Starting phenix.real_space_refine (version: dev) on Sun Feb 19 21:59:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/02_2023/7r87_24310.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/02_2023/7r87_24310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/02_2023/7r87_24310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/02_2023/7r87_24310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/02_2023/7r87_24310.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r87_24310/02_2023/7r87_24310.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 GLU 77": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C ARG 108": "NH1" <-> "NH2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" 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: 10793 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4608 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 21, 'TRANS': 564} Chain breaks: 2 Chain: "B" Number of atoms: 4481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4481 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 539} Chain breaks: 4 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Time building chain proxies: 6.56, per 1000 atoms: 0.61 Number of scatterers: 10793 At special positions: 0 Unit cell: (113.288, 104.958, 126.616, 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 67 16.00 O 1933 8.00 N 1827 7.00 C 6966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " 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: 4.46 Conformation dependent library (CDL) restraints added in 1.7 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 53.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.390A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.504A pdb=" N VAL A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 331 removed outlier: 3.583A pdb=" N GLU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.916A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.571A pdb=" N VAL A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.134A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.567A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.562A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.277A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 4.157A pdb=" N PHE A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 617 removed outlier: 4.239A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 619 through 649 removed outlier: 4.577A pdb=" N ILE A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 4.572A pdb=" N HIS A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 removed outlier: 3.556A pdb=" N VAL B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 244 through 261 removed outlier: 3.518A pdb=" N GLY B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.639A pdb=" N LEU B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.925A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.615A pdb=" N GLU B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 458 through 473 removed outlier: 4.333A pdb=" N ASN B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 removed outlier: 3.516A pdb=" N GLY B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 513 removed outlier: 4.628A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.685A pdb=" N TRP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 3.511A pdb=" N TRP B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.592A pdb=" N SER B 637 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR B 638 " --> pdb=" O LEU B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.640A pdb=" N ASP D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.936A pdb=" N LYS A 70 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR A 45 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.936A pdb=" N LYS A 70 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR A 45 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA A 43 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 110 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.522A pdb=" N THR A 248 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 81 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA A 264 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS A 83 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU A 266 " --> pdb=" O CYS A 83 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 85 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 96 removed outlier: 7.445A pdb=" N PHE B 93 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG B 50 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 95 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU B 48 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.620A pdb=" N SER B 268 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 105 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET B 100 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU B 284 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 102 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET B 286 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 104 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.537A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.736A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 107 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3438 1.34 - 1.46: 2397 1.46 - 1.58: 5083 1.58 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 11025 Sorted by residual: bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.05e+00 bond pdb=" CB PRO B 514 " pdb=" CG PRO B 514 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.47e-01 bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.51e-02 4.39e+03 7.01e-01 bond pdb=" CA ILE B 459 " pdb=" C ILE B 459 " ideal model delta sigma weight residual 1.524 1.533 -0.008 1.05e-02 9.07e+03 6.53e-01 bond pdb=" CA PRO B 514 " pdb=" CB PRO B 514 " ideal model delta sigma weight residual 1.531 1.536 -0.005 6.20e-03 2.60e+04 5.94e-01 ... (remaining 11020 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.30: 327 107.30 - 113.97: 6146 113.97 - 120.64: 4710 120.64 - 127.31: 3641 127.31 - 133.98: 96 Bond angle restraints: 14920 Sorted by residual: angle pdb=" N ILE A 416 " pdb=" CA ILE A 416 " pdb=" C ILE A 416 " ideal model delta sigma weight residual 112.96 109.27 3.69 1.00e+00 1.00e+00 1.36e+01 angle pdb=" N ILE B 307 " pdb=" CA ILE B 307 " pdb=" C ILE B 307 " ideal model delta sigma weight residual 113.07 108.80 4.27 1.36e+00 5.41e-01 9.88e+00 angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 122.08 126.15 -4.07 1.47e+00 4.63e-01 7.66e+00 angle pdb=" C MET B 513 " pdb=" N PRO B 514 " pdb=" CA PRO B 514 " ideal model delta sigma weight residual 121.65 119.14 2.51 1.01e+00 9.80e-01 6.16e+00 angle pdb=" C ASN A 551 " pdb=" N ILE A 552 " pdb=" CA ILE A 552 " ideal model delta sigma weight residual 120.62 124.60 -3.98 1.64e+00 3.72e-01 5.90e+00 ... (remaining 14915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6085 17.58 - 35.16: 394 35.16 - 52.73: 66 52.73 - 70.31: 13 70.31 - 87.89: 7 Dihedral angle restraints: 6565 sinusoidal: 2612 harmonic: 3953 Sorted by residual: dihedral pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " pdb=" OE1 GLU A 452 " ideal model delta sinusoidal sigma weight residual 0.00 -85.10 85.10 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CA ARG A 157 " pdb=" CB ARG A 157 " pdb=" CG ARG A 157 " pdb=" CD ARG A 157 " ideal model delta sinusoidal sigma weight residual -180.00 -121.93 -58.07 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLN A 126 " pdb=" CB GLN A 126 " pdb=" CG GLN A 126 " pdb=" CD GLN A 126 " ideal model delta sinusoidal sigma weight residual 60.00 113.64 -53.64 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 6562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1143 0.027 - 0.054: 342 0.054 - 0.082: 118 0.082 - 0.109: 73 0.109 - 0.136: 22 Chirality restraints: 1698 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA THR A 430 " pdb=" N THR A 430 " pdb=" C THR A 430 " pdb=" CB THR A 430 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE C 90 " pdb=" N ILE C 90 " pdb=" C ILE C 90 " pdb=" CB ILE C 90 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1695 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 555 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO A 556 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 556 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 556 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO B 491 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.016 5.00e-02 4.00e+02 2.50e-02 9.97e-01 pdb=" N PRO A 277 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.014 5.00e-02 4.00e+02 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3492 2.83 - 3.35: 9734 3.35 - 3.87: 17750 3.87 - 4.38: 19445 4.38 - 4.90: 35334 Nonbonded interactions: 85755 Sorted by model distance: nonbonded pdb=" O SER B 288 " pdb=" OG SER B 288 " model vdw 2.317 2.440 nonbonded pdb=" O LYS B 605 " pdb=" OG SER B 609 " model vdw 2.327 2.440 nonbonded pdb=" O ARG A 550 " pdb=" NH1 ARG A 550 " model vdw 2.343 2.520 nonbonded pdb=" OE1 GLN A 417 " pdb=" ND2 ASN B 579 " model vdw 2.349 2.520 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.355 2.440 ... (remaining 85750 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 67 5.16 5 C 6966 2.51 5 N 1827 2.21 5 O 1933 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 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: 1.050 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: 6.140 Check model and map are aligned: 0.150 Process input model: 31.520 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.002 0.043 11025 Z= 0.104 Angle : 0.437 6.734 14920 Z= 0.252 Chirality : 0.036 0.136 1698 Planarity : 0.002 0.025 1879 Dihedral : 12.082 87.888 4020 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.21), residues: 1349 helix: 0.27 (0.18), residues: 701 sheet: -1.06 (0.36), residues: 181 loop : -2.90 (0.24), residues: 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 1.393 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 266 average time/residue: 0.2741 time to fit residues: 98.8574 Evaluate side-chains 183 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1175 time to fit residues: 2.6839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 116 ASN A 134 GLN A 165 GLN A 206 GLN A 392 GLN A 437 ASN A 462 GLN A 470 HIS A 510 HIS A 528 ASN A 578 ASN A 604 GLN A 607 GLN B 99 GLN B 153 GLN B 183 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 302 GLN B 438 HIS B 462 ASN B 526 GLN B 607 GLN C 75 ASN D 47 GLN D 58 GLN D 65 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11025 Z= 0.280 Angle : 0.612 9.844 14920 Z= 0.307 Chirality : 0.043 0.244 1698 Planarity : 0.004 0.065 1879 Dihedral : 3.477 15.326 1498 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -0.30 (0.22), residues: 1349 helix: 1.18 (0.19), residues: 718 sheet: -1.00 (0.34), residues: 190 loop : -2.15 (0.27), residues: 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.161 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 184 average time/residue: 0.2460 time to fit residues: 63.0716 Evaluate side-chains 155 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1058 time to fit residues: 4.2080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 526 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN D 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11025 Z= 0.195 Angle : 0.512 9.196 14920 Z= 0.255 Chirality : 0.039 0.170 1698 Planarity : 0.003 0.046 1879 Dihedral : 3.303 16.610 1498 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.47 (0.23), residues: 1349 helix: 1.83 (0.20), residues: 709 sheet: -0.70 (0.35), residues: 190 loop : -1.76 (0.28), residues: 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.229 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 157 average time/residue: 0.2671 time to fit residues: 57.9287 Evaluate side-chains 139 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1823 time to fit residues: 3.