Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 12:50:05 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/01_2021/6kkr_0701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/01_2021/6kkr_0701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/01_2021/6kkr_0701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/01_2021/6kkr_0701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/01_2021/6kkr_0701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkr_0701/01_2021/6kkr_0701_updated.pdb" } resolution = 2.9 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= 0.006 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 8416 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 140 Unusual residues: {'BGC': 2, 'NAG': 4, ' CL': 2, ' K': 1, 'GLC': 2, 'DU0': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 140 Unusual residues: {'BGC': 2, 'NAG': 4, ' CL': 2, ' K': 1, 'GLC': 2, 'DU0': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.98, per 1000 atoms: 0.59 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 116 through 652 or resid 1101 through 1107 or resid 1111 t \ hrough 1112)) selection = (chain 'B' and (resid 116 through 652 or resid 1101 through 1107 or resid 1111 t \ hrough 1112)) } Number of scatterers: 8416 At special positions: 0 Unit cell: (77.064, 100.386, 102.414, 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 2 19.00 Cl 4 17.00 S 68 16.00 O 1514 8.00 N 1284 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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=4, symmetry=0 Links applied ALPHA1-4 " BGC A1109 " - " GLC A1110 " " BGC A1111 " - " GLC A1112 " " BGC B1108 " - " GLC B1109 " " BGC B1111 " - " GLC B1112 " BETA1-4 " NAG A1101 " - " NAG A1102 " " NAG A1103 " - " NAG A1104 " " NAG B1101 " - " NAG B1102 " " NAG B1103 " - " NAG B1104 " NAG-ASN " NAG A1102 " - " ASN A 312 " " NAG A1104 " - " ASN A 361 " " NAG B1102 " - " ASN B 312 " " NAG B1104 " - " ASN B 361 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 4 sheets defined 62.8% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... 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 125 through 132 Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 141 through 175 removed outlier: 7.052A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 195 through 226 removed outlier: 3.694A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 removed outlier: 3.713A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 279 through 300 removed outlier: 3.661A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.842A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.602A pdb=" N GLU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.679A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Proline residue: A 429 - end of helix Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 447 through 476 removed outlier: 3.640A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.593A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 505 through 535 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 540 through 546 removed outlier: 5.316A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.577A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 601 Proline residue: A 579 - end of helix removed outlier: 3.893A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 633 removed outlier: 3.691A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 651 removed outlier: 3.533A pdb=" N LEU A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 141 through 175 removed outlier: 7.052A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 195 through 226 removed outlier: 3.694A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 268 removed outlier: 3.713A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 279 through 300 removed outlier: 3.661A pdb=" N VAL B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.842A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.602A pdb=" N GLU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 420 through 430 removed outlier: 3.679A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Proline residue: B 429 - end of helix Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 447 through 476 removed outlier: 3.640A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.593A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 505 through 535 Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 540 through 546 removed outlier: 5.316A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.577A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 601 Proline residue: B 579 - end of helix removed outlier: 3.893A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 633 removed outlier: 3.691A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 651 removed outlier: 3.533A pdb=" N LEU B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 650 " --> pdb=" O GLY B 646 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 306 through 310 Processing sheet with id= B, first strand: chain 'A' and resid 326 through 329 Processing sheet with id= C, first strand: chain 'B' and resid 306 through 310 Processing sheet with id= D, first strand: chain 'B' and resid 326 through 329 418 hydrogen bonds defined for protein. 