Starting phenix.real_space_refine on Sat Sep 28 10:56:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/09_2024/6zfo_11184_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/09_2024/6zfo_11184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/09_2024/6zfo_11184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/09_2024/6zfo_11184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/09_2024/6zfo_11184_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/09_2024/6zfo_11184_trim.cif" } resolution = 4.4 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= 0.022 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 6128 2.51 5 N 1612 2.21 5 O 1900 1.98 5 H 9310 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2986 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3272 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "L" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3222 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2986 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3272 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3222 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.62, per 1000 atoms: 0.61 Number of scatterers: 18988 At special positions: 0 Unit cell: (78.02, 137.78, 170.15, 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 38 16.00 O 1900 8.00 N 1612 7.00 C 6128 6.00 H 9310 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 1.7 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 9.4% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.660A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.974A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 4.359A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 404 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.724A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.680A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.660A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.976A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.361A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.725A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.679A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.017A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.496A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.024A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.864A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.353A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.017A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.496A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 4 through 7 removed outlier: 6.025A pdb=" N THR C 69 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N GLN C 27 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N SER C 67 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N ILE C 29 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 11.535A pdb=" N SER C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 115 through 119 removed outlier: 5.864A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 154 through 156 removed outlier: 4.354A pdb=" N TRP C 149 " --> pdb=" O GLN C 156 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 948 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: 7.23 Time building geometry restraints manager: 6.36 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: 9310 1.03 - 1.23: 0 1.23 - 1.42: 4328 1.42 - 1.62: 5542 1.62 - 1.81: 44 Bond restraints: 19224 Sorted by residual: bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.48e-02 4.57e+03 1.73e+00 bond pdb=" C TYR E 505 " pdb=" N GLN E 506 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.48e-02 4.57e+03 1.71e+00 bond pdb=" C5 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.31e+00 ... (remaining 19219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.90: 34537 10.90 - 21.80: 0 21.80 - 32.70: 0 32.70 - 43.61: 0 43.61 - 54.51: 2 Bond angle restraints: 34539 Sorted by residual: angle pdb=" C SER B 120 " pdb=" N SER B 121 " pdb=" H SER B 121 " ideal model delta sigma weight residual 123.52 69.02 54.51 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA SER B 121 " pdb=" N SER B 121 " pdb=" H SER B 121 " ideal model delta sigma weight residual 113.22 60.29 52.93 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C SER H 120 " pdb=" N SER H 121 " pdb=" CA SER H 121 " ideal model delta sigma weight residual 123.25 129.32 -6.07 1.69e+00 3.50e-01 1.29e+01 angle pdb=" C SER B 120 " pdb=" N SER B 121 " pdb=" CA SER B 121 " ideal model delta sigma weight