Starting phenix.real_space_refine (version: dev) on Mon Feb 20 01:45:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/02_2023/7zre_14912_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/02_2023/7zre_14912.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/7zre_14912/02_2023/7zre_14912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/02_2023/7zre_14912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/02_2023/7zre_14912_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/02_2023/7zre_14912_updated.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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 101 atoms to isotropic. 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 43": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10996 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5001 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 26, 'TRANS': 646} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.54, per 1000 atoms: 0.59 Number of scatterers: 10996 At special positions: 0 Unit cell: (89.056, 112.332, 143.704, 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) K 9 19.00 S 62 16.00 P 6 15.00 O 1996 8.00 N 1818 7.00 C 7105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 5 sheets defined 56.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 134 through 156 removed outlier: 3.788A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.558A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.787A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 436 removed outlier: 4.365A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.513A pdb=" N LEU A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 507 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 2 through 33 Proline residue: C 6 - end of helix Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 148 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.272A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 64 through 102 removed outlier: 3.751A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 245 removed outlier: 4.048A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.761A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 266 through 285 removed outlier: 5.522A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 330 through 343 removed outlier: 4.528A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 367 through 370 No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 509 removed outlier: 4.481A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 557 through 594 removed outlier: 6.517A pdb=" N MET B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.654A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 630 removed outlier: 4.458A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 646 through 679 removed outlier: 4.327A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.522A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 531 through 535 removed outlier: 6.577A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ASP B 518 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 373 through 375 removed outlier: 4.346A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 317 through 323 removed outlier: 7.646A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1653 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: 3.20 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1771 1.31 - 1.44: 2725 1.44 - 1.57: 6563 1.57 - 1.69: 13 1.69 - 1.82: 112 Bond restraints: 11184 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.592 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.424 -0.090 1.10e-02 8.26e+03 6.76e+01 bond pdb=" CB7 CDL A 608 " pdb=" OB8 CDL A 608 " ideal model delta sigma weight residual 1.334 1.422 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CA7 CDL A 608 " pdb=" OA8 CDL A 608 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.43e+01 bond pdb=" CA7 CDL A 609 " pdb=" OA8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.414 -0.080 1.10e-02 8.26e+03 5.28e+01 ... (remaining 11179 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.81: 232 104.81 - 112.16: 5776 112.16 - 119.51: 3739 119.51 - 126.86: 5290 126.86 - 134.21: 140 Bond angle restraints: 15177 Sorted by residual: angle pdb=" C51 CDL A 609 " pdb=" CB5 CDL A 609 " pdb=" OB6 CDL A 609 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C11 CDL A 608 " pdb=" CA5 CDL A 608 " pdb=" OA6 CDL A 608 " ideal model delta sigma weight residual 111.33 120.12 -8.79 1.32e+00 5.72e-01 4.42e+01 angle pdb=" C11 CDL A 609 " pdb=" CA5 CDL A 609 " pdb=" OA6 CDL A 609 " ideal model delta sigma weight residual 111.33 119.83 -8.50 1.32e+00 5.72e-01 4.14e+01 angle pdb=" C51 CDL A 608 " pdb=" CB5 CDL A 608 " pdb=" OB6 CDL A 608 " ideal model delta sigma weight residual 111.33 119.63 -8.30 1.32e+00 5.72e-01 3.94e+01 angle pdb=" C71 CDL A 609 " pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 111.64 120.47 -8.83 1.65e+00 3.69e-01 2.88e+01 ... (remaining 