1230 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: 2.55 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2474 1.35 - 1.47: 2320 1.47 - 1.60: 3728 1.60 - 1.73: 0 1.73 - 1.85: 104 Bond restraints: 8626 Sorted by residual: bond pdb=" C3 BGC A1111 " pdb=" C4 BGC A1111 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.30e-02 5.92e+03 2.34e+01 bond pdb=" C3 BGC B1108 " pdb=" C4 BGC B1108 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.30e-02 5.92e+03 2.34e+01 bond pdb=" C5 GLC B1109 " pdb=" O5 GLC B1109 " ideal model delta sigma weight residual 1.410 1.503 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C5 GLC A1112 " pdb=" O5 GLC A1112 " ideal model delta sigma weight residual 1.410 1.503 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C4 BGC B1108 " pdb=" O4 BGC B1108 " ideal model delta sigma weight residual 1.423 1.466 -0.043 1.00e-02 1.00e+04 1.86e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.64: 154 103.64 - 111.32: 3566 111.32 - 119.00: 3553 119.00 - 126.68: 4397 126.68 - 134.36: 124 Bond angle restraints: 11794 Sorted by residual: angle pdb=" N VAL B 431 " pdb=" CA VAL B 431 " pdb=" C VAL B 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" C PRO B 230 " pdb=" N PRO B 231 " pdb=" CA PRO B 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C PRO A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C ILE A 571 " pdb=" N ALA A 572 " pdb=" CA ALA A 572 " ideal model delta sigma weight residual 122.40 128.23 -5.83 1.45e+00 4.76e-01 1.62e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.98: 4907 31.98 - 63.95: 47 63.95 - 95.93: 2 95.93 - 127.90: 2 127.90 - 159.88: 2 Dihedral angle restraints: 4960 sinusoidal: 1878 harmonic: 3082 Sorted by residual: dihedral pdb=" C26 DU0 A1108 " pdb=" C24 DU0 A1108 " pdb=" C25 DU0 A1108 " pdb=" O23 DU0 A1108 " ideal model delta sinusoidal sigma weight residual 178.12 18.24 159.88 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C26 DU0 B1110 " pdb=" C24 DU0 B1110 " pdb=" C25 DU0 B1110 " pdb=" O23 DU0 B1110 " ideal model delta sinusoidal sigma weight residual 178.12 18.24 159.88 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA VAL A 490 " pdb=" C VAL A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1264 0.083 - 0.167: 184 0.167 - 0.250: 14 0.250 - 0.333: 2 0.333 - 0.417: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG B1102 " pdb=" ND2 ASN B 312 " pdb=" C2 NAG B1102 " pdb=" O5 NAG B1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C1 NAG A1102 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG A1102 " pdb=" O5 NAG A1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C1 GLC B1109 " pdb=" O4 BGC B1108 " pdb=" C2 GLC B1109 " pdb=" O5 GLC B1109 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 1.68e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO B 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 473 " 0.011 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE A 473 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 473 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 473 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 473 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 473 " -0.000 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.35 - 3.18: 6948 3.18 - 4.01: 20407 4.01 - 4.84: 35506 4.84 - 5.67: 51476 5.67 - 6.50: 61037 Nonbonded interactions: 175374 Sorted by model distance: nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.348 2.440 nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.348 2.440 nonbonded pdb=" O2 GLC A1112 " pdb=" O4 GLC A1112 " model vdw 2.383 2.440 nonbonded pdb=" O2 GLC B1109 " pdb=" O4 GLC B1109 " model vdw 2.383 2.440 nonbonded pdb=" O GLU B 222 " pdb=" OG1 THR B 226 " model vdw 2.383 2.440 ... (remaining 175369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 8298 8416 True True 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 2 8.98 5 S 68 5.16 5 Cl 4 4.86 5 C 5544 2.51 5 N 1284 2.21 5 O 1514 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 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: 0.450 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.010 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.040 Process input model: 31.890 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.520 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.093 8626 Angle : 1.105 10.401 11794 Chirality : 0.060 0.417 1466 Planarity : 0.007 0.063 1404 Dihedral : 10.855 159.879 2974 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.23 % 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: -3.53 (0.20), residues: 1070 helix: -2.09 (0.16), residues: 632 sheet: None (None), residues: 0 loop : -2.58 (0.25), residues: 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.885 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 67 average time/residue: 0.9197 time to fit residues: 63.2285 Evaluate side-chains 54 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.0870 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0105 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.036 8626 Angle : 0.563 6.926 11794 Chirality : 0.042 0.330 1466 Planarity : 0.005 0.070 1404 Dihedral : 8.991 125.572 1242 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.11 % 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: -1.30 (0.24), residues: 1070 helix: -0.14 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -1.98 (0.27), residues: 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.852 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 1.0331 time to fit residues: 61.4151 Evaluate side-chains 52 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 40.0000 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 0.0050 chunk 32 optimal weight: 0.0170 chunk 77 optimal weight: 6.9990 overall best weight: 0.6234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN B 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0302 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.036 8626 Angle : 0.561 6.893 11794 Chirality : 0.041 0.281 1466 Planarity : 0.004 0.093 1404 Dihedral : 8.615 118.624 1242 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.23 % 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 (0.25), residues: 1070 helix: 0.81 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.54 (0.29), residues: 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.831 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 1.0097 time to fit residues: 64.1718 Evaluate side-chains 53 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0770 chunk 72 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 0.0270 chunk 27 optimal weight: 0.0570 chunk 85 optimal weight: 6.9990 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0290 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.036 