Starting phenix.real_space_refine on Wed Sep 25 03:02:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/09_2024/6qvb_4646.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/09_2024/6qvb_4646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/09_2024/6qvb_4646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/09_2024/6qvb_4646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/09_2024/6qvb_4646.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvb_4646/09_2024/6qvb_4646.cif" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6109 2.51 5 N 1482 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9237 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4617 Classifications: {'peptide': 596} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 566} Chain breaks: 3 Chain: "A" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4620 Classifications: {'peptide': 597} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 567} Chain breaks: 3 Time building chain proxies: 5.96, per 1000 atoms: 0.65 Number of scatterers: 9237 At special positions: 0 Unit cell: (110.21, 118.77, 108.07, 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 70 16.00 O 1576 8.00 N 1482 7.00 C 6109 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 - 3.00 Amino acid : True - 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 66.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'B' and resid 115 through 153 Processing helix chain 'B' and resid 158 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.499A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.283A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 323 removed outlier: 3.778A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 375 removed outlier: 3.717A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.546A pdb=" N LEU B 392 " --> pdb=" O HIS B 389 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 389 through 393' Processing helix chain 'B' and resid 394 through 404 removed outlier: 3.520A pdb=" N THR B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 455 through 477 removed outlier: 4.867A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.613A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.881A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 585 removed outlier: 3.723A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 632 removed outlier: 4.074A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 863 through 872 removed outlier: 3.947A pdb=" N GLY B 872 " --> pdb=" O LYS B 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 153 Processing helix chain 'A' and resid 158 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.492A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 209 through 224 removed outlier: 4.269A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 323 removed outlier: 3.872A pdb=" N TYR A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 375 removed outlier: 3.692A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.549A pdb=" N LEU A 392 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 393 " --> pdb=" O ARG A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 393' Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.670A pdb=" N THR A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 455 through 477 removed outlier: 4.763A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 4.738A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 4.060A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.696A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 632 removed outlier: 4.082A pdb=" N THR A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 872 removed outlier: 3.830A pdb=" N LEU A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640 removed outlier: 6.078A pdb=" N LEU B 637 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 651 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 639 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 5.978A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640 removed outlier: 6.020A pdb=" N LEU A 637 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 651 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 639 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 5.979A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2735 1.34 - 1.46: 2230 1.46 - 1.58: 4384 1.58 - 1.70: 2 1.70 - 1.82: 116 Bond restraints: 9467 Sorted by residual: bond pdb=" CB MET B 414 " pdb=" CG MET B 414 " ideal model delta