Starting phenix.real_space_refine on Thu Jan 18 19:47:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/01_2024/7dsv_30847_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/01_2024/7dsv_30847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/01_2024/7dsv_30847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/01_2024/7dsv_30847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/01_2024/7dsv_30847_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/01_2024/7dsv_30847_neut_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 6194 2.51 5 N 1522 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9340 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3672 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 15, 'TRANS': 447} Chain breaks: 1 Chain: "B" Number of atoms: 3672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3672 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 15, 'TRANS': 447} Chain breaks: 1 Chain: "D" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 915 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 499 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 13, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 372 Chain: "C" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 915 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 499 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 13, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 372 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 83 Unusual residues: {'LBN': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'LBN:plan-2': 8, 'LBN:plan-3': 5, 'LBN:plan-1': 8} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 83 Unusual residues: {'LBN': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'LBN:plan-2': 8, 'LBN:plan-3': 5, 'LBN:plan-1': 8} Unresolved non-hydrogen planarities: 76 Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" C10 LBN A 601 " occ=0.00 ... (8 atoms not shown) pdb=" C7 LBN A 601 " occ=0.00 residue: pdb=" C11 LBN A 602 " occ=0.00 ... (13 atoms not shown) pdb=" C8 LBN A 602 " occ=0.00 residue: pdb=" C11 LBN A 603 " occ=0.00 ... (10 atoms not shown) pdb=" C8 LBN A 603 " occ=0.00 residue: pdb=" C11 LBN A 604 " occ=0.00 ... (10 atoms not shown) pdb=" C8 LBN A 604 " occ=0.00 residue: pdb=" C11 LBN A 605 " occ=0.00 ... (6 atoms not shown) pdb=" C8 LBN A 605 " occ=0.00 residue: pdb=" C11 LBN A 606 " occ=0.00 ... (6 atoms not shown) pdb=" C8 LBN A 606 " occ=0.00 residue: pdb=" C11 LBN A 607 " occ=0.00 ... (6 atoms not shown) pdb=" C8 LBN A 607 " occ=0.00 residue: pdb=" C34 LBN A 608 " occ=0.00 ... (8 atoms not shown) pdb=" C5 LBN A 608 " occ=0.00 residue: pdb=" C34 LBN B 801 " occ=0.00 ... (8 atoms not shown) pdb=" C5 LBN B 801 " occ=0.00 residue: pdb=" C10 LBN B 802 " occ=0.00 ... (8 atoms not shown) pdb=" C7 LBN B 802 " occ=0.00 residue: pdb=" C11 LBN B 803 " occ=0.00 ... (13 atoms not shown) pdb=" C8 LBN B 803 " occ=0.00 residue: pdb=" C11 LBN B 804 " occ=0.00 ... (10 atoms not shown) pdb=" C8 LBN B 804 " occ=0.00 ... (remaining 4 not shown) Time building chain proxies: 5.29, per 1000 atoms: 0.57 Number of scatterers: 9340 At special positions: 0 Unit cell: (143, 73, 101, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1596 8.00 N 1522 7.00 C 6194 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: 4.84 Conformation dependent library (CDL) restraints added in 1.8 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 0 sheets defined 65.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 131 through 149 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 186 through 213 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.549A pdb=" N PHE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.644A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 319 removed outlier: 3.745A pdb=" N PHE A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.586A pdb=" N VAL A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 366 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 373 through 403 Processing helix chain 'A' and resid 411 through 437 Processing helix chain 'A' and resid 446 through 453 Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 500 through 503 No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 518 through 538 Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 131 through 149 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 186 through 213 Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.549A pdb=" N PHE B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 253 through 282 removed outlier: 3.644A pdb=" N ILE B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 319 removed outlier: 3.745A pdb=" N PHE B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 347 removed outlier: 3.587A pdb=" N VAL B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 366 Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 373 through 403 Processing helix chain 'B' and resid 411 through 437 Processing helix chain 'B' and resid 446 through 453 Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 518 through 538 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 25 through 39 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.196A pdb=" N HIS D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 111 through 122 removed outlier: 3.743A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.645A pdb=" N LYS D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 188 No H-bonds generated for 'chain 'D' and resid 185 through 188' Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 80 through 90 removed outlier: 4.195A pdb=" N HIS C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 111 through 122 removed outlier: 3.743A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 149 through 163 Processing helix chain 'C' and resid 173 through 181 removed outlier: 3.644A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 188 No H-bonds generated for 'chain 'C' and resid 185 through 188' 578 hydrogen bonds defined for protein. 1716 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: 2.39 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1470 1.31 - 1.44: 2546 1.44 - 1.56: 5446 1.56 - 1.69: 22 1.69 - 1.81: 44 Bond restraints: 9528 Sorted by residual: bond pdb=" C GLU D 16 " pdb=" O GLU D 16 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.19e-02 7.06e+03 1.79e+01 bond pdb=" C GLU C 16 " pdb=" O GLU C 16 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.77e+01 bond pdb=" N ASP C 95 " pdb=" CA ASP C 95 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.29e+01 bond pdb=" N ASP D 95 " pdb=" CA ASP D 95 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" C5 LBN B 805 " pdb=" C8 LBN B 805 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 9523 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.45: 191 106.45 - 113.40: 5413 113.40 - 120.35: 3700 120.35 - 127.29: 3560 127.29 - 134.24: 96 Bond angle restraints: 12960 Sorted by residual: angle pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N SER C 99 " ideal model delta sigma weight residual 118.38 108.99 9.39 1.30e+00 5.92e-01 5.22e+01 angle pdb=" CA LYS D 98 " pdb=" C LYS D 98 " pdb=" N SER D 99 " ideal model delta sigma weight residual 118.38 109.05 9.33 1.30e+00 5.92e-01 5.15e+01 angle pdb=" C LYS D 98 " pdb=" N SER D 99 " pdb=" CA SER D 99 " ideal model delta sigma weight residual 122.09 132.86 -10.77 1.79e+00 3.12e-01 3.62e+01 angle pdb=" C LYS C 98 " pdb=" N SER C 99 " pdb=" CA SER C 99 " ideal model delta sigma weight residual 122.09 132.82 -10.73 1.79e+00 3.12e-01 3.59e+01 angle pdb=" O LYS C 98 " pdb=" C LYS C 98 " pdb=" N SER C 99 " ideal model delta sigma weight residual 122.42 130.08 -7.66 1.31e+00 5.83e-01 3.42e+01 ... (remaining 12955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 4795 14.30 - 28.61: 464 28.61 - 42.91: 155 42.91 - 57.21: 32 57.21 - 71.52: 12 Dihedral angle restraints: 5458 sinusoidal: 1734 harmonic: 3724 Sorted by residual: dihedral pdb=" CA ALA D 171 " pdb=" C ALA D 171 " pdb=" N SER D 172 " pdb=" CA SER D 172 " ideal model delta harmonic sigma weight residual -180.00 -152.32 -27.68 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA C 171 " pdb=" C ALA C 171 " pdb=" N SER C 172 " pdb=" CA SER C 172 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA LYS D 129 " pdb=" C LYS D 129 " pdb=" N ILE D 130 " pdb=" CA ILE D 130 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1216 0.064 - 0.127: 292 0.127 - 0.191: 45 0.191 - 0.254: 11 0.254 - 0.318: 8 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA GLU C 20 " pdb=" N GLU C 20 " pdb=" C GLU C 20 " pdb=" CB GLU C 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA GLU D 20 " pdb=" N GLU D 20 " pdb=" C GLU D 20 " pdb=" CB GLU D 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ASN C 109 " pdb=" N ASN