15172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5878 17.92 - 35.85: 612 35.85 - 53.77: 144 53.77 - 71.70: 37 71.70 - 89.62: 11 Dihedral angle restraints: 6682 sinusoidal: 2585 harmonic: 4097 Sorted by residual: dihedral pdb=" C PHD B 307 " pdb=" N PHD B 307 " pdb=" CA PHD B 307 " pdb=" CB PHD B 307 " ideal model delta harmonic sigma weight residual -122.60 -137.22 14.62 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" N PHD B 307 " pdb=" C PHD B 307 " pdb=" CA PHD B 307 " pdb=" CB PHD B 307 " ideal model delta harmonic sigma weight residual 122.80 134.98 -12.18 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 6679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1729 0.104 - 0.207: 73 0.207 - 0.311: 4 0.311 - 0.414: 0 0.414 - 0.518: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA PHD B 307 " pdb=" N PHD B 307 " pdb=" C PHD B 307 " pdb=" CB PHD B 307 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA LEU B 342 " pdb=" N LEU B 342 " pdb=" C LEU B 342 " pdb=" CB LEU B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE B 393 " pdb=" CA ILE B 393 " pdb=" CG1 ILE B 393 " pdb=" CG2 ILE B 393 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1804 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.054 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO A 362 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 360 " 0.011 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE B 360 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 360 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 360 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 360 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 360 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 360 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 18 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C THR C 18 " -0.037 2.00e-02 2.50e+03 pdb=" O THR C 18 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 2998 2.81 - 3.39: 12628 3.39 - 3.98: 22007 3.98 - 4.56: 30532 4.56 - 5.14: 44185 Nonbonded interactions: 112350 Sorted by model distance: nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR A 339 " pdb=" O CYS A 344 " model vdw 2.248 2.440 nonbonded pdb=" O TYR C 22 " pdb=" OG1 THR C 26 " model vdw 2.270 2.440 nonbonded pdb=" OG SER B 612 " pdb=" OD1 ASP B 614 " model vdw 2.271 2.440 nonbonded pdb=" OG SER A 241 " pdb=" O ILE A 348 " model vdw 2.278 2.440 ... (remaining 112345 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: 6 Type Number sf(0) Gaussians K 9 8.98 5 P 6 5.49 5 S 62 5.16 5 C 7105 2.51 5 N 1818 2.21 5 O 1996 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.170 Process input model: 31.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.006 0.224 11184 Z= 0.400 Angle : 0.929 11.183 15177 Z= 0.471 Chirality : 0.049 0.518 1807 Planarity : 0.006 0.080 1905 Dihedral : 15.965 89.620 4050 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1433 helix: 0.17 (0.16), residues: 884 sheet: -1.05 (0.58), residues: 82 loop : -1.79 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.084 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2124 time to fit residues: 49.1409 Evaluate side-chains 133 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.0040 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11184 Z= 0.161 Angle : 0.522 7.256 15177 Z= 0.262 Chirality : 0.039 0.150 1807 Planarity : 0.004 0.065 1905 Dihedral : 9.750 59.453 1674 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1433 helix: 0.98 (0.17), residues: 881 sheet: -0.99 (0.59), residues: 80 loop : -1.71 (0.25), residues: 472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.127 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 0.1990 time to fit residues: 43.5746 Evaluate side-chains 131 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1051 time to fit residues: 2.4075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 0.0980 chunk 129 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 11184 Z= 0.243 Angle : 0.561 8.250 15177 Z= 0.283 Chirality : 0.041 0.154 1807 Planarity : 0.004 0.058 1905 Dihedral : 8.851 59.953 1674 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1433 helix: 1.09 (0.17), residues: 879 sheet: -1.09 (0.58), residues: 80 loop : -1.52 (0.25), residues: 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.149 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 144 average time/residue: 0.1951 time to fit residues: 42.7341 Evaluate side-chains 135 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0986 time to fit residues: 2.6711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 138 optimal weight: 0.0670 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11184 Z= 0.137 Angle : 0.493 7.343 15177 Z= 0.249 Chirality : 0.039 0.143 1807 Planarity : 0.004 0.047 1905 Dihedral : 8.176 59.043 1674 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1433 helix: 1.38 (0.18), residues: 873 sheet: -1.02 (0.57), residues: 82 