sigma weight residual 1.520 1.389 0.131 3.00e-02 1.11e+03 1.91e+01 bond pdb=" CB TYR A 302 " pdb=" CG TYR A 302 " ideal model delta sigma weight residual 1.512 1.429 0.083 2.20e-02 2.07e+03 1.42e+01 bond pdb=" CG TYR A 302 " pdb=" CD1 TYR A 302 " ideal model delta sigma weight residual 1.389 1.320 0.069 2.10e-02 2.27e+03 1.07e+01 bond pdb=" CE1 TYR A 302 " pdb=" CZ TYR A 302 " ideal model delta sigma weight residual 1.378 1.304 0.074 2.40e-02 1.74e+03 9.49e+00 bond pdb=" CD1 TYR A 302 " pdb=" CE1 TYR A 302 " ideal model delta sigma weight residual 1.382 1.291 0.091 3.00e-02 1.11e+03 9.26e+00 ... (remaining 9462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 12470 4.26 - 8.53: 320 8.53 - 12.79: 53 12.79 - 17.05: 15 17.05 - 21.31: 3 Bond angle restraints: 12861 Sorted by residual: angle pdb=" C TYR B 589 " pdb=" N LEU B 593 " pdb=" CA LEU B 593 " ideal model delta sigma weight residual 121.70 135.34 -13.64 1.80e+00 3.09e-01 5.74e+01 angle pdb=" C TYR A 589 " pdb=" N LEU A 593 " pdb=" CA LEU A 593 " ideal model delta sigma weight residual 121.70 135.33 -13.63 1.80e+00 3.09e-01 5.73e+01 angle pdb=" CA TRP A 469 " pdb=" CB TRP A 469 " pdb=" CG TRP A 469 " ideal model delta sigma weight residual 113.60 127.33 -13.73 1.90e+00 2.77e-01 5.22e+01 angle pdb=" CA TYR B 589 " pdb=" C TYR B 589 " pdb=" N LEU B 593 " ideal model delta sigma weight residual 116.84 128.50 -11.66 1.71e+00 3.42e-01 4.65e+01 angle pdb=" CA TYR A 589 " pdb=" C TYR A 589 " pdb=" N LEU A 593 " ideal model delta sigma weight residual 116.84 128.38 -11.54 1.71e+00 3.42e-01 4.55e+01 ... (remaining 12856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 4914 14.51 - 29.02: 466 29.02 - 43.53: 120 43.53 - 58.04: 23 58.04 - 72.55: 4 Dihedral angle restraints: 5527 sinusoidal: 2104 harmonic: 3423 Sorted by residual: dihedral pdb=" CA LYS A 324 " pdb=" C LYS A 324 " pdb=" N ASP A 325 " pdb=" CA ASP A 325 " ideal model delta harmonic sigma weight residual 180.00 -137.16 -42.84 0 5.00e+00 4.00e-02 7.34e+01 dihedral pdb=" CA LYS B 324 " pdb=" C LYS B 324 " pdb=" N ASP B 325 " pdb=" CA ASP B 325 " ideal model delta harmonic sigma weight residual -180.00 -137.26 -42.74 0 5.00e+00 4.00e-02 7.31e+01 dihedral pdb=" CA ARG B 670 " pdb=" C ARG B 670 " pdb=" N LEU B 671 " pdb=" CA LEU B 671 " ideal model delta harmonic sigma weight residual 180.00 -137.73 -42.27 0 5.00e+00 4.00e-02 7.15e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1183 0.094 - 0.188: 270 0.188 - 0.282: 47 0.282 - 0.377: 9 0.377 - 0.471: 10 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CG LEU B 671 " pdb=" CB LEU B 671 " pdb=" CD1 LEU B 671 " pdb=" CD2 LEU B 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA PHE B 488 " pdb=" N PHE B 488 " pdb=" C PHE B 488 " pdb=" CB PHE B 488 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 1516 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 517 " 0.068 2.00e-02 2.50e+03 5.24e-02 5.49e+01 pdb=" CG TYR B 517 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 TYR B 517 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 517 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 517 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 517 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 517 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR B 517 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " 0.068 2.00e-02 2.50e+03 5.22e-02 5.46e+01 pdb=" CG TYR A 517 " -0.126 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 469 " -0.056 2.00e-02 2.50e+03 4.11e-02 4.22e+01 pdb=" CG TRP A 469 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 TRP A 469 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 469 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 469 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 469 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 469 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 469 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 469 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 469 " -0.004 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 535 2.70 - 3.25: 9654 3.25 - 3.80: 15800 3.80 - 4.35: 18494 4.35 - 4.90: 29057 Nonbonded interactions: 73540 Sorted by model distance: nonbonded pdb=" OH TYR B 302 " pdb=" O GLU A 291 " model vdw 2.153 3.040 nonbonded pdb=" O ILE B 401 " pdb=" OG1 THR B 405 " model vdw 2.156 3.040 nonbonded pdb=" O CYS A 179 " pdb=" OG SER A 183 " model vdw 2.194 3.040 nonbonded pdb=" O CYS B 