C 109 " pdb=" C ASN C 109 " pdb=" CB ASN C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1569 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 99 " 0.037 2.00e-02 2.50e+03 7.16e-02 5.13e+01 pdb=" C SER D 99 " -0.124 2.00e-02 2.50e+03 pdb=" O SER D 99 " 0.044 2.00e-02 2.50e+03 pdb=" N LYS D 100 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 99 " 0.037 2.00e-02 2.50e+03 7.16e-02 5.12e+01 pdb=" C SER C 99 " -0.124 2.00e-02 2.50e+03 pdb=" O SER C 99 " 0.044 2.00e-02 2.50e+03 pdb=" N LYS C 100 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 96 " 0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASN D 96 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN D 96 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU D 97 " 0.021 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 610 2.72 - 3.27: 10125 3.27 - 3.81: 15407 3.81 - 4.36: 18319 4.36 - 4.90: 31177 Nonbonded interactions: 75638 Sorted by model distance: nonbonded pdb=" O VAL B 367 " pdb=" CG GLU B 368 " model vdw 2.180 3.440 nonbonded pdb=" O VAL A 367 " pdb=" CG GLU A 368 " model vdw 2.181 3.440 nonbonded pdb=" O SER A 375 " pdb=" OG1 THR A 378 " model vdw 2.274 2.440 nonbonded pdb=" O SER B 375 " pdb=" OG1 THR B 378 " model vdw 2.275 2.440 nonbonded pdb=" O PHE B 162 " pdb=" OH TYR B 342 " model vdw 2.305 2.440 ... (remaining 75633 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' and (resid 87 through 558 or resid 601 or resid 603 through 607)) selection = (chain 'B' and (resid 87 through 558 or resid 801 or (resid 803 through 804 and \ (name C11 or name C14 or name C17 or name C20 or name C22 or name C23 or name C2 \ 4 or name C40 or name C41 or name C42 or name C5 or name C8 )) or (resid 805 thr \ ough 807 and (name C11 or name C14 or name C17 or name C20 or name C22 or name C \ 23 or name C24 or name C8 )))) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=0.98 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: 0.890 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: 0.010 Extract box with map and model: 3.870 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.680 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.008 0.070 9528 Z= 0.570 Angle : 1.061 10.769 12960 Z= 0.658 Chirality : 0.061 0.318 1572 Planarity : 0.006 0.072 1620 Dihedral : 13.922 71.516 3054 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.75 % Allowed : 1.37 % Favored : 96.88 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1284 helix: -0.25 (0.16), residues: 920 sheet: None (None), residues: 0 loop : -2.20 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 386 HIS 0.003 0.001 HIS A 545 PHE 0.018 0.002 PHE A 119 TYR 0.012 0.001 TYR A 283 ARG 0.012 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ILE cc_start: 0.8509 (tt) cc_final: 0.8269 (tt) REVERT: A 419 LEU cc_start: 0.8807 (tt) cc_final: 0.8520 (tt) REVERT: A 546 TRP cc_start: 0.3155 (OUTLIER) cc_final: 0.2616 (m100) REVERT: B 125 ILE cc_start: 0.8493 (tt) cc_final: 0.8228 (tt) REVERT: B 546 TRP cc_start: 0.2826 (OUTLIER) cc_final: 0.2393 (m100) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.1906 time to fit residues: 33.4585 Evaluate side-chains 97 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 546 TRP Chi-restraints excluded: chain B residue 549 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 50.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS A 519 ASN A 544 HIS A 545 HIS B 250 HIS B 519 ASN B 544 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9528 Z= 0.213 Angle : 0.530 5.701 12960 Z= 0.283 Chirality : 0.042 0.204 1572 Planarity : 0.004 0.056 1620 Dihedral : 7.574 63.828 1474 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.25 % Allowed : 8.98 % Favored : 89.78 % 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: 0.26 (0.24), residues: 1284 helix: 1.01 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.81 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 386 HIS 0.005 0.000 HIS A 545 PHE 0.014 0.001 PHE B 382 TYR 0.010 0.001 TYR A 274 ARG 0.006 0.001 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.963 Fit side-chains REVERT: A 125 ILE cc_start: 0.8533 (tt) cc_final: 0.8332 (tt) REVERT: A 419 LEU cc_start: 0.8818 (tt) cc_final: 0.8586 (tt) REVERT: B 125 ILE cc_start: 0.8500 (tt) cc_final: 0.8289 (tt) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1584 time to fit residues: 25.2309 Evaluate side-chains 98 