Starting phenix.real_space_refine on Thu Jun 27 00:49:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/06_2024/8toi_41453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/06_2024/8toi_41453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/06_2024/8toi_41453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/06_2024/8toi_41453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/06_2024/8toi_41453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/06_2024/8toi_41453_updated.pdb" } resolution = 2.64 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= 0.057 sd= 0.508 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 34 5.49 5 S 40 5.16 5 C 7502 2.51 5 N 1724 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 87": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5160 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5160 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 547 Unusual residues: {' CA': 2, 'PGW': 18} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PGW:plan-3': 9} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 547 Unusual residues: {' CA': 2, 'PGW': 18} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PGW:plan-3': 9} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 6.33, per 1000 atoms: 0.55 Number of scatterers: 11414 At special positions: 0 Unit cell: (91.575, 137.775, 106.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 40 16.00 P 34 15.00 O 2110 8.00 N 1724 7.00 C 7502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 4 sheets defined 65.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 33 through 47 removed outlier: 3.644A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 102 through 105 removed outlier: 3.833A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.896A pdb=" N VAL A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 218 through 245 Processing helix chain 'A' and resid 281 through 319 removed outlier: 4.023A pdb=" N LEU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 331 through 357 Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 363 through 391 removed outlier: 6.230A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 412 Processing helix chain 'A' and resid 432 through 452 removed outlier: 3.814A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 500 through 517 Processing helix chain 'A' and resid 524 through 544 removed outlier: 3.987A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 584 removed outlier: 4.497A pdb=" N LEU A 571 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER A 576 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER A 577 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A 583 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 624 Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 667 through 684 Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.644A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 102 through 105 removed outlier: 3.834A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 183 through 211 removed outlier: 3.896A pdb=" N VAL B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 281 through 319 removed outlier: 4.024A pdb=" N LEU B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Proline residue: B 293 - end of helix Processing helix chain 'B' and resid 331 through 357 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 363 through 391 removed outlier: 6.230A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 412 Processing helix chain 'B' and resid 432 through 452 removed outlier: 3.814A pdb=" N THR B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 500 through 517 Processing helix chain 'B' and resid 524 through 544 removed outlier: 3.986A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 584 removed outlier: 4.496A pdb=" N LEU B 571 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER B 576 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER B 577 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS B 583 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 624 Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 667 through 684 Processing helix chain 'B' and resid 689 through 693 Processing helix chain 'B' and resid 702 through 715 Processing sheet with id= A, first strand: chain 'A' and resid 147 through 149 Processing sheet with