179 " pdb=" OG SER B 183 " model vdw 2.194 3.040 nonbonded pdb=" O CYS A 546 " pdb=" OG1 THR A 550 " model vdw 2.227 3.040 ... (remaining 73535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 115 through 671 or resid 819 through 872)) selection = (chain 'B' and (resid 115 through 671 or resid 819 through 872)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.010 0.131 9467 Z= 0.621 Angle : 1.720 21.313 12861 Z= 0.891 Chirality : 0.090 0.471 1519 Planarity : 0.012 0.073 1573 Dihedral : 12.748 72.553 3325 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.28 % Favored : 89.55 % Rotamer: Outliers : 3.10 % Allowed : 8.91 % Favored : 87.99 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 1.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.19), residues: 1177 helix: -2.20 (0.15), residues: 740 sheet: -3.20 (0.60), residues: 44 loop : -4.22 (0.23), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.008 TRP A 469 HIS 0.017 0.003 HIS A 555 PHE 0.073 0.006 PHE B 341 TYR 0.127 0.007 TYR B 517 ARG 0.017 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 LEU cc_start: 0.9691 (mt) cc_final: 0.9371 (mt) REVERT: B 267 LEU cc_start: 0.9701 (mp) cc_final: 0.9500 (tt) REVERT: B 307 PHE cc_start: 0.9541 (t80) cc_final: 0.9098 (t80) REVERT: B 417 GLU cc_start: 0.9011 (tt0) cc_final: 0.8712 (tm-30) REVERT: B 464 PHE cc_start: 0.9589 (t80) cc_final: 0.9352 (t80) REVERT: B 559 MET cc_start: 0.9560 (ptp) cc_final: 0.9270 (ptm) REVERT: B 565 LEU cc_start: 0.9672 (mt) cc_final: 0.9365 (tt) REVERT: B 660 LEU cc_start: 0.9761 (tt) cc_final: 0.9554 (mt) REVERT: B 854 MET cc_start: 0.8638 (tmm) cc_final: 0.8354 (tmm) REVERT: A 128 MET cc_start: 0.9708 (tpp) cc_final: 0.9052 (tpp) REVERT: A 143 LEU cc_start: 0.9459 (tp) cc_final: 0.9067 (tp) REVERT: A 399 PHE cc_start: 0.8710 (m-80) cc_final: 0.8463 (m-80) REVERT: A 417 GLU cc_start: 0.9197 (tt0) cc_final: 0.8670 (tm-30) REVERT: A 419 MET cc_start: 0.9507 (mmp) cc_final: 0.9178 (mmt) REVERT: A 466 MET cc_start: 0.9174 (tpt) cc_final: 0.8961 (tpt) REVERT: A 473 VAL cc_start: 0.9609 (p) cc_final: 0.9392 (m) REVERT: A 488 PHE cc_start: 0.9396 (m-10) cc_final: 0.9189 (m-10) REVERT: A 559 MET cc_start: 0.9558 (ptp) cc_final: 0.9253 (ptm) REVERT: A 564 ILE cc_start: 0.9757 (mm) cc_final: 0.9505 (mm) REVERT: A 565 LEU cc_start: 0.9633 (mt) cc_final: 0.9215 (tt) REVERT: A 854 MET cc_start: 0.8894 (tmm) cc_final: 0.8600 (tmm) outliers start: 31 outliers final: 9 residues processed: 265 average time/residue: 0.1922 time to fit residues: 71.6310 Evaluate side-chains 165 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS B 823 GLN A 379 HIS A 823 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9467 Z= 0.256 Angle : 0.927 9.958 12861 Z= 0.484 Chirality : 0.051 0.236 1519 Planarity : 0.006 0.051 1573 Dihedral : 8.017 55.704 1260 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.40 % Allowed : 6.11 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -2.61 (0.22), residues: 1177 helix: -0.60 (0.17), residues: 758 sheet: -2.93 (0.61), residues: 44 loop : -3.91 (0.27), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 469 HIS 0.005 0.001 HIS B 369 PHE 0.059 0.003 PHE B 488 TYR 0.023 0.002 TYR A 517 ARG 0.007 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 246 LEU cc_start: 0.9535 (tp) cc_final: 0.9198 (mt) REVERT: B 250 MET cc_start: 0.9317 (tmm) cc_final: 0.9017 (tmm) REVERT: B 267 LEU cc_start: 0.9735 (mp) cc_final: 0.9485 (tp) REVERT: B 307 PHE cc_start: 0.9452 (t80) cc_final: 0.9198 (t80) REVERT: B 399 PHE cc_start: 0.8762 (m-80) cc_final: 0.8512 (m-10) REVERT: B 410 MET cc_start: 0.9671 (tpt) cc_final: 0.9341 (tpp) REVERT: B 414 MET cc_start: 0.9357 (tmm) cc_final: 0.8950 (tmm) REVERT: B 417 GLU cc_start: 0.8989 (tt0) cc_final: 0.8592 (tm-30) REVERT: B 429 ASP cc_start: 0.8924 (t70) cc_final: 0.8333 (p0) REVERT: B 464 PHE cc_start: 0.9617 (t80) cc_final: 0.9388 (t80) REVERT: B 470 MET cc_start: 0.8820 (ppp) cc_final: 0.8548 (ppp) REVERT: B 548 GLU cc_start: 0.8670 (pp20) cc_final: 0.8287 (pp20) REVERT: B 559 MET cc_start: 0.9393 (ptp) cc_final: 0.9150 (ptm) REVERT: B 560 MET cc_start: 0.9338 (mpp) cc_final: 0.9116 (mpp) REVERT: B 564 ILE cc_start: 0.9724 (mm) cc_final: 0.9518 (mm) REVERT: B 565 LEU cc_start: 0.9602 (mt) cc_final: 0.9205 (tt) REVERT: B 609 MET cc_start: 0.8807 (mmp) cc_final: 0.8309 (mmp) REVERT: B 646 MET cc_start: 0.9680 (mmp) cc_final: 0.9478 (mmm) REVERT: A 235 PHE cc_start: 0.8670 (t80) cc_final: 0.7863 (t80) REVERT: A 250 MET cc_start: 0.9256 (tmm) cc_final: 0.8898 (tmm) REVERT: A 399 PHE cc_start: 0.8860 (m-80) cc_final: 0.8283 (m-80) REVERT: A 404 PHE cc_start: 0.8840 (p90) cc_final: 0.8540 (p90) REVERT: A 410 MET cc_start: 0.9674 (tpt) cc_final: 0.9243 (tpp) REVERT: A 449 TRP cc_start: 0.9209 (m100) cc_final: 0.8963 (m100) REVERT: A 466 MET cc_start: 0.9130 (tpt) cc_final: 0.8851 (tpt) REVERT: A 488 PHE cc_start: 0.9253 (m-10) cc_final: 0.8563 (m-10) REVERT: A 559 MET cc_start: 0.9488 (ptp) cc_final: 0.9283 (ptm) REVERT: A 564 ILE cc_start: 0.9666 (mm) cc_final: 0.9461 (mm) REVERT: A 565 LEU cc_start: 0.9581 (mt) cc_final: 0.9193 (tt) REVERT: A 609 MET cc_start: 0.8793 (mmp) cc_final: 0.8389 (mmp) REVERT: A 646 MET cc_start: 0.9646 (mmp) cc_final: 0.9335 (mtt) REVERT: A 854 MET cc_start: 0.8732 (tmm) cc_final: 0.8485 (tmm) outliers start: 4 outliers final: 1 residues processed: 211 average time/residue: 0.1772 time to fit residues: 54.5331 Evaluate side-chains 164 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 369 HIS B 567 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9467 Z= 0.270 Angle : 0.892 10.676 12861 Z= 0.465 Chirality : 0.049 0.355 1519 Planarity : 0.005 0.042 1573 Dihedral : 7.606 56.244 1260 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.30 % Allowed : 6.01 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.77 (0.23), residues: 1177 helix: 0.11 (0.18), residues: 756 sheet: -2.80 (0.68), residues: 44 loop : -3.68 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 469 HIS 0.006 0.002 HIS B 369 PHE 0.049 0.003 PHE B 488 TYR 0.020 0.002 TYR A 517 ARG 0.005 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9612 (pp) cc_final: 0.9166 (pp) REVERT: B 128 MET cc_start: 0.9676 (mmt) cc_final: 0.9422 (mmm) REVERT: B 250 MET cc_start: 0.9318 (tmm) cc_final: 0.9073 (tmm) REVERT: B 267 LEU cc_start: 0.9730 (mp) cc_final: 0.9476 (tt) REVERT: B 307 PHE cc_start: 0.9472 (t80) cc_final: 0.9191 (t80) REVERT: B 410 MET cc_start: 0.9642 (tpt) cc_final: 0.9263 (tpp) REVERT: B 414 MET cc_start: 0.9452 (tmm) cc_final: 0.9157 (tmm) REVERT: B 470 MET cc_start: 0.8791 (ppp) cc_final: 0.8567 (ppp) REVERT: B 559 MET cc_start: 0.9377 (ptp) cc_final: 0.9168 (ptm) REVERT: B 560 MET cc_start: 0.9337 (mpp) cc_final: 0.9135 (mpp) REVERT: B 565 LEU cc_start: 0.9570 (mt) cc_final: 0.9167 (tt) REVERT: B 609 MET cc_start: 0.8907 (mmp) cc_final: 0.8470 (mmp) REVERT: B 646 MET cc_start: 0.9698 (mmp) cc_final: 0.9491 (mmm) REVERT: A 128 MET cc_start: 0.9428 (mtm) cc_final: 0.9106 (mtp) REVERT: A 235 PHE cc_start: 0.8858 (t80) cc_final: 0.7978 (t80) REVERT: A 339 MET cc_start: 0.8801 (pmm) cc_final: 0.8447 (pmm) REVERT: A 399 PHE cc_start: 0.8857 (m-80) cc_final: 0.8297 (m-80) REVERT: A 410 MET cc_start: 0.9624 (tpt) cc_final: 0.9235 (tpp) REVERT: A 449 TRP cc_start: 0.9121 (m100) cc_final: 0.8869 (m100) REVERT: A 548 GLU cc_start: 0.8594 (pp20) cc_final: 0.8195 (pp20) REVERT: A 564 ILE cc_start: 0.9683 (mm) cc_final: 0.9452 (mm) REVERT: A 565 LEU cc_start: 0.9546 (mt) cc_final: 0.9158 (tt) REVERT: A 609 MET cc_start: 0.9328 (mmp) cc_final: 0.8720 (mmp) REVERT: A 646 MET cc_start: 0.9646 (mmp) cc_final: 0.9335 (mtp) outliers start: 3 outliers final: 2 residues processed: 200 average time/residue: 0.1751 time to fit residues: 51.5945 Evaluate side-chains 155 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9467 Z= 0.218 Angle : 0.865 11.563 12861 Z= 0.440 Chirality : 0.048 0.340 1519 Planarity : 0.005 0.042 1573 Dihedral : 7.166 53.518 1260 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.30 % Allowed : 4.50 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.38 (0.24), residues: 1177 helix: 0.46 (0.18), residues: 761 sheet: -2.40 (0.75), residues: 44 loop : -3.71 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 469 HIS 0.005 0.001 HIS A 379 PHE 0.044 0.002 PHE B 488 TYR 0.046 0.002 TYR A 589 ARG 0.002 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 LEU cc_start: 0.9368 (tp) cc_final: 0.9072 (pp) REVERT: B 174 PHE cc_start: 0.9579 (m-10) cc_final: 0.9338 (m-80) REVERT: B 250 MET cc_start: 0.9320 (tmm) cc_final: 0.9095 (tmm) REVERT: B 267 LEU cc_start: 0.9721 (mp) cc_final: 0.9471 (tt) REVERT: B 307 PHE cc_start: 0.9467 (t80) cc_final: 0.9190 (t80) REVERT: B 339 MET cc_start: 0.8864 (ptp) cc_final: 0.8454 (ptp) REVERT: B 374 LEU cc_start: 0.9140 (tp) cc_final: 0.8898 (mt) REVERT: B 410 MET cc_start: 0.9632 (tpt) cc_final: 0.9231 (tpp) REVERT: B 414 MET