residual 123.25 129.31 -6.06 1.69e+00 3.50e-01 1.29e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" C ALA L 51 " ideal model delta sigma weight residual 110.80 116.44 -5.64 2.13e+00 2.20e-01 7.01e+00 ... (remaining 34534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 8649 16.15 - 32.30: 435 32.30 - 48.45: 173 48.45 - 64.60: 53 64.60 - 80.75: 6 Dihedral angle restraints: 9316 sinusoidal: 4942 harmonic: 4374 Sorted by residual: dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TRP H 111 " pdb=" C TRP H 111 " pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASP H 73 " pdb=" CB ASP H 73 " pdb=" CG ASP H 73 " pdb=" OD1 ASP H 73 " ideal model delta sinusoidal sigma weight residual -30.00 -83.26 53.26 1 2.00e+01 2.50e-03 9.64e+00 ... (remaining 9313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 848 0.029 - 0.059: 455 0.059 - 0.088: 60 0.088 - 0.117: 101 0.117 - 0.146: 28 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL E 433 " pdb=" N VAL E 433 " pdb=" C VAL E 433 " pdb=" CB VAL E 433 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1489 not shown) Planarity restraints: 2914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO H 157 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 157 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 402 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C ILE A 402 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE A 402 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG A 403 " -0.007 2.00e-02 2.50e+03 ... (remaining 2911 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 213 2.03 - 2.67: 27339 2.67 - 3.31: 53693 3.31 - 3.96: 72610 3.96 - 4.60: 111007 Nonbonded interactions: 264862 Sorted by model distance: nonbonded pdb=" H SER B 121 " pdb=" HA SER B 121 " model vdw 1.382 1.816 nonbonded pdb="HE22 GLN L 6 " pdb=" O TYR L 86 " model vdw 1.548 2.450 nonbonded pdb="HE22 GLN C 6 " pdb=" O TYR C 86 " model vdw 1.553 2.450 nonbonded pdb="HE21 GLN L 90 " pdb=" OG1 THR L 98 " model vdw 1.619 2.450 nonbonded pdb="HE21 GLN C 90 " pdb=" OG1 THR C 98 " model vdw 1.621 2.450 ... (remaining 264857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 333 through 465 or (resid 466 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH12 or name HH21)) or resid 467 t \ hrough 526 or resid 601)) selection = (chain 'E' and (resid 333 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) o \ r resid 358 through 395 or (resid 396 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z or name OH or name H or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2)) or resid 397 through 526 or resid 601)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 40.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 47.390 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 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 : 0.003 0.032 9914 Z= 0.188 Angle : 0.556 6.068 13482 Z= 0.317 Chirality : 0.043 0.146 1492 Planarity : 0.003 0.040 1730 Dihedral : 10.427 80.747 3552 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.30 % Allowed : 4.37 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.66 (0.24), residues: 1236 helix: -1.91 (0.57), residues: 68 sheet: -0.18 (0.23), residues: 482 loop : -0.37 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 353 HIS 0.003 0.001 HIS B 208 PHE 0.009 0.001 PHE A 400 TYR 0.007 0.001 TYR L 49 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 241 time to evaluate : 1.560 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: 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: 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: 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: 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: 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: E 389 ASP cc_start: 0.7275 (p0) cc_final: 0.5739 (t0) REVERT: L 95 LEU cc_start: 0.6508 (mt) cc_final: 0.5298 (tt) REVERT: L 123 ASP cc_start: 0.8255 (m-30) cc_final: 0.7598 (p0) REVERT: A 429 PHE cc_start: 0.7413 (t80) cc_final: 0.6941 (t80) REVERT: A 505 TYR cc_start: 0.6490 (m-80) cc_final: 0.6052 (m-10) REVERT: B 34 MET cc_start: 0.5530 (mmm) cc_final: 0.5016 (mmt) REVERT: B 38 ARG cc_start: 0.5186 (ptt180) cc_final: 0.4883 (ptt90) REVERT: C 54 LEU cc_start: 0.7889 (tp) cc_final: 0.7638 (mm) outliers start: 14 outliers final: 4 residues processed: 253 average time/residue: 0.6482 time to fit residues: 211.2109 Evaluate side-chains 163 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 156 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9914 Z= 0.246 Angle : 0.579 15.856 13482 Z= 0.317 Chirality : 0.045 0.160 1492 Planarity : 0.005 0.082 1730 Dihedral : 4.810 30.369 1406 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.19 % Allowed : 2.97 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.82 (0.23), residues: 1236 helix: -2.14 (0.51), residues: 70 sheet: -0.16 (0.22), residues: 476 loop : -0.57 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.005 0.001 HIS A 519 PHE 0.019 0.001 PHE E 377 TYR 0.018 0.002 TYR H 107 ARG 0.003 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 1.538 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7320 (p0) cc_final: 0.5769 (t0) REVERT: L 29 ILE cc_start: 0.6928 (pt) cc_final: 0.5514 (pt) REVERT: L 90 GLN cc_start: 0.5647 (pp30) cc_final: 0.5065 (tt0) REVERT: L 95 LEU cc_start: 0.7114 (mt) cc_final: 0.5518 (tt) REVERT: L 123 ASP cc_start: 0.8485 (m-30) cc_final: 0.7938 (p0) REVERT: A 408 ARG cc_start: 0.7619 (tpm170) cc_final: 0.7200 (tpm170) REVERT: A 429 PHE cc_start: 0.8128 (t80) cc_final: 0.7584 (t80) REVERT: A 505 TYR cc_start: 0.6365 (m-80) cc_final: 0.6020 (m-10) REVERT: B 116 LEU cc_start: 0.6209 (tp) cc_final: 0.5655 (tt) REVERT: C 54 LEU cc_start: 0.7983 (tp) cc_final: 0.7739 (tt) outliers start: 2 outliers final: 2 residues processed: 196 average time/residue: 0.6119 time to fit residues: 156.4348 Evaluate side-chains 152 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 0.0040 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9914 Z= 0.357 Angle : 0.659 15.443 13482 Z= 0.360 Chirality : 0.046 0.173 1492 Planarity : 0.005 0.079 1730 Dihedral : 5.063 26.303 1406 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.20 (0.23), residues: 1236 helix: -2.22 (0.51), residues: 68 sheet: -0.29 (0.23), residues: 466 loop : -0.97 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 162 HIS 0.003 0.001 HIS B 172 PHE 0.022 0.002 PHE E 377 TYR 0.024 0.003 TYR H 107 ARG 0.009 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.621 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 375 SER cc_start: 0.9142 (m) cc_final: 0.8904 (t) REVERT: H 83 MET cc_start: -0.2507 (mtm) cc_final: -0.2827 (mtm) REVERT: L 123 ASP cc_start: 0.8664 (m-30) cc_final: 0.8021 (p0) REVERT: L 171 ASP cc_start: 0.8624 (t0) cc_final: 0.8311 (t0) REVERT: A 429 PHE cc_start: 0.8308 (t80) cc_final: 0.7785 (t80) REVERT: A 505 TYR cc_start: 0.6720 (m-80) cc_final: 0.6352 (m-10) REVERT: B 116 LEU cc_start: 0.6546 (tp) cc_final: 0.6123 (tt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.6376 time to fit residues: 147.1249 Evaluate side-chains 143 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 414 GLN H 172 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 156 GLN A 439 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9914 Z= 0.346 Angle : 0.641 15.663 13482 Z= 0.353 Chirality : 0.046 0.163 1492 Planarity : 0.005 0.067 1730 Dihedral : 5.152 27.595 1406 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.41 (0.23), residues: 1236 helix: -2.05 (0.51), residues: 68 sheet: -0.40 (0.23), residues: 468 loop : -1.18 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.027 0.002 PHE E 377 TYR 0.030 0.003 TYR A 495 ARG 0.006 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.116 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: -0.3503 (mtm) cc_final: -0.3762 (mtt) REVERT: L 123 ASP cc_start: 0.8597 (m-30) cc_final: 0.7961 (p0) REVERT: L 171 ASP cc_start: 0.8720 (t0) cc_final: 0.8333 (t0) REVERT: A 429 PHE cc_start: 0.8348 (t80) cc_final: 0.7909 (t80) REVERT: A 505 TYR cc_start: 0.6730 (m-80) cc_final: 0.6391 (m-10) REVERT: B 38 ARG cc_start: 0.5755 (ptt180) cc_final: 0.5504 (ptt180) REVERT: B 104 TRP cc_start: 0.6553 (m-10) cc_final: 0.6277 (m-10) REVERT: B 116 LEU cc_start: 0.6618 (tp) cc_final: 0.6149 (tt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.6422 time to fit residues: 137.9987 Evaluate side-chains 130 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9914 Z= 0.214 Angle : 0.546 15.520 13482 Z= 0.296 Chirality : 0.044 0.152 1492 Planarity : 0.004 0.062 1730 Dihedral : 4.818 24.084 1406 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.29 (0.23), residues: 1236 helix: -1.70 (0.53), residues: 68 sheet: -0.34 (0.23), residues: 484 loop : -1.11 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 162 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE B 68 TYR 0.021 0.002 TYR H 60 ARG 0.005 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.570 