id= B, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.784A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 147 through 149 Processing sheet with id= D, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.784A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1722 1.31 - 1.44: 3226 1.44 - 1.57: 6564 1.57 - 1.70: 68 1.70 - 1.83: 66 Bond restraints: 11646 Sorted by residual: bond pdb=" C1 PGW A 820 " pdb=" O01 PGW A 820 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1 PGW A 809 " pdb=" O01 PGW A 809 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 PGW B 820 " pdb=" O01 PGW B 820 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C1 PGW B 809 " pdb=" O01 PGW B 809 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C1 PGW A 817 " pdb=" O01 PGW A 817 " ideal model delta sigma weight residual 1.332 1.427 -0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 11641 not shown) Histogram of bond angle deviations from ideal: 80.14 - 96.20: 4 96.20 - 112.25: 6172 112.25 - 128.31: 9324 128.31 - 144.36: 120 144.36 - 160.42: 2 Bond angle restraints: 15622 Sorted by residual: angle pdb=" C2 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O01 PGW A 805 " ideal model delta sigma weight residual 110.92 160.42 -49.50 3.00e+00 1.11e-01 2.72e+02 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O01 PGW B 805 " ideal model delta sigma weight residual 110.92 160.38 -49.46 3.00e+00 1.11e-01 2.72e+02 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O02 PGW B 805 " ideal model delta sigma weight residual 125.44 80.14 45.30 3.00e+00 1.11e-01 2.28e+02 angle pdb=" C2 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O02 PGW A 805 " ideal model delta sigma weight residual 125.44 80.21 45.23 3.00e+00 1.11e-01 2.27e+02 angle pdb=" O01 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O02 PGW A 805 " ideal model delta sigma weight residual 123.63 80.21 43.42 3.00e+00 1.11e-01 2.09e+02 ... (remaining 15617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.20: 6550 33.20 - 66.41: 400 66.41 - 99.61: 58 99.61 - 132.82: 20 132.82 - 166.02: 28 Dihedral angle restraints: 7056 sinusoidal: 3268 harmonic: 3788 Sorted by residual: dihedral pdb=" CA ILE A 101 " pdb=" C ILE A 101 " pdb=" N ALA A 102 " pdb=" CA ALA A 102 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE B 101 " pdb=" C ILE B 101 " pdb=" N ALA B 102 " pdb=" CA ALA B 102 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" O01 PGW B 815 " pdb=" C01 PGW B 815 " pdb=" C02 PGW B 815 " pdb=" O03 PGW B 815 " ideal model delta sinusoidal sigma weight residual 59.30 -106.72 166.02 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 7053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1242 0.054 - 0.109: 292 0.109 - 0.163: 74 0.163 - 0.217: 20 0.217 - 0.272: 4 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 111 " pdb=" CA VAL B 111 " pdb=" CG1 VAL B 111 " pdb=" CG2 VAL B 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1629 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 396 " 0.014 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE B 396 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 396 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 396 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 396 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 396 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 396 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 396 " -0.014 2.00e-02 2.50e+03 1.85e-02 5.98e+00 pdb=" CG PHE A 396 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 396 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 396 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 396 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 396 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 396 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 134 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C VAL B 134 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL B 134 " -0.016 2.00e-02 2.50e+03 pdb=" N THR B 135 " -0.014 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3428 2.83 - 3.35: 10115 3.35 - 3.87: 18918 3.87 - 4.38: 21237 4.38 - 4.90: 36821 Nonbonded interactions: 90519 Sorted by model distance: nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.318 2.440 nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.318 