cc_start: 0.9391 (tmm) cc_final: 0.9181 (tmm) REVERT: B 559 MET cc_start: 0.9390 (ptp) cc_final: 0.9188 (ptm) REVERT: B 560 MET cc_start: 0.9377 (mpp) cc_final: 0.9175 (mpp) REVERT: B 565 LEU cc_start: 0.9547 (mt) cc_final: 0.9175 (tt) REVERT: B 609 MET cc_start: 0.9079 (mmp) cc_final: 0.8700 (mmp) REVERT: B 646 MET cc_start: 0.9713 (mmp) cc_final: 0.9491 (mmm) REVERT: A 128 MET cc_start: 0.9365 (mtm) cc_final: 0.8994 (mtp) REVERT: A 164 TRP cc_start: 0.9584 (t-100) cc_final: 0.9321 (t-100) REVERT: A 178 PHE cc_start: 0.9328 (m-10) cc_final: 0.8946 (m-80) REVERT: A 235 PHE cc_start: 0.8781 (t80) cc_final: 0.7873 (t80) REVERT: A 339 MET cc_start: 0.8872 (pmm) cc_final: 0.8511 (pmm) REVERT: A 399 PHE cc_start: 0.8856 (m-80) cc_final: 0.8315 (m-80) REVERT: A 400 VAL cc_start: 0.9713 (p) cc_final: 0.9476 (p) REVERT: A 410 MET cc_start: 0.9597 (tpt) cc_final: 0.9185 (tpp) REVERT: A 466 MET cc_start: 0.9374 (tpt) cc_final: 0.9122 (tpt) REVERT: A 559 MET cc_start: 0.9678 (ptm) cc_final: 0.8962 (ppp) REVERT: A 564 ILE cc_start: 0.9675 (mm) cc_final: 0.9443 (mm) REVERT: A 565 LEU cc_start: 0.9522 (mt) cc_final: 0.9139 (tt) REVERT: A 609 MET cc_start: 0.9359 (mmp) cc_final: 0.8793 (mmp) REVERT: A 646 MET cc_start: 0.9670 (mmp) cc_final: 0.9373 (mtp) outliers start: 3 outliers final: 0 residues processed: 200 average time/residue: 0.1724 time to fit residues: 51.0133 Evaluate side-chains 151 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9467 Z= 0.219 Angle : 0.844 10.298 12861 Z= 0.430 Chirality : 0.047 0.223 1519 Planarity : 0.005 0.063 1573 Dihedral : 6.866 46.199 1260 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.20 % Allowed : 3.70 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -0.96 (0.24), residues: 1177 helix: 0.81 (0.18), residues: 765 sheet: -2.23 (0.77), residues: 44 loop : -3.67 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 469 HIS 0.004 0.001 HIS A 538 PHE 0.045 0.002 PHE B 488 TYR 0.027 0.002 TYR B 589 ARG 0.002 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9715 (pp) cc_final: 0.9397 (pp) REVERT: B 128 MET cc_start: 0.9684 (mmp) cc_final: 0.9398 (mmm) REVERT: B 143 LEU cc_start: 0.9378 (tp) cc_final: 0.9093 (pp) REVERT: B 174 PHE cc_start: 0.9613 (m-10) cc_final: 0.9386 (m-80) REVERT: B 250 MET cc_start: 0.9342 (tmm) cc_final: 0.9118 (tmm) REVERT: B 267 LEU cc_start: 0.9739 (mp) cc_final: 0.9512 (tp) REVERT: B 307 PHE cc_start: 0.9470 (t80) cc_final: 0.9214 (t80) REVERT: B 373 MET cc_start: 0.9099 (mmp) cc_final: 0.8696 (mtp) REVERT: B 374 LEU cc_start: 0.9135 (tp) cc_final: 0.8899 (mt) REVERT: B 399 PHE cc_start: 0.8884 (m-80) cc_final: 0.8371 (m-80) REVERT: B 410 MET cc_start: 0.9613 (tpt) cc_final: 0.9270 (tpp) REVERT: B 414 MET cc_start: 0.9353 (tmm) cc_final: 0.9070 (tmm) REVERT: B 470 MET cc_start: 0.8859 (ppp) cc_final: 0.8527 (tmm) REVERT: B 560 MET cc_start: 0.9312 (mpp) cc_final: 0.9011 (mpp) REVERT: B 609 MET cc_start: 0.9019 (mmp) cc_final: 0.8646 (mmp) REVERT: B 646 MET cc_start: 0.9717 (mmp) cc_final: 0.9505 (mmm) REVERT: A 128 MET cc_start: 0.9388 (mtm) cc_final: 0.8977 (mtp) REVERT: A 164 TRP cc_start: 0.9620 (t-100) cc_final: 0.9382 (t-100) REVERT: A 174 PHE cc_start: 0.9584 (m-10) cc_final: 0.9347 (m-80) REVERT: A 235 PHE cc_start: 0.8599 (t80) cc_final: 0.7703 (t80) REVERT: A 399 PHE cc_start: 0.8833 (m-80) cc_final: 0.8333 (m-80) REVERT: A 400 VAL cc_start: 0.9722 (p) cc_final: 0.9520 (p) REVERT: A 410 MET cc_start: 0.9557 (tpt) cc_final: 0.9192 (tpp) REVERT: A 429 ASP cc_start: 0.9084 (t70) cc_final: 0.8392 (p0) REVERT: A 466 MET cc_start: 0.9317 (tpt) cc_final: 0.9067 (tpt) REVERT: A 470 MET cc_start: 0.8948 (ppp) cc_final: 0.8689 (ppp) REVERT: A 609 MET cc_start: 0.9254 (mmp) cc_final: 0.8787 (mmp) REVERT: A 646 MET cc_start: 0.9672 (mmp) cc_final: 0.9378 (mtp) outliers start: 2 outliers final: 0 residues processed: 195 average time/residue: 0.1709 time to fit residues: 49.2652 Evaluate side-chains 143 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS B 451 HIS B 567 ASN B 827 GLN A 379 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9467 Z= 0.204 Angle : 0.839 10.974 12861 Z= 0.422 Chirality : 0.047 0.171 1519 Planarity : 0.005 0.056 1573 Dihedral : 6.528 40.477 1260 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.20 % Allowed : 2.40 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.74 (0.25), residues: 1177 helix: 0.96 (0.19), residues: 767 sheet: -2.27 (0.87), residues: 34 loop : -3.54 