Starting phenix.real_space_refine on Fri Aug 9 09:33:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/08_2024/7tdf_25827.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/08_2024/7tdf_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_25827/08_2024/7tdf_25827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/08_2024/7tdf_25827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/08_2024/7tdf_25827.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdf_25827/08_2024/7tdf_25827.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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-5409/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: 9.41, per 1000 atoms: 0.48 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: 14.47 Conformation dependent library (CDL) restraints added in 1.9 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: 1.60 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: 7.72 Time building geometry restraints manager: 15.26 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: 8572 17.99 - 35.98: 460 35.98 - 53.98: 144 53.98 - 71.97: 142 71.97 - 89.96: 6 Dihedral angle restraints: 9324 sinusoidal: 4840 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 9321 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 2.450 nonbonded pdb=" O GLN B 54 " pdb=" HG SER B 55 " model vdw 1.568 2.450 nonbonded pdb=" HG1 THR A 452 " pdb=" OD1 ASN A 454 " model vdw 1.569 2.450 nonbonded pdb="HH11 ARG B 104 " pdb=" O GLY B 110 " model vdw 1.574 2.450 nonbonded pdb="HH11 ARG A 104 " pdb=" O GLY A 110 " model vdw 1.583 2.450 ... (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 Time spend for trying shortcut: 0.00 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 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.290 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 62.590 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 % Allowed : 5.29 % Favored : 94.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 271 HIS 0.003 0.001 HIS B 27 PHE 0.016 0.003 PHE B 57 TYR 0.025 0.005 TYR A 532 ARG 0.016 0.003 ARG B 279 *********************** 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 : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7863 (t0) cc_final: 0.7452 (t0) REVERT: A 208 LEU cc_start: 0.8415 (tt) cc_final: 0.8192 (tp) REVERT: A 490 ASN cc_start: 0.8097 (t0) cc_final: 0.7777 (t0) REVERT: A 538 MET cc_start: 0.6634 (tmt) cc_final: 0.6314 (tmt) REVERT: B 324 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7224 (mtp85) REVERT: B 538 MET cc_start: 0.6887 (tmt) cc_final: 0.6379 (tmt) outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 2.8247 time to fit residues: 790.6924 Evaluate side-chains 226 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE 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: 0.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7490 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10030 Z= 0.279 Angle : 0.600 6.459 13634 Z= 0.326 Chirality : 0.039 0.135 1552 Planarity : 0.004 0.044 1666 Dihedral : 4.825 28.087 1292 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.32 % Allowed : 11.81 % Favored : 86.86 % 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: 1.40 (0.25), residues: 1164 helix: 1.02 (0.17), residues: 882 sheet: None (None), residues: 0 loop : 1.02 (0.43), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 223 HIS 0.002 0.001 HIS B 27 PHE 0.015 0.002 PHE A 599 TYR 0.016 0.002 TYR A 568 ARG 0.010 0.001 ARG B 325 *********************** 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 238 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 224 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7976 (t0) cc_final: 0.7630 (t0) REVERT: A 490 ASN cc_start: 0.8091 (t0) cc_final: 0.7720 (t0) REVERT: A 531 ARG cc_start: 0.6737 (ttm-80) cc_final: 0.6464 (ttm-80) REVERT: A 538 MET cc_start: 0.6597 (tmt) cc_final: 0.6312 (tmt) REVERT: B 39 ASP cc_start: 0.6986 (t0) cc_final: 0.6765 (t70) REVERT: B 66 ILE cc_start: 0.8261 (pt) cc_final: 0.7689 (mt) REVERT: B 69 ARG cc_start: 0.7201 (ttm170) cc_final: 0.6999 (mtm110) REVERT: B 538 MET cc_start: 0.6859 (tmt) cc_final: 0.6337 (tmt) outliers start: 14 outliers final: 6 residues processed: 230 average time/residue: 2.5500 time to fit residues: 627.4134 Evaluate side-chains 211 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 605 GLU 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: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10030 Z= 0.299 Angle : 0.556 6.152 13634 Z= 0.303 Chirality : 0.038 0.136 1552 Planarity : 0.004 0.059 1666 Dihedral : 4.581 27.014 1292 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.61 % Allowed : 13.61 % Favored : 84.78 % 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: 1.78 (0.25), residues: 1164 helix: 1.38 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.82 (0.44), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 223 HIS 0.003 0.001 HIS B 27 PHE 0.021 0.002 PHE B 399 TYR 0.017 0.002 TYR A 568 ARG 0.004 0.000 ARG B 325 *********************** 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 225 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8032 (t0) cc_final: 0.7658 (t0) REVERT: A 323 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7646 (ttpp) REVERT: A 490 ASN cc_start: 0.8092 (t0) cc_final: 0.7727 (t0) REVERT: A 531 ARG cc_start: 0.6800 (ttm-80) cc_final: 0.6516 (ttm-80) REVERT: A 538 MET cc_start: 0.6620 (tmt) cc_final: 0.6334 (tmt) REVERT: B 39 ASP cc_start: 0.7024 (t0) cc_final: 0.6795 (t70) REVERT: B 65 PHE cc_start: 0.7744 (m-80) cc_final: 0.7507 (m-80) REVERT: B 66 ILE cc_start: 0.8258 (pt) cc_final: 0.8005 (mt) REVERT: B 94 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: B 538 MET cc_start: 0.6892 (tmt) cc_final: 0.6390 (tmt) REVERT: B 680 ASP cc_start: 0.7138 (m-30) cc_final: 0.6922 (m-30) outliers start: 17 outliers final: 5 residues processed: 217 average time/residue: 2.9899 time to fit residues: 692.3422 Evaluate side-chains 200 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: