Starting phenix.real_space_refine (version: dev) on Sun Feb 26 03:34:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/02_2023/7tdf_25827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/02_2023/7tdf_25827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/02_2023/7tdf_25827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/02_2023/7tdf_25827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/02_2023/7tdf_25827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/02_2023/7tdf_25827.pdb" } resolution = 2.7 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7502 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19566 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 9783 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 577} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 9783 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 577} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 9.09, per 1000 atoms: 0.46 Number of scatterers: 19566 At special positions: 0 Unit cell: (111.055, 86.005, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1708 8.00 N 1502 7.00 C 6520 6.00 H 9792 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 101 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 83.8% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.826A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.752A pdb=" N GLU A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.688A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 150 through 172 removed outlier: 3.891A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.567A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 3.579A pdb=" N GLY A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.535A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.365A pdb=" N PHE A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.671A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.000A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 452 removed outlier: 4.200A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 487 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.795A pdb=" N PHE A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.687A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.743A pdb=" N ALA A 553 " --> pdb=" O GLN A 549 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.676A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 4.211A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 686 Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.667A pdb=" N ARG B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.798A pdb=" N GLU B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.589A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 150 through 172 removed outlier: 3.937A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.540A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 238 removed outlier: 3.532A pdb=" N MET B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLY B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.540A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.721A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 335 Processing helix chain 'B' and resid 343 through 356 Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.669A pdb=" N ILE B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 removed outlier: 4.089A pdb=" N TYR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 487 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.697A pdb=" N PHE B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.503A pdb=" N LEU B 533 " --> pdb=" O TRP B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 548 through 565 removed outlier: 4.639A pdb=" N ALA B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE B 554 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 565 through 588 Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.718A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 4.187A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 686 Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 673 hydrogen bonds defined for protein. 1965 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: 7.92 Time building geometry restraints manager: 16.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9780 1.03 - 1.23: 62 1.23 - 1.42: 4316 1.42 - 1.62: 5592 1.62 - 1.82: 72 Bond restraints: 19822 Sorted by residual: bond pdb=" N GLY B 527 " pdb=" CA GLY B 527 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.31e+00 bond pdb=" N GLY A 527 " pdb=" CA GLY A 527 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.12e+00 bond pdb=" CB PRO A 99 " pdb=" CG PRO A 99 " ideal model delta sigma weight residual 1.506 1.427 0.079 3.90e-02 6.57e+02 4.15e+00 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.506 1.434 0.072 3.90e-02 6.57e+02 3.41e+00 bond pdb=" N TRP A 464 " pdb=" CA TRP A 464 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 ... (remaining 19817 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.27: 786 107.27 - 113.97: 22351 113.97 - 120.68: 7919 120.68 - 127.39: 4588 127.39 - 134.09: 100 Bond angle restraints: 35744 Sorted by residual: angle pdb=" N ASN B 96 " pdb=" CA ASN B 96 " pdb=" C ASN B 96 " ideal model delta sigma weight residual 109.81 116.25 -6.44 2.21e+00 2.05e-01 8.50e+00 angle pdb=" N VAL B 586 " pdb=" CA VAL B 586 " pdb=" C VAL B 586 " ideal model delta sigma weight residual 109.34 115.12 -5.78 2.08e+00 2.31e-01 7.71e+00 angle pdb=" CA TYR B 123 " pdb=" CB TYR B 123 " pdb=" CG TYR B 123 " ideal model delta sigma weight residual 113.90 118.80 -4.90 1.80e+00 3.09e-01 7.41e+00 angle pdb=" N ASN A 96 " pdb=" CA ASN A 96 " pdb=" C ASN A 96 " ideal model delta sigma weight residual 109.81 115.57 -5.76 2.21e+00 2.05e-01 6.80e+00 angle pdb=" CA TYR A 123 " pdb=" CB TYR A 123 " pdb=" CG TYR A 123 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 ... (remaining 35739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7445 17.99 - 35.98: 405 35.98 - 53.98: 90 53.98 - 71.97: 118 71.97 - 89.96: 6 Dihedral angle restraints: 8064 sinusoidal: 3580 harmonic: 4484 Sorted by residual: dihedral pdb=" CA GLU A 600 " pdb=" C GLU A 600 " pdb=" N THR A 601 " pdb=" CA THR A 601 " ideal model delta harmonic sigma weight residual -180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLN A 400 " pdb=" C GLN A 400 " pdb=" N LYS A 401 " pdb=" CA LYS A 401 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ARG A 20 " pdb=" C ARG A 20 " pdb=" N ARG A 21 " pdb=" CA ARG A 21 " ideal model delta harmonic sigma weight residual -180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 8061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 861 0.035 - 0.069: 524 0.069 - 0.104: 125 0.104 - 0.139: 28 0.139 - 0.173: 14 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CA PRO A 563 " pdb=" N PRO A 563 " pdb=" C PRO A 563 " pdb=" CB PRO A 563 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA ARG B 358 " pdb=" N ARG B 358 " pdb=" C ARG B 358 " pdb=" CB ARG B 358 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA PRO A 138 " pdb=" N PRO A 138 " pdb=" C PRO A 138 " pdb=" CB PRO A 138 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1549 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 400 " 0.029 2.00e-02 2.50e+03 3.73e-02 2.09e+01 pdb=" CD GLN A 400 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 400 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 400 " -0.061 2.00e-02 2.50e+03 pdb="HE21 GLN A 400 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 400 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 353 " -0.025 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" CD GLN A 353 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN A 353 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN A 353 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN A 353 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 353 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 618 " 0.029 2.00e-02 2.50e+03 3.46e-02 1.79e+01 pdb=" CG ASN B 618 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 618 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN B 618 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN B 618 " 0.052 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 757 2.17 - 2.77: 37991 2.77 - 3.38: 55461 3.38 - 3.99: 69546 3.99 - 4.60: 109924 Nonbonded interactions: 273679 Sorted by model distance: nonbonded pdb=" HG1 THR B 452 " pdb=" OD1 ASN B 454 " model vdw 1.556 1.850 nonbonded pdb=" O GLN B 54 " pdb=" HG SER B 55 " model vdw 1.568 1.850 nonbonded pdb=" HG1 THR A 452 " pdb=" OD1 ASN A 454 " model vdw 1.569 1.850 nonbonded pdb="HH11 ARG B 104 " pdb=" O GLY B 110 " model vdw 1.574 1.850 nonbonded pdb="HH11 ARG A 104 " pdb=" O GLY A 110 " model vdw 1.583 1.850 ... (remaining 273674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 6520 2.51 5 N 1502 2.21 5 O 1708 1.98 5 H 9792 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.300 Extract box with map and model: 12.860 Check model and map are aligned: 0.270 Process input model: 63.240 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 10030 Z= 0.388 Angle : 0.735 6.444 13634 Z= 0.454 Chirality : 0.046 0.173 1552 Planarity : 0.008 0.131 1666 Dihedral : 12.557 89.961 3514 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.06 (0.24), residues: 1164 helix: -0.11 (0.16), residues: 864 sheet: None (None), residues: 0 loop : 1.07 (0.43), residues: 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 1.662 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 outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 2.8516 time to fit residues: 797.3574 Evaluate side-chains 225 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.8697 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 10030 Z= 0.308 Angle : 0.596 6.221 13634 Z= 0.321 Chirality : 0.039 0.140 1552 Planarity : 0.004 0.043 1666 Dihedral : 4.781 28.683 1290 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.44 (0.25), residues: 1164 helix: 1.05 (0.17), residues: 882 sheet: None (None), residues: 0 loop : 1.03 (0.43), residues: 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 224 average time/residue: 2.9764 time to fit residues: 711.0839 Evaluate side-chains 214 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 1.0632 time to fit residues: 6.9498 ------------------------------------------------------------------------------- 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: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 10030 Z= 0.355 Angle : 0.573 6.043 13634 Z= 0.311 Chirality : 0.040 0.142 1552 Planarity : 0.005 0.079 1666 Dihedral : 4.634 27.482 1290 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.67 (0.25), residues: 1164 helix: 1.30 (0.17), residues: 882 sheet: None (None), residues: 0 loop : 0.79 (0.44), residues: 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 225 average time/residue: 2.9866 time to fit residues: 715.0040 Evaluate side-chains 206 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 3.9709 time to fit residues: 6.1607 ------------------------------------------------------------------------------- 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: 0.4980 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7721 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10030 Z= 0.275 Angle : 0.538 5.998 13634 Z= 0.291 Chirality : 0.037 0.131 