8626 Angle : 0.514 6.032 11794 Chirality : 0.040 0.222 1466 Planarity : 0.003 0.032 1404 Dihedral : 7.951 109.040 1242 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.11 % 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: 0.57 (0.26), residues: 1070 helix: 1.44 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.32 (0.30), residues: 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.859 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.1109 time to fit residues: 69.3396 Evaluate side-chains 52 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0796 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.053 8626 Angle : 0.718 9.902 11794 Chirality : 0.046 0.227 1466 Planarity : 0.005 0.092 1404 Dihedral : 8.031 107.425 1242 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.00 % 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 (0.25), residues: 1070 helix: 1.18 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -1.44 (0.27), residues: 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.807 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.0848 time to fit residues: 61.1624 Evaluate side-chains 50 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 439 ASN A 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0901 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.039 8626 Angle : 0.691 9.286 11794 Chirality : 0.045 0.192 1466 Planarity : 0.004 0.034 1404 Dihedral : 7.864 100.060 1242 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.00 % 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: 0.15 (0.25), residues: 1070 helix: 1.20 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -1.48 (0.27), residues: 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.954 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.0398 time to fit residues: 60.8223 Evaluate side-chains 54 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0813 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.034 8626 Angle : 0.586 6.884 11794 Chirality : 0.041 0.163 1466 Planarity : 0.004 0.052 1404 Dihedral : 7.382 98.772 1242 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.00 % 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: 0.67 (0.26), residues: 1070 helix: 1.70 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.888 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.1177 time to fit residues: 66.4894 Evaluate side-chains 55 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0904 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.084 8626 Angle : 0.620 8.287 11794 Chirality : 0.041 0.148 1466 Planarity : 0.005 0.125 1404 Dihedral : 7.056 86.926 1242 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.00 % 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: 0.77 (0.26), residues: 1070 helix: 1.80 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.888 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 1.1178 time to fit residues: 72.0159 Evaluate side-chains 58 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0874 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.037 8626 Angle : 0.591 7.778 11794 Chirality : 0.041 0.225 1466 Planarity : 0.004 0.052 1404 Dihedral : 6.274 79.396 1242 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.00 % 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: 0.95 (0.26), residues: 1070 helix: 1.88 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.29 (0.29), residues: 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.920 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 1.0830 time to fit residues: 67.6452 Evaluate side-chains 59 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 89 optimal weight: 0.0770 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0790 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.079 8626 Angle : 0.544 7.652 11794 Chirality : 0.040 0.206 1466 Planarity : 0.005 0.116 1404 Dihedral : 5.461 52.906 1242 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.00 % 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: 1.28 (0.27), residues: 1070 helix: 2.14 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 438 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield and 0 Emsley and 1070 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 1.1331 time to fit residues: 68.4755 Evaluate side-chains 55 residues out of total 882 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 0.0870 chunk 23 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.340382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.332367 restraints weight = 10979.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.335442 restraints weight = 5739.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5247 r_free = 0.5247 target = 0.337254 restraints weight = 3267.659| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.034 8626 ANGLE : 0.563 7.635 11794 CHIRALITY : 0.041 0.182 1466 PLANARITY : 0.004 0.045 1404 DIHEDRAL : 5.458 49.817 1242 MIN NONBONDED DISTANCE : 2.160 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 8.87 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 3.27 % FAVORED : 96.73 % ROTAMER OUTLIERS : 0.00 % 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: 1.24 (0.27), RESIDUES: 1070 HELIX: 2.14 (0.21), RESIDUES: 630 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -1.22 (0.29), RESIDUES: 440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0900 moved from start: 0.6488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.034 8626 Angle : 0.563 7.635 11794 Chirality : 0.041 0.182 1466 Planarity : 0.004 0.045 1404 Dihedral : 5.458 49.817 1242 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.00 % 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: 1.24 (0.27), residues: 1070 helix: 2.14 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 440 =============================================================================== Job complete usr+sys time: 2138.72 seconds wall clock time: 39 minutes 28.66 seconds (2368.66 seconds total)