2.440 nonbonded pdb=" O TRP B 570 " pdb=" OG SER B 573 " model vdw 2.353 2.440 nonbonded pdb=" O TRP A 570 " pdb=" OG SER A 573 " model vdw 2.353 2.440 nonbonded pdb=" OE2 GLU B 358 " pdb=" OH TYR B 360 " model vdw 2.360 2.440 ... (remaining 90514 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.670 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.840 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.096 11646 Z= 0.560 Angle : 1.856 49.496 15622 Z= 0.718 Chirality : 0.054 0.272 1632 Planarity : 0.006 0.053 1914 Dihedral : 24.382 166.024 4596 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1274 helix: -0.55 (0.15), residues: 888 sheet: -1.94 (0.77), residues: 44 loop : -1.97 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 141 HIS 0.004 0.001 HIS B 366 PHE 0.043 0.002 PHE B 396 TYR 0.017 0.002 TYR B 457 ARG 0.003 0.000 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.175 Fit side-chains REVERT: A 320 TYR cc_start: 0.8068 (t80) cc_final: 0.7754 (t80) REVERT: B 55 GLU cc_start: 0.7866 (tp30) cc_final: 0.7066 (mm-30) REVERT: B 320 TYR cc_start: 0.8143 (t80) cc_final: 0.7800 (t80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 1.2566 time to fit residues: 225.0465 Evaluate side-chains 131 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 30.0000 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 153 HIS A 265 HIS A 310 ASN A 366 HIS A 696 GLN A 698 GLN B 79 GLN B 153 HIS B 265 HIS B 310 ASN B 366 HIS B 696 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11646 Z= 0.176 Angle : 1.058 46.415 15622 Z= 0.405 Chirality : 0.039 0.158 1632 Planarity : 0.004 0.043 1914 Dihedral : 26.001 161.673 2250 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.87 % Allowed : 9.05 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1274 helix: 0.92 (0.16), residues: 892 sheet: -1.54 (0.81), residues: 44 loop : -1.66 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 235 HIS 0.003 0.001 HIS B 479 PHE 0.023 0.001 PHE A 406 TYR 0.011 0.001 TYR A 383 ARG 0.003 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.165 Fit side-chains REVERT: B 282 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7898 (tpp) outliers start: 20 outliers final: 4 residues processed: 140 average time/residue: 1.1296 time to fit residues: 172.5420 Evaluate side-chains 134 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN B 479 HIS B 696 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11646 Z= 0.160 Angle : 1.034 46.405 15622 Z= 0.394 Chirality : 0.039 0.157 1632 Planarity : 0.004 0.037 1914 Dihedral : 24.463 165.012 2250 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.33 % Allowed : 12.03 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1274 helix: 1.51 (0.17), residues: 896 sheet: -1.19 (0.85), residues: 44 loop : -1.37 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 235 HIS 0.004 0.001 HIS B 366 PHE 0.012 0.001 PHE B 396 TYR 0.011 0.001 TYR B 26 ARG 0.007 0.000 ARG B 699 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.918 Fit side-chains REVERT: A 33 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8205 (ttp80) REVERT: A 400 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6527 (pp) REVERT: B 33 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8129 (ttp80) REVERT: B 282 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7835 (tpp) REVERT: B 320 TYR cc_start: 0.7797 (t80) cc_final: 0.7455 (t80) REVERT: B 325 LYS cc_start: 0.8405 (tppt) cc_final: 0.8125 (tppt) REVERT: B 400 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6511 (pp) outliers start: 25 outliers final: 5 residues processed: 151 average time/residue: 1.1265 time to fit residues: 185.1503 Evaluate side-chains 138 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 510 GLN A 531 ASN A 633 GLN A 641 GLN A 696 GLN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN B 641 GLN B 696 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11646 Z= 0.400 Angle : 1.083 46.113 15622 Z= 0.427 Chirality : 0.044 0.168 1632 Planarity : 0.004 0.039 1914 Dihedral : 23.931 164.586 2250 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.52 % Allowed : 14.83 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1274 helix: 1.63 (0.17), residues: 896 sheet: -1.06 (0.88), residues: 44 loop : -1.42 