1552 Planarity : 0.004 0.056 1666 Dihedral : 4.427 25.837 1290 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.97 (0.26), residues: 1164 helix: 1.55 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.77 (0.45), residues: 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 202 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 213 average time/residue: 3.0112 time to fit residues: 682.8296 Evaluate side-chains 207 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.2560 time to fit residues: 5.0073 ------------------------------------------------------------------------------- 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: 0.1980 chunk 1 optimal weight: 0.0980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10030 Z= 0.185 Angle : 0.503 5.928 13634 Z= 0.272 Chirality : 0.035 0.180 1552 Planarity : 0.004 0.054 1666 Dihedral : 4.185 24.243 1290 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.31 (0.26), residues: 1164 helix: 1.82 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.79 (0.45), residues: 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 219 average time/residue: 2.9282 time to fit residues: 684.9519 Evaluate side-chains 209 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 202 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.8811 ------------------------------------------------------------------------------- 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: 5.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 10030 Z= 0.328 Angle : 0.545 5.646 13634 Z= 0.296 Chirality : 0.038 0.143 1552 Planarity : 0.004 0.047 1666 Dihedral : 4.289 24.783 1290 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.12 (0.26), residues: 1164 helix: 1.73 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.57 (0.44), residues: 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 215 average time/residue: 2.9580 time to fit residues: 677.4400 Evaluate side-chains 205 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 196 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.2905 time to fit residues: 2.5284 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 10030 Z= 0.206 Angle : 0.509 5.647 13634 Z= 0.274 Chirality : 0.035 0.124 1552 Planarity : 0.004 0.063 1666 Dihedral : 4.135 23.912 1290 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.35 (0.26), residues: 1164 helix: 1.90 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.60 (0.44), residues: 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 215 average time/residue: 2.9341 time to fit residues: 672.8166 Evaluate side-chains 215 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.2433 time to fit residues: 3.4974 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 ASN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 10030 Z= 0.307 Angle : 0.543 5.607 13634 Z= 0.293 Chirality : 0.038 0.139 1552 Planarity : 0.004 0.061 1666 Dihedral : 4.202 24.302 1290 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.19 (0.26), residues: 1164 helix: 1.82 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.45 (0.44), residues: 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 209 average time/residue: 2.9474 time to fit residues: 656.2279 Evaluate side-chains 205 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.1096 ------------------------------------------------------------------------------- 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: 0.8980 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 83 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 10030 Z= 0.214 Angle : 0.514 5.768 13634 Z= 0.277 Chirality : 0.035 0.126 1552 Planarity : 0.005 0.085 1666 Dihedral : 4.105 23.726 1290 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.37 (0.26), residues: 1164 helix: 1.95 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.51 (0.44), residues: 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 215 average time/residue: 2.8500 time to fit residues: 655.7302 Evaluate side-chains 217 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.2634 time to fit residues: 2.9371 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 ASN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 10030 Z= 0.361 Angle : 0.563 5.708 13634 Z= 0.304 Chirality : 0.040 0.220 1552 Planarity : 0.005 0.086 1666 Dihedral : 4.243 24.817 1290 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.12 (0.25), residues: 1164 helix: 1.77 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.38 (0.44), residues: 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 215 average time/residue: 2.8622 time to fit residues: 657.3699 Evaluate side-chains 209 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 202 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.8212 ------------------------------------------------------------------------------- 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: 0.9990 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 82 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118379 restraints weight = 35357.728| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.69 r_work: 0.3342 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10030 Z= 0.222 Angle : 0.525 5.910 13634 Z= 0.282 Chirality : 0.035 0.129 1552 Planarity : 0.005 0.088 1666 Dihedral : 4.127 24.456 1290 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.22 (0.26), residues: 1164 helix: 1.87 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.25 (0.45), residues: 266 =============================================================================== Job complete usr+sys time: 10290.44 seconds wall clock time: 180 minutes 24.85 seconds (10824.85 seconds total)