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: 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: 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: 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: 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: symmetry clash REVERT: H 83 MET cc_start: -0.3635 (mtm) cc_final: -0.3974 (mtt) REVERT: L 123 ASP cc_start: 0.8553 (m-30) cc_final: 0.7978 (p0) REVERT: L 171 ASP cc_start: 0.8726 (t0) cc_final: 0.8319 (t0) REVERT: A 429 PHE cc_start: 0.8164 (t80) cc_final: 0.7811 (t80) REVERT: A 505 TYR cc_start: 0.6719 (m-80) cc_final: 0.6456 (m-10) REVERT: B 38 ARG cc_start: 0.5327 (ptt180) cc_final: 0.4822 (ptt180) REVERT: B 116 LEU cc_start: 0.6472 (tp) cc_final: 0.6072 (tt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.6017 time to fit residues: 135.6162 Evaluate side-chains 139 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN L 199 HIS A 394 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9914 Z= 0.248 Angle : 0.553 15.612 13482 Z= 0.302 Chirality : 0.044 0.158 1492 Planarity : 0.004 0.060 1730 Dihedral : 4.825 25.507 1406 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.20 (0.23), residues: 1236 helix: -1.53 (0.56), residues: 68 sheet: -0.20 (0.23), residues: 474 loop : -1.14 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 436 HIS 0.017 0.002 HIS H 35 PHE 0.014 0.001 PHE B 108 TYR 0.024 0.002 TYR H 60 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.383 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 150 VAL cc_start: 0.8306 (t) cc_final: 0.7992 (t) REVERT: H 153 TYR cc_start: 0.4797 (p90) cc_final: 0.4537 (p90) REVERT: L 123 ASP cc_start: 0.8609 (m-30) cc_final: 0.8044 (p0) REVERT: L 171 ASP cc_start: 0.8756 (t0) cc_final: 0.8343 (t0) REVERT: A 429 PHE cc_start: 0.8232 (t80) cc_final: 0.7849 (t80) REVERT: A 505 TYR cc_start: 0.6649 (m-80) cc_final: 0.6392 (m-10) REVERT: B 38 ARG cc_start: 0.5562 (ptt180) cc_final: 0.5092 (ptt180) REVERT: B 116 LEU cc_start: 0.6546 (tp) cc_final: 0.6124 (tt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.6163 time to fit residues: 131.7044 Evaluate side-chains 134 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9914 Z= 0.191 Angle : 0.521 15.595 13482 Z= 0.283 Chirality : 0.044 0.155 1492 Planarity : 0.004 0.059 1730 Dihedral : 4.624 23.705 1406 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.17 (0.24), residues: 1236 helix: -2.09 (0.50), residues: 84 sheet: -0.10 (0.23), residues: 474 loop : -1.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 36 HIS 0.003 0.001 HIS B 35 PHE 0.009 0.001 PHE A 490 TYR 0.025 0.002 TYR H 60 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.751 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: 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: 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: 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: 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: E 355 ARG cc_start: 0.5707 (ttm170) cc_final: 0.5297 (ttp-170) REVERT: H 150 VAL cc_start: 0.8317 (t) cc_final: 0.8001 (t) REVERT: H 153 TYR cc_start: 0.4750 (p90) cc_final: 0.4535 (p90) REVERT: L 123 ASP cc_start: 0.8607 (m-30) cc_final: 0.8054 (p0) REVERT: L 171 ASP cc_start: 0.8697 (t0) cc_final: 0.8292 (t0) REVERT: A 365 TYR cc_start: 0.5390 (m-80) cc_final: 0.4979 (m-80) REVERT: A 429 PHE cc_start: 0.8174 (t80) cc_final: 0.7797 (t80) REVERT: B 38 ARG cc_start: 0.5376 (ptt180) cc_final: 0.4915 (ptt180) REVERT: B 116 LEU cc_start: 0.6502 (tp) cc_final: 0.6108 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.6444 time to fit residues: 142.2980 Evaluate side-chains 134 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9914 Z= 0.216 Angle : 0.535 15.611 13482 Z= 0.289 Chirality : 0.044 0.155 1492 Planarity : 0.004 0.058 1730 Dihedral : 4.611 23.408 1406 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.15 (0.24), residues: 1236 helix: -2.09 (0.50), residues: 84 sheet: -0.08 (0.23), residues: 474 loop : -1.