UDP B 801 " pdb=" O1A UDP B 801 " ideal model delta sigma weight residual 106.70 111.06 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" O2A UDP B 801 " pdb=" PA UDP B 801 " pdb=" O3A UDP B 801 " ideal model delta sigma weight residual 105.97 110.21 -4.24 1.00e+00 1.00e+00 1.80e+01 angle pdb=" O5' UDP B 801 " pdb=" PA UDP B 801 " pdb=" O2A UDP B 801 " ideal model delta sigma weight residual 110.83 107.01 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" O1A UDP B 801 " pdb=" PA UDP B 801 " pdb=" O3A UDP B 801 " ideal model delta sigma weight residual 109.95 106.28 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" O GLU A 320 " ideal model delta sigma weight residual 121.28 117.36 3.92 1.07e+00 8.73e-01 1.34e+01 ... (remaining 13247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 5490 17.11 - 34.22: 277 34.22 - 51.34: 46 51.34 - 68.45: 4 68.45 - 85.56: 4 Dihedral angle restraints: 5821 sinusoidal: 2410 harmonic: 3411 Sorted by residual: dihedral pdb=" CA ARG B 673 " pdb=" CB ARG B 673 " pdb=" CG ARG B 673 " pdb=" CD ARG B 673 " ideal model delta sinusoidal sigma weight residual 60.00 119.48 -59.48 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS A 321 " pdb=" CA LYS A 321 " pdb=" CB LYS A 321 " pdb=" CG LYS A 321 " ideal model delta sinusoidal sigma weight residual -180.00 -120.76 -59.24 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG B 149 " pdb=" CB ARG B 149 " pdb=" CG ARG B 149 " pdb=" CD ARG B 149 " ideal model delta sinusoidal sigma weight residual -60.00 -118.53 58.53 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1205 0.054 - 0.108: 200 0.108 - 0.162: 36 0.162 - 0.216: 4 0.216 - 0.270: 3 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE B 542 " pdb=" N ILE B 542 " pdb=" C ILE B 542 " pdb=" CB ILE B 542 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE B 537 " pdb=" N ILE B 537 " pdb=" C ILE B 537 " pdb=" CB ILE B 537 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1445 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 399 " -0.019 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR B 399 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 399 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 399 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 399 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 399 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 399 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 399 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 479 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 480 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 480 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 480 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 448 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 449 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " -0.016 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 24 2.38 - 3.01: 5236 3.01 - 3.64: 14435 3.64 - 4.27: 22268 4.27 - 4.90: 36615 Nonbonded interactions: 78578 Sorted by model distance: nonbonded pdb=" O1A UDP B 801 " pdb="MN MN B 802 " model vdw 1.752 2.320 nonbonded pdb=" O ALA A 377 " pdb=" OG1 THR A 408 " model vdw 2.205 2.440 nonbonded pdb=" OG SER A 547 " pdb=" OD1 ASP A 647 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.217 2.440 nonbonded pdb=" O GLU A 587 " pdb=" OH TYR A 630 " model vdw 2.237 2.440 ... (remaining 78573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 3.850 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.100 Find NCS groups from input model: 0.270 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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 : 0.003 0.046 9746 Z= 0.175 Angle : 0.524 6.152 13252 Z= 0.297 Chirality : 0.045 0.270 1448 Planarity : 0.003 0.035 1675 Dihedral : 10.227 85.558 3590 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1138 helix: 1.40 (0.28), residues: 358 sheet: -1.03 (0.44), residues: 142 loop : -0.17 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 396 HIS 0.002 0.001 HIS B 623 PHE 0.009 0.001 PHE B 400 TYR 0.019 0.001 TYR B 399 ARG 0.001 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.2736 time to fit residues: 102.3946 Evaluate side-chains 253 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0890 time to fit residues: 1.7063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.0030 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS A 406 GLN A 431 GLN A 658 ASN B 276 HIS B 412 GLN B 430 ASN B 517 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9746 Z= 0.167 Angle : 0.526 8.546 13252 Z= 0.262 Chirality : 0.043 0.167 1448 Planarity : 0.004 0.034 1675 Dihedral : 4.122 41.752 1330 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.94 % Allowed : 11.15 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1138 helix: 1.26 (0.28), residues: 360 sheet: -0.88 (0.43), residues: 140 loop : -0.16 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 374 HIS 0.004 0.001 HIS B 88 PHE 0.020 0.001 PHE B 551 TYR 0.022 0.001 TYR A 319 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 262 average time/residue: 0.2622 time to fit residues: 91.7866 Evaluate side-chains 257 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1195 time to fit residues: 3.7983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 113 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9746 Z= 0.182 Angle : 0.526 8.259 13252 Z= 0.263 Chirality : 0.043 0.187 1448 Planarity : 0.004 0.031 1675 Dihedral : 3.967 32.563 1330 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.65 % Allowed : 12.71 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1138 helix: 1.20 (0.28), residues: 360 sheet: -0.99 (0.43), residues: 139 loop : -0.26 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 374 HIS 0.003 0.001 HIS B 88 PHE 0.028 0.002 PHE B 551 TYR 0.019 0.001 TYR A 319 ARG 0.006 0.001 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 248 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 256 average time/residue: 0.2634 time to fit residues: 89.6467 Evaluate side-chains 255 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0995 time to fit residues: 2.9957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9746 Z= 0.194 Angle : 0.531 6.986 13252 Z= 0.266 Chirality : 0.043 0.245 1448 Planarity : 0.004 0.031 1675 Dihedral : 3.899 23.898 1330 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.36 % Allowed : 13.87 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1138 helix: 1.05 (0.27), residues: 366 sheet: -1.00 (0.43), residues: 139 