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 469 HIS 0.004 0.001 HIS A 451 PHE 0.050 0.002 PHE B 488 TYR 0.019 0.002 TYR A 589 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 LEU cc_start: 0.9397 (tp) cc_final: 0.9096 (pp) REVERT: B 174 PHE cc_start: 0.9627 (m-10) cc_final: 0.9403 (m-80) REVERT: B 267 LEU cc_start: 0.9723 (mp) cc_final: 0.9498 (tt) REVERT: B 307 PHE cc_start: 0.9462 (t80) cc_final: 0.8612 (t80) REVERT: B 374 LEU cc_start: 0.9205 (tp) cc_final: 0.9003 (mt) REVERT: B 399 PHE cc_start: 0.8978 (m-80) cc_final: 0.8540 (m-80) REVERT: B 410 MET cc_start: 0.9574 (tpt) cc_final: 0.9290 (tpp) REVERT: B 414 MET cc_start: 0.9352 (tmm) cc_final: 0.9067 (tmm) REVERT: B 470 MET cc_start: 0.8872 (ppp) cc_final: 0.8437 (tmm) REVERT: B 560 MET cc_start: 0.9298 (mpp) cc_final: 0.9052 (mpp) REVERT: B 567 ASN cc_start: 0.9392 (OUTLIER) cc_final: 0.9108 (m-40) REVERT: B 609 MET cc_start: 0.9055 (mmp) cc_final: 0.8735 (mmp) REVERT: B 646 MET cc_start: 0.9711 (mmp) cc_final: 0.9493 (mmm) REVERT: A 128 MET cc_start: 0.9349 (mtm) cc_final: 0.8918 (mtp) REVERT: A 164 TRP cc_start: 0.9579 (t-100) cc_final: 0.9338 (t-100) REVERT: A 174 PHE cc_start: 0.9564 (m-10) cc_final: 0.9329 (m-80) REVERT: A 181 LEU cc_start: 0.8434 (mm) cc_final: 0.8076 (mt) REVERT: A 235 PHE cc_start: 0.8540 (t80) cc_final: 0.7566 (t80) REVERT: A 399 PHE cc_start: 0.8938 (m-80) cc_final: 0.8432 (m-80) REVERT: A 400 VAL cc_start: 0.9728 (p) cc_final: 0.9528 (p) REVERT: A 410 MET cc_start: 0.9528 (tpt) cc_final: 0.9127 (tpp) REVERT: A 414 MET cc_start: 0.9124 (tmm) cc_final: 0.8761 (tmm) REVERT: A 470 MET cc_start: 0.9006 (ppp) cc_final: 0.8753 (ppp) REVERT: A 609 MET cc_start: 0.9248 (mmp) cc_final: 0.8731 (mmp) REVERT: A 646 MET cc_start: 0.9665 (mmp) cc_final: 0.9364 (mtp) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.1804 time to fit residues: 50.8256 Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9467 Z= 0.204 Angle : 0.868 12.701 12861 Z= 0.431 Chirality : 0.047 0.184 1519 Planarity : 0.005 0.048 1573 Dihedral : 6.420 43.294 1260 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.10 % Allowed : 2.40 % Favored : 97.50 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1177 helix: 1.03 (0.19), residues: 766 sheet: -2.09 (0.89), residues: 34 loop : -3.49 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 469 HIS 0.005 0.001 HIS A 451 PHE 0.051 0.002 PHE B 488 TYR 0.066 0.002 TYR B 589 ARG 0.003 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9305 (mtm) cc_final: 0.9055 (mtt) REVERT: B 143 LEU cc_start: 0.9367 (tp) cc_final: 0.9075 (pp) REVERT: B 174 PHE cc_start: 0.9608 (m-10) cc_final: 0.9385 (m-80) REVERT: B 191 ILE cc_start: 0.9728 (pt) cc_final: 0.9342 (pt) REVERT: B 246 LEU cc_start: 0.9329 (tp) cc_final: 0.9109 (tp) REVERT: B 250 MET cc_start: 0.8708 (mmp) cc_final: 0.8437 (mmm) REVERT: B 267 LEU cc_start: 0.9744 (mp) cc_final: 0.9526 (tp) REVERT: B 373 MET cc_start: 0.8941 (mmp) cc_final: 0.8605 (mtp) REVERT: B 374 LEU cc_start: 0.9189 (tp) cc_final: 0.8982 (mt) REVERT: B 399 PHE cc_start: 0.8982 (m-80) cc_final: 0.8535 (m-80) REVERT: B 410 MET cc_start: 0.9549 (tpt) cc_final: 0.9248 (tpp) REVERT: B 414 MET cc_start: 0.9307 (tmm) cc_final: 0.9051 (tmm) REVERT: B 470 MET cc_start: 0.8850 (ppp) cc_final: 0.8420 (tmm) REVERT: B 609 MET cc_start: 0.9030 (mmp) cc_final: 0.8541 (mmp) REVERT: B 646 MET cc_start: 0.9702 (mmp) cc_final: 0.9490 (mmm) REVERT: A 128 MET cc_start: 0.9359 (mtm) cc_final: 0.8960 (mtp) REVERT: A 164 TRP cc_start: 0.9610 (t-100) cc_final: 0.9372 (t-100) REVERT: A 174 PHE cc_start: 0.9550 (m-10) cc_final: 0.9309 (m-80) REVERT: A 181 LEU cc_start: 0.8444 (mm) cc_final: 0.8106 (mt) REVERT: A 399 PHE cc_start: 0.8841 (m-80) cc_final: 0.8377 (m-80) REVERT: A 410 MET cc_start: 0.9516 (tpt) cc_final: 0.9136 (tpp) REVERT: A 466 MET cc_start: 0.9356 (tpt) cc_final: 0.9140 (tpt) REVERT: A 559 MET cc_start: 0.9772 (ttt) cc_final: 0.9277 (ppp) REVERT: A 560 MET cc_start: 0.9695 (mtm) cc_final: 0.8787 (ptp) REVERT: A 609 MET cc_start: 0.9235 (mmp) cc_final: 0.8655 (mmp) REVERT: A 646 MET cc_start: 0.9660 (mmp) cc_final: 0.9360 (mtp) outliers start: 1 outliers final: 1 residues processed: 195 average time/residue: 0.1674 time to fit residues: 48.2395 Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.0050 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9467 Z= 0.214 Angle : 0.886 11.948 12861 Z= 0.439 Chirality : 0.047 0.180 1519 Planarity : 0.005 0.046 1573 Dihedral : 6.223 35.240 1260 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.53 (0.25), residues: 1177 helix: 1.06 (0.19), residues: 771 sheet: -2.27 (1.03), residues: 24 loop : -3.33 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 469 HIS 0.004 0.001 HIS A 451 PHE 0.052 0.002 PHE B 488 TYR 0.055 0.002 TYR B 589 ARG 0.005 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9360 (mtm) cc_final: 0.9097 (mtt) REVERT: B 143 LEU cc_start: 0.9335 (tp) cc_final: 0.9035 (pp) REVERT: B 174 PHE cc_start: 0.9602 (m-10) cc_final: 0.9371 (m-80) REVERT: B 246 LEU cc_start: 0.9303 (tp) cc_final: 0.9081 (tp) REVERT: B 250 MET cc_start: 0.8659 (mmp) cc_final: 0.8391 (mmm) REVERT: B 267 LEU cc_start: 0.9762 (mp) cc_final: 0.9546 (tp) REVERT: B 307 PHE cc_start: 0.9427 (t80) cc_final: 0.8383 (t80) REVERT: B 374 LEU cc_start: 0.9215 (tp) cc_final: 0.8992 (mt) REVERT: B 399 PHE cc_start: 0.8961 (m-80) cc_final: 0.8529 (m-80) REVERT: B 410 MET cc_start: 0.9538 (tpt) cc_final: 0.9213 (tpp) REVERT: B 414 MET cc_start: 0.9310 (tmm) cc_final: 0.9068 (tmm) REVERT: B 470 MET cc_start: 0.8857 (ppp) cc_final: 0.8469 (tmm) REVERT: B 609 MET cc_start: 0.9161 (mmp) cc_final: 0.8750 (mmp) REVERT: B 646 MET cc_start: 0.9694 (mmp) cc_final: 0.9482 (mmm) REVERT: B 868 LYS cc_start: 0.9636 (tmtt) cc_final: 0.9428 (tptp) REVERT: A 128 MET cc_start: 0.9314 (mtm) cc_final: 0.8920 (mtp) REVERT: A 164 TRP cc_start: 0.9575 (t-100) cc_final: 0.9357 (t-100) REVERT: A 174 PHE cc_start: 0.9543 (m-10) cc_final: 0.9298 (m-80) REVERT: A 181 LEU cc_start: 0.8485 (mm) cc_final: 0.8258 (mm) REVERT: A 339 MET cc_start: 0.8733 (ptp) cc_final: 0.8133 (ptp) REVERT: A 399 PHE cc_start: 0.8826 (m-80) cc_final: 0.8349 (m-80) REVERT: A 410 MET cc_start: 0.9475 (tpt) cc_final: 0.9068 (tpp) REVERT: A 414 MET cc_start: 0.8979 (tmm) cc_final: 0.8634 (tmm) REVERT: A 449 TRP cc_start: 0.8945 (m100) cc_final: 0.8669 (m100) REVERT: A 466 MET cc_start: 0.9375 (tpt) cc_final: 0.8990 (tpt) REVERT: A 470 MET cc_start: 0.8866 (ppp) cc_final: 0.8654 (ppp) REVERT: A 485 MET cc_start: 0.9394 (mmp) cc_final: 0.9182 (mmm) REVERT: A 559 MET cc_start: 0.9749 (ttt) cc_final: 0.9264 (ppp) REVERT: A 560 MET cc_start: 0.9641 (mtm) cc_final: 0.8791 (ptp) REVERT: A 609 MET cc_start: 0.8244 (mmp) cc_final: 0.7994 (mmp) REVERT: A 646 MET cc_start: 0.9671 (mmp) cc_final: 0.9359 (mtp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1637 time to fit residues: 47.9034 Evaluate side-chains 139 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.0170 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.0070 chunk 95 optimal weight: 0.0020 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 838 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9467 Z= 0.213 Angle : 0.899 11.489 12861 Z= 0.442 Chirality : 0.047 0.178 1519 Planarity : 0.005 0.076 1573 Dihedral : 6.087 33.364 1260 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1177 helix: 0.97 (0.19), residues: 771 sheet: -2.19 (1.05), residues: 24 loop : -3.25 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 469 HIS 0.008 0.001 HIS B 555 PHE 0.050 0.002 PHE B 488 TYR 0.050 0.002 TYR B 589 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9393 (mtm) cc_final: 0.9039 (mtp) REVERT: B 135 MET cc_start: 0.9539 (ptp) cc_final: 0.9269 (ppp) REVERT: B 143 LEU cc_start: 0.9269 (tp) cc_final: 0.9018 (pp) REVERT: B 174 PHE cc_start: 0.9589 (m-10) cc_final: 0.9364 (m-80) REVERT: B 194 MET cc_start: 0.9228 (ptp) cc_final: 0.9026 (ptp) REVERT: B 246 LEU cc_start: 0.9292 (tp) cc_final: 0.9072 (tp) REVERT: B 250 MET cc_start: 0.8640 (mmp) cc_final: 0.8378 (mmm) REVERT: B 399 PHE cc_start: 0.8936 (m-80) cc_final: 0.8543 (m-80) REVERT: B 410 MET cc_start: 0.9518 (tpt) cc_final: 0.9208 (tpp) REVERT: B 414 MET cc_start: 0.9215 (tmm) cc_final: 0.8891 (tmm) REVERT: B 435 LYS cc_start: 0.9802 (mmmt) cc_final: 0.9413 (tmmt) REVERT: B 470 MET cc_start: 0.8854 (ppp) cc_final: 0.8476 (tmm) REVERT: B 609 MET cc_start: 0.9115 (mmp) cc_final: 0.8687 (mmp) REVERT: B 646 MET cc_start: 0.9685 (mmp) cc_final: 0.9469 (mmm) REVERT: A 128 MET cc_start: 0.9354 (mtm) cc_final: 0.8934 (mtp) REVERT: A 174 PHE cc_start: 0.9532 (m-10) cc_final: 0.9275 (m-80) REVERT: A 181 LEU cc_start: 0.8470 (mm) cc_final: 0.8241 (mm) REVERT: A 319 LEU cc_start: 0.9672 (tp) cc_final: 0.9384 (tt) REVERT: A 339 MET cc_start: 0.8742 (ptp) cc_final: 0.8049 (ptp) REVERT: A 399 PHE cc_start: 0.8785 (m-80) cc_final: 0.8309 (m-80) REVERT: A 410 MET cc_start: 0.9449 (tpt) cc_final: 0.9030 (tpp) REVERT: A 414 MET cc_start: 0.8859 (tmm) cc_final: 0.8562 (tmm) REVERT: A 449 TRP cc_start: 0.8918 (m100) cc_final: 0.8665 (m100) REVERT: A 466 MET cc_start: 0.9361 (tpt) cc_final: 0.8976 (tpt) REVERT: A 485 MET cc_start: 0.9426 (mmp) cc_final: 0.9184 (mmt) REVERT: A 559 MET cc_start: 0.9724 (ttt) cc_final: 0.9276 (ppp) REVERT: A 560 MET cc_start: 0.9640 (mtm) cc_final: 0.8834 (ptp) REVERT: A 609 MET cc_start: 0.8447 (mmp) cc_final: 0.8168 (mmp) REVERT: A 646 MET cc_start: 0.9662 (mmp) cc_final: 0.9348 (mtp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1642 time to fit residues: 48.1660 Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 108 optimal weight: 0.0170 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS ** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9467 Z= 0.235 Angle : 0.878 11.161 12861 Z= 0.440 Chirality : 0.047 0.177 1519 Planarity : 0.005 0.061 1573 Dihedral : 6.036 31.198 1260 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1177 helix: 1.07 (0.19), residues: 769 sheet: -2.28 (1.02), residues: 24 loop : -3.17 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 469 HIS 0.012 0.001 HIS B 555 PHE 0.053 0.002 PHE B 488 TYR 0.048 0.002 TYR B 589 ARG 0.003 0.000 ARG B 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9462 (mtm) cc_final: 0.9151 (mtp) REVERT: B 135 MET cc_start: 0.9552 (ptp) cc_final: 0.9285 (ppp) REVERT: B 136 ASP cc_start: 0.8892 (p0) cc_final: 0.8642 (p0) REVERT: B 143 LEU cc_start: 0.9280 (tp) cc_final: 0.9032 (pp) REVERT: B 174 PHE cc_start: 0.9597 (m-10) cc_final: 0.9375 (m-80) REVERT: B 181 LEU cc_start: 0.8705 (mm) cc_final: 0.8350 (mt) REVERT: B 246 LEU cc_start: 0.9335 (tp) cc_final: 0.9121 (tp) REVERT: B 250 MET cc_start: 0.8610 (mmp) cc_final: 0.8326 (mmm) REVERT: B 307 PHE cc_start: 0.9455 (t80) cc_final: 0.9170 (t80) REVERT: B 399 PHE cc_start: 0.8921 (m-80) cc_final: 0.8532 (m-80) REVERT: B 410 MET cc_start: 0.9533 (tpt) cc_final: 0.9295 (tpp) REVERT: B 414 MET cc_start: 0.9214 (tmm) cc_final: 0.9003 (tmm) REVERT: B 470 MET cc_start: 0.8871 (ppp) cc_final: 0.8487 (tmm) REVERT: B 559 MET cc_start: 0.9765 (ttt) cc_final: 0.9275 (ppp) REVERT: B 560 MET cc_start: 0.9399 (mpp) cc_final: 0.8246 (mpp) REVERT: B 609 MET cc_start: 0.9109 (mmp) cc_final: 0.8688 (mmp) REVERT: B 646 MET cc_start: 0.9697 (mmp) cc_final: 0.9488 (mmm) REVERT: A 128 MET cc_start: 0.9369 (mtm) cc_final: 0.9075 (mtp) REVERT: A 136 ASP cc_start: 0.8845 (p0) cc_final: 0.8513 (p0) REVERT: A 164 TRP cc_start: 0.9574 (t-100) cc_final: 0.9325 (t-100) REVERT: A 174 PHE cc_start: 0.9530 (m-10) cc_final: 0.9283 (m-80) REVERT: A 181 LEU cc_start: 0.8375 (mm) cc_final: 0.8129 (mm) REVERT: A 191 ILE cc_start: 0.9761 (pt) cc_final: 0.9424 (mm) REVERT: A 311 PHE cc_start: 0.8763 (m-80) cc_final: 0.8319 (m-80) REVERT: A 399 PHE cc_start: 0.8782 (m-80) cc_final: 0.8306 (m-80) REVERT: A 410 MET cc_start: 0.9483 (tpt) cc_final: 0.9110 (tpp) REVERT: A 466 MET cc_start: 0.9399 (tpt) cc_final: 0.8969 (tpt) REVERT: A 470 MET cc_start: 0.8849 (ppp) cc_final: 0.8641 (ppp) REVERT: A 559 MET cc_start: 0.9754 (ttt) cc_final: 0.9327 (ppp) REVERT: A 560 MET cc_start: 0.9648 (mtm) cc_final: 0.8848 (ptp) REVERT: A 609 MET cc_start: 0.8416 (mmp) cc_final: 0.8138 (mmp) REVERT: A 646 MET cc_start: 0.9667 (mmp) cc_final: 0.9422 (mmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1610 time to fit residues: 44.6388 Evaluate side-chains 140 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 6.9990 chunk 86 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050957 restraints weight = 56555.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052458 restraints weight = 37657.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053364 restraints weight = 27429.052| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9467 Z= 0.208 Angle : 0.881 11.375 12861 Z= 0.431 Chirality : 0.047 0.179 1519 Planarity : 0.005 0.056 1573 Dihedral : 5.912 30.043 1260 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.07 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.39 (0.25), residues: 1177 helix: 1.11 (0.19), residues: 760 sheet: -1.88 (1.09), residues: 24 loop : -3.03 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 469 HIS 0.010 0.001 HIS B 555 PHE 0.055 0.002 PHE B 488 TYR 0.045 0.002 TYR B 589 ARG 0.003 0.000 ARG B 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.23 seconds wall clock time: 37 minutes 9.83 seconds (2229.83 seconds total)