loop : -1.46 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.338 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 143 average time/residue: 0.2063 time to fit residues: 44.4508 Evaluate side-chains 132 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1114 time to fit residues: 2.0460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11184 Z= 0.198 Angle : 0.525 7.801 15177 Z= 0.264 Chirality : 0.040 0.149 1807 Planarity : 0.004 0.046 1905 Dihedral : 8.056 57.330 1674 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1433 helix: 1.38 (0.18), residues: 872 sheet: -1.01 (0.59), residues: 77 loop : -1.42 (0.25), residues: 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.286 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 145 average time/residue: 0.2133 time to fit residues: 46.4172 Evaluate side-chains 137 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1030 time to fit residues: 2.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 11184 Z= 0.156 Angle : 0.509 9.574 15177 Z= 0.255 Chirality : 0.039 0.146 1807 Planarity : 0.004 0.041 1905 Dihedral : 7.831 57.056 1674 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1433 helix: 1.46 (0.18), residues: 873 sheet: -0.99 (0.58), residues: 77 loop : -1.37 (0.25), residues: 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.245 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 144 average time/residue: 0.2233 time to fit residues: 48.9398 Evaluate side-chains 132 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1091 time to fit residues: 1.8388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.0370 chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 11184 Z= 0.151 Angle : 0.516 9.366 15177 Z= 0.254 Chirality : 0.039 0.167 1807 Planarity : 0.003 0.041 1905 Dihedral : 7.640 58.390 1674 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1433 helix: 1.51 (0.18), residues: 873 sheet: -1.06 (0.58), residues: 79 loop : -1.32 (0.26), residues: 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.263 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 139 average time/residue: 0.2081 time to fit residues: 43.7735 Evaluate side-chains 133 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1028 time to fit residues: 2.6407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 252 ASN B 30 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 11184 Z= 0.150 Angle : 0.525 14.833 15177 Z= 0.258 Chirality : 0.039 0.192 1807 Planarity : 0.003 0.040 1905 Dihedral : 7.498 55.726 1674 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1433 helix: 1.61 (0.18), residues: 862 sheet: -1.08 (0.58), residues: 79 loop : -1.21 (0.26), residues: 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.275 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 135 average time/residue: 0.2134 time to fit residues: 43.9314 Evaluate side-chains 132 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1348 time to fit residues: 2.1100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 77 optimal weight: 0.0470 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.3980 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 11184 Z= 0.141 Angle : 0.517 13.476 15177 Z= 0.254 Chirality : 0.039 0.171 1807 Planarity : 0.003 0.040 1905 Dihedral : 7.335 55.992 1674 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1433 helix: 1.63 (0.18), residues: 868 sheet: -1.10 (0.58), residues: 79 loop : -1.23 (0.26), residues: 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.451 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 134 average time/residue: 0.2241 time to fit residues: 45.5690 Evaluate side-chains 133 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0998 time to fit residues: 2.1440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 11184 Z= 0.151 Angle : 0.528 12.509 15177 Z= 0.258 Chirality : 0.039 0.163 1807 Planarity : 0.003 0.040 1905 Dihedral : 7.279 55.827 1674 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1433 helix: 1.63 (0.18), residues: 863 sheet: -1.08 (0.58), residues: 79 loop : -1.22 (0.26), residues: 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.495 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2287 time to fit residues: 45.8656 Evaluate side-chains 129 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109652 restraints weight = 14211.652| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.33 r_work: 0.3075 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 11184 Z= 0.140 Angle : 0.517 11.996 15177 Z= 0.253 Chirality : 0.039 0.153 1807 Planarity : 0.003 0.040 1905 Dihedral : 7.172 56.264 1674 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1433 helix: 1.67 (0.18), residues: 863 sheet: -1.11 (0.58), residues: 80 loop : -1.19 (0.26), residues: 490 =============================================================================== Job complete usr+sys time: 2159.96 seconds wall clock time: 40 minutes 31.16 seconds (2431.16 seconds total)