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 36 HIS 0.003 0.001 HIS B 35 PHE 0.013 0.001 PHE A 377 TYR 0.026 0.002 TYR H 60 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.524 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 355 ARG cc_start: 0.5877 (ttm170) cc_final: 0.5448 (ttp-170) REVERT: H 34 MET cc_start: 0.5031 (mmm) cc_final: 0.4597 (mmm) REVERT: H 150 VAL cc_start: 0.8330 (t) cc_final: 0.8006 (t) REVERT: H 153 TYR cc_start: 0.4795 (p90) cc_final: 0.4537 (p90) REVERT: L 123 ASP cc_start: 0.8605 (m-30) cc_final: 0.8068 (p0) REVERT: L 171 ASP cc_start: 0.8726 (t0) cc_final: 0.8306 (t0) REVERT: A 429 PHE cc_start: 0.8224 (t80) cc_final: 0.7877 (t80) REVERT: B 38 ARG cc_start: 0.5433 (ptt180) cc_final: 0.4910 (ptt180) REVERT: B 116 LEU cc_start: 0.6531 (tp) cc_final: 0.6160 (tt) REVERT: C 171 ASP cc_start: 0.8281 (t0) cc_final: 0.7990 (t0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.6708 time to fit residues: 146.9557 Evaluate side-chains 135 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9914 Z= 0.229 Angle : 0.538 15.698 13482 Z= 0.293 Chirality : 0.044 0.158 1492 Planarity : 0.005 0.058 1730 Dihedral : 4.665 22.669 1406 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.16 (0.24), residues: 1236 helix: -2.08 (0.49), residues: 84 sheet: -0.04 (0.23), residues: 470 loop : -1.10 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 104 HIS 0.002 0.001 HIS B 35 PHE 0.012 0.001 PHE C 99 TYR 0.021 0.002 TYR H 60 ARG 0.008 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.610 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 355 ARG cc_start: 0.5976 (ttm170) cc_final: 0.5554 (ttp-170) REVERT: H 34 MET cc_start: 0.5193 (mmm) cc_final: 0.4685 (mmm) REVERT: H 150 VAL cc_start: 0.8334 (t) cc_final: 0.8019 (t) REVERT: H 153 TYR cc_start: 0.4733 (p90) cc_final: 0.4456 (p90) REVERT: L 4 MET cc_start: 0.6769 (mmm) cc_final: 0.6419 (mmm) REVERT: L 123 ASP cc_start: 0.8575 (m-30) cc_final: 0.8056 (p0) REVERT: L 171 ASP cc_start: 0.8735 (t0) cc_final: 0.8322 (t0) REVERT: A 429 PHE cc_start: 0.8246 (t80) cc_final: 0.7906 (t80) REVERT: B 38 ARG cc_start: 0.5382 (ptt180) cc_final: 0.4840 (ptt180) REVERT: B 43 LYS cc_start: 0.8377 (mmpt) cc_final: 0.8171 (mmmt) REVERT: B 116 LEU cc_start: 0.6583 (tp) cc_final: 0.6199 (tt) REVERT: C 171 ASP cc_start: 0.8249 (t0) cc_final: 0.8001 (t0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.6079 time to fit residues: 129.7206 Evaluate side-chains 132 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9914 Z= 0.228 Angle : 0.538 15.645 13482 Z= 0.293 Chirality : 0.044 0.157 1492 Planarity : 0.004 0.058 1730 Dihedral : 4.660 23.103 1406 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.15 (0.24), residues: 1236 helix: -2.03 (0.50), residues: 84 sheet: -0.05 (0.23), residues: 470 loop : -1.09 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 436 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 377 TYR 0.030 0.002 TYR A 453 ARG 0.004 0.000 ARG H 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.799 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 355 ARG cc_start: 0.6028 (ttm170) cc_final: 0.5577 (ttp-170) REVERT: H 34 MET cc_start: 0.5239 (mmm) cc_final: 0.4743 (mmm) REVERT: H 150 VAL cc_start: 0.8363 (t) cc_final: 0.8032 (t) REVERT: H 153 TYR cc_start: 0.4761 (p90) cc_final: 0.4479 (p90) REVERT: L 90 GLN cc_start: 0.6305 (pp30) cc_final: 0.5935 (pp30) REVERT: L 123 ASP cc_start: 0.8587 (m-30) cc_final: 0.8063 (p0) REVERT: L 171 ASP cc_start: 0.8729 (t0) cc_final: 0.8300 (t0) REVERT: A 374 PHE cc_start: 0.6813 (m-10) cc_final: 0.6277 (m-80) REVERT: A 429 PHE cc_start: 0.8248 (t80) cc_final: 0.7891 (t80) REVERT: B 38 ARG cc_start: 0.5377 (ptt180) cc_final: 0.4810 (ptt180) REVERT: B 43 LYS cc_start: 0.8385 (mmpt) cc_final: 0.8175 (mmmt) REVERT: B 116 LEU cc_start: 0.6595 (tp) cc_final: 0.6226 (tt) REVERT: C 171 ASP cc_start: 0.8184 (t0) cc_final: 0.7920 (t0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.6279 time to fit residues: 134.4469 Evaluate side-chains 138 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.217321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.183458 restraints weight = 48950.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.183632 restraints weight = 58292.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.185369 restraints weight = 44154.525| |-----------------------------------------------------------------------------| r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9914 Z= 0.194 Angle : 0.520 15.588 13482 Z= 0.281 Chirality : 0.044 0.157 1492 Planarity : 0.004 0.058 1730 Dihedral : 4.588 22.673 1406 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.09 (0.24), residues: 1236 helix: -2.04 (0.49), residues: 86 sheet: -0.02 (0.23), residues: 470 loop : -1.02 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.002 0.001 HIS H 208 PHE 0.010 0.001 PHE E 377 TYR 0.023 0.002 TYR A 453 ARG 0.004 0.000 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5435.22 seconds wall clock time: 100 minutes 26.02 seconds (6026.02 seconds total)