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.0030 chunk 58 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 11025 Z= 0.436 Angle : 0.650 11.015 14920 Z= 0.327 Chirality : 0.044 0.187 1698 Planarity : 0.004 0.045 1879 Dihedral : 3.960 17.893 1498 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.40 (0.23), residues: 1349 helix: 1.63 (0.19), residues: 707 sheet: -0.41 (0.36), residues: 188 loop : -1.65 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.379 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 146 average time/residue: 0.2802 time to fit residues: 56.8145 Evaluate side-chains 130 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1787 time to fit residues: 4.2296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11025 Z= 0.171 Angle : 0.529 11.141 14920 Z= 0.260 Chirality : 0.039 0.152 1698 Planarity : 0.003 0.046 1879 Dihedral : 3.572 15.403 1498 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.90 (0.24), residues: 1349 helix: 2.12 (0.20), residues: 696 sheet: -0.15 (0.37), residues: 188 loop : -1.51 (0.29), residues: 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.277 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 134 average time/residue: 0.2718 time to fit residues: 50.9516 Evaluate side-chains 121 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1728 time to fit residues: 3.4522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 0.0040 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11025 Z= 0.202 Angle : 0.546 11.329 14920 Z= 0.266 Chirality : 0.040 0.187 1698 Planarity : 0.003 0.047 1879 Dihedral : 3.549 15.694 1498 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1349 helix: 2.21 (0.20), residues: 697 sheet: -0.02 (0.37), residues: 193 loop : -1.40 (0.29), residues: 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.314 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 123 average time/residue: 0.2559 time to fit residues: 44.3119 Evaluate side-chains 116 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1214 time to fit residues: 2.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 0.0030 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11025 Z= 0.171 Angle : 0.535 11.138 14920 Z= 0.259 Chirality : 0.039 0.191 1698 Planarity : 0.003 0.047 1879 Dihedral : 3.488 15.577 1498 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1349 helix: 2.26 (0.20), residues: 703 sheet: 0.21 (0.39), residues: 187 loop : -1.29 (0.30), residues: 459 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.383 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 123 average time/residue: 0.2613 time to fit residues: 45.2317 Evaluate side-chains 113 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0953 time to fit residues: 2.2271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11025 Z= 0.209 Angle : 0.553 11.274 14920 Z= 0.267 Chirality : 0.040 0.199 1698 Planarity : 0.003 0.048 1879 Dihedral : 3.539 15.720 1498 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1349 helix: 2.25 (0.20), residues: 704 sheet: 0.27 (0.39), residues: 187 loop : -1.23 (0.30), residues: 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.204 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 115 average time/residue: 0.2647 time to fit residues: 42.9131 Evaluate side-chains 116 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1078 time to fit residues: 2.7978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 11025 Z= 0.444 Angle : 0.668 11.779 14920 Z= 0.330 Chirality : 0.044 0.206 1698 Planarity : 0.004 0.049 1879 Dihedral : 4.053 17.234 1498 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.88 (0.23), residues: 1349 helix: 1.87 (0.19), residues: 704 sheet: 0.00 (0.38), residues: 195 loop : -1.24 (0.30), residues: 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.387 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 125 average time/residue: 0.2833 time to fit residues: 49.7153 Evaluate side-chains 115 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1019 time to fit residues: 2.5894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 chunk 85 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11025 Z= 0.171 Angle : 0.556 11.124 14920 Z= 0.269 Chirality : 0.039 0.191 1698 Planarity : 0.003 0.049 1879 Dihedral : 3.684 15.822 1498 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1349 helix: 2.20 (0.20), residues: 703 sheet: 0.17 (0.38), residues: 195 loop : -1.15 (0.30), residues: 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.365 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 120 average time/residue: 0.2553 time to fit residues: 43.6450 Evaluate side-chains 112 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0959 time to fit residues: 1.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.0040 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.103095 restraints weight = 13788.359| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.68 r_work: 0.2936 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11025 Z= 0.173 Angle : 0.553 11.250 14920 Z= 0.265 Chirality : 0.039 0.199 1698 Planarity : 0.003 0.048 1879 Dihedral : 3.560 15.903 1498 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1349 helix: 2.31 (0.20), residues: 703 sheet: 0.25 (0.39), residues: 195 loop : -1.09 (0.31), residues: 451 =============================================================================== Job complete usr+sys time: 2272.22 seconds wall clock time: 42 minutes 16.43 seconds (2536.43 seconds total)