loop : -0.26 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 374 HIS 0.004 0.001 HIS A 241 PHE 0.036 0.002 PHE A 577 TYR 0.026 0.002 TYR B 582 ARG 0.006 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 246 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 253 average time/residue: 0.2589 time to fit residues: 86.7811 Evaluate side-chains 249 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 239 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0893 time to fit residues: 3.0639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS A 352 GLN A 431 GLN A 706 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9746 Z= 0.164 Angle : 0.531 9.124 13252 Z= 0.265 Chirality : 0.043 0.253 1448 Planarity : 0.004 0.031 1675 Dihedral : 3.761 21.228 1330 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.07 % Allowed : 14.74 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1138 helix: 1.10 (0.28), residues: 360 sheet: -0.98 (0.43), residues: 139 loop : -0.29 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 396 HIS 0.004 0.001 HIS A 241 PHE 0.038 0.002 PHE A 577 TYR 0.026 0.001 TYR B 582 ARG 0.006 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 250 average time/residue: 0.2570 time to fit residues: 86.1820 Evaluate side-chains 240 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 235 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1609 time to fit residues: 2.6806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.0050 chunk 21 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9746 Z= 0.146 Angle : 0.524 7.022 13252 Z= 0.266 Chirality : 0.042 0.236 1448 Planarity : 0.004 0.033 1675 Dihedral : 3.598 18.949 1330 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.78 % Allowed : 14.84 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1138 helix: 1.29 (0.28), residues: 352 sheet: -0.88 (0.43), residues: 140 loop : -0.28 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 396 HIS 0.004 0.001 HIS A 241 PHE 0.024 0.001 PHE A 577 TYR 0.023 0.001 TYR A 319 ARG 0.007 0.001 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 245 average time/residue: 0.2565 time to fit residues: 84.0373 Evaluate side-chains 243 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0845 time to fit residues: 2.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9746 Z= 0.227 Angle : 0.570 9.310 13252 Z= 0.288 Chirality : 0.044 0.211 1448 Planarity : 0.004 0.032 1675 Dihedral : 3.824 18.454 1330 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.16 % Allowed : 16.10 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1138 helix: 1.02 (0.27), residues: 359 sheet: -1.00 (0.43), residues: 141 loop : -0.28 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 374 HIS 0.004 0.001 HIS A 448 PHE 0.022 0.002 PHE A 577 TYR 0.024 0.002 TYR A 319 ARG 0.006 0.001 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 249 average time/residue: 0.2662 time to fit residues: 88.1824 Evaluate side-chains 244 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1436 time to fit residues: 3.1490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9746 Z= 0.226 Angle : 0.572 8.938 13252 Z= 0.291 Chirality : 0.044 0.202 1448 Planarity : 0.004 0.032 1675 Dihedral : 3.930 17.570 1330 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.78 % Allowed : 16.39 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1138 helix: 0.90 (0.27), residues: 360 sheet: -0.93 (0.43), residues: 140 loop : -0.23 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 374 HIS 0.004 0.001 HIS B 571 PHE 0.026 0.002 PHE A 577 TYR 0.025 0.002 TYR A 319 ARG 0.007 0.001 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 245 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 248 average time/residue: 0.2688 time to fit residues: 88.4985 Evaluate side-chains 245 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 238 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0953 time to fit residues: 2.7304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9746 Z= 0.253 Angle : 0.594 9.265 13252 Z= 0.304 Chirality : 0.045 0.189 1448 Planarity : 0.004 0.033 1675 Dihedral : 4.097 18.146 1330 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.29 % Allowed : 17.75 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1138 helix: 0.72 (0.27), residues: 360 sheet: -0.94 (0.43), residues: 141 loop : -0.29 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 711 HIS 0.010 0.001 HIS A 631 PHE 0.017 0.002 PHE B 680 TYR 0.028 0.002 TYR A 319 ARG 0.007 0.001 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 251 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 251 average time/residue: 0.2753 time to fit residues: 91.0718 Evaluate side-chains 245 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3690 time to fit residues: 2.5682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 0.0030 chunk 55 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9746 Z= 0.174 Angle : 0.595 9.755 13252 Z= 0.301 Chirality : 0.043 0.171 1448 Planarity : 0.004 0.034 1675 Dihedral : 3.965 19.535 1330 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.10 % Allowed : 18.72 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1138 helix: 0.96 (0.28), residues: 346 sheet: -0.84 (0.44), residues: 139 loop : -0.30 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.019 0.001 PHE B 633 TYR 0.021 0.001 TYR A 714 ARG 0.008 0.001 ARG B 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 233 average time/residue: 0.2890 time to fit residues: 88.7364 Evaluate side-chains 236 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1048 time to fit residues: 1.8323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.151029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130139 restraints weight = 14352.167| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.53 r_work: 0.3520 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9746 Z= 0.226 Angle : 0.618 9.701 13252 Z= 0.313 Chirality : 0.044 0.179 1448 Planarity : 0.004 0.040 1675 Dihedral : 4.104 20.337 1330 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.39 % Allowed : 18.62 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1138 helix: 0.73 (0.27), residues: 360 sheet: -0.94 (0.43), residues: 142 loop : -0.30 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 711 HIS 0.004 0.001 HIS A 437 PHE 0.024 0.002 PHE B 680 TYR 0.023 0.002 TYR A 319 ARG 0.010 0.001 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2645.94 seconds wall clock time: 48 minutes 33.03 seconds (2913.03 seconds total)