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 235 HIS 0.006 0.001 HIS A 366 PHE 0.029 0.002 PHE A 406 TYR 0.014 0.002 TYR A 220 ARG 0.006 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.146 Fit side-chains REVERT: A 320 TYR cc_start: 0.8007 (t80) cc_final: 0.7801 (t80) REVERT: B 33 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8243 (ttp80) REVERT: B 320 TYR cc_start: 0.8088 (t80) cc_final: 0.7804 (t80) outliers start: 27 outliers final: 4 residues processed: 142 average time/residue: 1.1576 time to fit residues: 179.2065 Evaluate side-chains 124 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 696 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 633 GLN B 696 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11646 Z= 0.182 Angle : 1.044 46.299 15622 Z= 0.400 Chirality : 0.040 0.152 1632 Planarity : 0.003 0.034 1914 Dihedral : 23.127 166.289 2250 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.15 % Allowed : 15.76 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1274 helix: 1.82 (0.17), residues: 896 sheet: -1.03 (0.89), residues: 44 loop : -1.34 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 235 HIS 0.003 0.001 HIS A 366 PHE 0.009 0.001 PHE A 379 TYR 0.013 0.001 TYR A 457 ARG 0.004 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.152 Fit side-chains REVERT: A 320 TYR cc_start: 0.7957 (t80) cc_final: 0.7654 (t80) REVERT: A 325 LYS cc_start: 0.8466 (tppt) cc_final: 0.8156 (tppt) REVERT: B 320 TYR cc_start: 0.8032 (t80) cc_final: 0.7566 (t80) REVERT: B 325 LYS cc_start: 0.8458 (tppt) cc_final: 0.8103 (tppt) outliers start: 23 outliers final: 9 residues processed: 141 average time/residue: 1.1193 time to fit residues: 172.0584 Evaluate side-chains 137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 627 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 0.0060 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 633 GLN A 696 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 633 GLN B 696 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11646 Z= 0.152 Angle : 1.037 46.261 15622 Z= 0.394 Chirality : 0.039 0.152 1632 Planarity : 0.003 0.033 1914 Dihedral : 22.118 166.885 2250 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.77 % Allowed : 16.88 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1274 helix: 2.02 (0.17), residues: 896 sheet: -1.00 (0.89), residues: 44 loop : -1.25 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 141 HIS 0.003 0.001 HIS B 366 PHE 0.030 0.001 PHE B 406 TYR 0.015 0.001 TYR B 457 ARG 0.004 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.179 Fit side-chains REVERT: A 282 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7795 (tpp) REVERT: A 320 TYR cc_start: 0.7953 (t80) cc_final: 0.7729 (t80) REVERT: A 701 MET cc_start: 0.7702 (tpp) cc_final: 0.7234 (tpt) REVERT: B 33 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8190 (ttp80) REVERT: B 282 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7828 (tpp) REVERT: B 320 TYR cc_start: 0.8007 (t80) cc_final: 0.7662 (t80) outliers start: 19 outliers final: 7 residues processed: 149 average time/residue: 1.1173 time to fit residues: 181.5557 Evaluate side-chains 135 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 627 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 0.0670 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 77 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 633 GLN A 696 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN B 310 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 633 GLN B 696 GLN B 698 GLN B 715 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11646 Z= 0.162 Angle : 1.044 46.227 15622 Z= 0.398 Chirality : 0.039 0.151 1632 Planarity : 0.003 0.035 1914 Dihedral : 21.661 166.489 2250 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.52 % Allowed : 16.98 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1274 helix: 2.07 (0.17), residues: 894 sheet: -0.98 (0.90), residues: 44 loop : -1.23 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 235 HIS 0.003 0.001 HIS B 366 PHE 0.010 0.001 PHE A 379 TYR 0.014 0.001 TYR A 457 ARG 0.004 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 0.919 Fit side-chains REVERT: A 282 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7776 (tpp) REVERT: A 320 TYR cc_start: 0.7865 (t80) cc_final: 0.7592 (t80) REVERT: A 701 MET cc_start: 0.7711 (tpp) cc_final: 0.7342 (tpt) REVERT: B 282 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7803 (tpp) REVERT: B 320 TYR cc_start: 0.7930 (t80) cc_final: 0.7589 (t80) REVERT: B 701 MET cc_start: 0.7896 (tpp) cc_final: 0.7526 (tpt) outliers start: 27 outliers final: 8 residues processed: 143 average time/residue: 1.1711 time to fit residues: 182.3496 Evaluate side-chains 133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 627 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 479 HIS A 633 GLN A 666 HIS A 696 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN B 479 HIS B 633 GLN B 666 HIS B 696 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11646 Z= 0.237 Angle : 1.057 46.111 15622 Z= 0.407 Chirality : 0.041 0.154 1632 Planarity : 0.004 0.033 1914 Dihedral : 21.123 164.853 2250 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.96 % Allowed : 17.72 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1274 helix: 1.95 (0.17), residues: 908 sheet: -0.91 (0.89), residues: 44 loop : -1.36 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 141 HIS 0.004 0.001 HIS A 366 PHE 0.017 0.001 PHE B 406 TYR 0.015 0.001 TYR A 457 ARG 0.004 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.230 Fit side-chains REVERT: A 88 TRP cc_start: 0.8554 (t60) cc_final: 0.8336 (t60) REVERT: A 320 TYR cc_start: 0.7979 (t80) cc_final: 0.7691 (t80) REVERT: A 701 MET cc_start: 0.7716 (tpp) cc_final: 0.7404 (tpt) REVERT: B 88 TRP cc_start: 0.8520 (t60) cc_final: 0.8270 (t60) REVERT: B 282 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7832 (tpp) REVERT: B 320 TYR cc_start: 0.8006 (t80) cc_final: 0.7744 (t80) REVERT: B 701 MET cc_start: 0.7937 (tpp) cc_final: 0.7639 (tpt) outliers start: 21 outliers final: 8 residues processed: 136 average time/residue: 1.1273 time to fit residues: 167.3728 Evaluate side-chains 133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 627 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8328 > 50: distance: 110 - 139: 10.343 distance: 117 - 148: 8.389 distance: 134 - 139: 7.992 distance: 135 - 167: 10.948 distance: 139 - 140: 6.431 distance: 140 - 141: 3.832 distance: 140 - 143: 12.096 distance: 141 - 142: 9.141 distance: 141 - 148: 6.414 distance: 142 - 173: 23.978 distance: 143 - 144: 8.793 distance: 144 - 145: 14.885 distance: 145 - 146: 9.011 distance: 145 - 147: 17.897 distance: 148 - 149: 17.539 distance: 149 - 150: 13.799 distance: 149 - 152: 7.127 distance: 150 - 151: 44.321 distance: 150 - 156: 35.899 distance: 152 - 153: 15.216 distance: 153 - 154: 7.910 distance: 153 - 155: 4.406 distance: 156 - 157: 7.572 distance: 157 - 158: 32.090 distance: 157 - 160: 27.657 distance: 158 - 159: 11.078 distance: 158 - 167: 26.254 distance: 159 - 186: 25.670 distance: 160 - 161: 35.797 distance: 161 - 162: 31.873 distance: 162 - 163: 22.527 distance: 163 - 164: 20.068 distance: 164 - 165: 8.468 distance: 164 - 166: 10.798 distance: 167 - 168: 9.479 distance: 168 - 169: 6.377 distance: 168 - 171: 12.559 distance: 169 - 170: 11.338 distance: 169 - 173: 4.404 distance: 170 - 194: 9.585 distance: 171 - 172: 17.191 distance: 173 - 174: 4.142 distance: 174 - 175: 8.393 distance: 175 - 176: 14.664 distance: 175 - 181: 5.076 distance: 176 - 203: 22.321 distance: 177 - 178: 5.201 distance: 178 - 179: 8.756 distance: 178 - 180: 12.024 distance: 181 - 182: 5.235 distance: 182 - 183: 6.489 distance: 182 - 185: 4.351 distance: 183 - 184: 16.526 distance: 183 - 186: 9.601 distance: 184 - 211: 31.426 distance: 186 - 187: 4.211 distance: 187 - 188: 5.058 distance: 187 - 190: 4.157 distance: 188 - 189: 8.950 distance: 188 - 194: 14.661 distance: 190 - 191: 10.664 distance: 191 - 192: 3.970 distance: 191 - 193: 17.238 distance: 194 - 195: 4.700 distance: 195 - 196: 4.331 distance: 195 - 198: 12.398 distance: 196 - 197: 15.481 distance: 196 - 203: 8.978 distance: 198 - 199: 17.324 distance: 199 - 200: 14.354 distance: 200 - 201: 10.185 distance: 201 - 202: 16.271 distance: 203 - 204: 6.211 distance: 204 - 205: 20.312 distance: 204 - 207: 10.770 distance: 205 - 206: 19.900 distance: 205 - 211: 21.472 distance: 207 - 208: 6.524 distance: 207 - 209: 21.122 distance: 208 - 210: 18.214 distance: 211 - 212: 13.572 distance: 212 - 213: 6.757 distance: 212 - 215: 9.116 distance: 213 - 214: 7.083