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.6980 chunk 36 optimal weight: 0.0370 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 40.0000 chunk 103 optimal weight: 0.4980 chunk 115 optimal weight: 30.0000 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9528 Z= 0.177 Angle : 0.487 6.973 12960 Z= 0.257 Chirality : 0.041 0.205 1572 Planarity : 0.004 0.053 1620 Dihedral : 6.490 62.602 1454 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.62 % Allowed : 11.22 % Favored : 87.16 % 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: 0.93 (0.24), residues: 1284 helix: 1.48 (0.18), residues: 908 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 386 HIS 0.003 0.001 HIS A 540 PHE 0.016 0.001 PHE B 382 TYR 0.007 0.001 TYR A 274 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.962 Fit side-chains REVERT: A 125 ILE cc_start: 0.8514 (tt) cc_final: 0.8278 (tt) REVERT: A 346 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6979 (mm-30) REVERT: A 364 ARG cc_start: 0.8152 (ttt90) cc_final: 0.7870 (ttt180) REVERT: A 422 LEU cc_start: 0.8500 (tp) cc_final: 0.8288 (tp) REVERT: B 125 ILE cc_start: 0.8504 (tt) cc_final: 0.8267 (tt) REVERT: B 346 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6966 (mm-30) REVERT: B 364 ARG cc_start: 0.8106 (ttt90) cc_final: 0.7775 (ttt180) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.1748 time to fit residues: 29.2186 Evaluate side-chains 108 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 20.0000 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 0.0570 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 50.0000 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS A 519 ASN B 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9528 Z= 0.211 Angle : 0.495 6.306 12960 Z= 0.261 Chirality : 0.041 0.191 1572 Planarity : 0.004 0.052 1620 Dihedral : 6.755 64.579 1454 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.00 % Allowed : 12.84 % Favored : 85.16 % 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: 0.93 (0.24), residues: 1284 helix: 1.47 (0.18), residues: 916 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 386 HIS 0.002 0.001 HIS B 545 PHE 0.013 0.001 PHE B 382 TYR 0.009 0.001 TYR A 274 ARG 0.003 0.001 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.985 Fit side-chains REVERT: A 125 ILE cc_start: 0.8564 (tt) cc_final: 0.8311 (tt) REVERT: A 346 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7010 (mm-30) REVERT: B 125 ILE cc_start: 0.8617 (tt) cc_final: 0.8371 (tt) REVERT: B 346 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7024 (mm-30) outliers start: 16 outliers final: 12 residues processed: 107 average time/residue: 0.1575 time to fit residues: 26.5624 Evaluate side-chains 112 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 40.0000 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.0060 chunk 92 optimal weight: 30.0000 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 30.0000 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9528 Z= 0.185 Angle : 0.476 6.932 12960 Z= 0.249 Chirality : 0.040 0.192 1572 Planarity : 0.004 0.051 1620 Dihedral : 6.497 64.733 1454 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.62 % Allowed : 12.97 % Favored : 84.41 % 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: 1.18 (0.24), residues: 1284 helix: 1.68 (0.18), residues: 908 sheet: None (None), residues: 0 loop : -1.48 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.002 0.000 HIS B 540 PHE 0.012 0.001 PHE A 119 TYR 0.008 0.001 TYR A 274 ARG 0.004 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.027 Fit side-chains REVERT: A 125 ILE cc_start: 0.8553 (tt) cc_final: 0.8319 (tt) REVERT: A 346 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7038 (mm-30) REVERT: B 125 ILE cc_start: 0.8567 (tt) cc_final: 0.8310 (tt) REVERT: B 346 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7015 (mm-30) outliers start: 21 outliers final: 14 residues processed: 117 average time/residue: 0.1726 time to fit residues: 31.0206 Evaluate side-chains 119 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9528 Z= 0.366 Angle : 0.579 7.658 12960 Z= 0.299 Chirality : 0.044 0.182 1572 Planarity : 0.004 0.054 1620 Dihedral : 7.501 68.695 1454 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.62 % Allowed : 13.59 % Favored : 82.79 % 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: 0.73 (0.24), residues: 1284 helix: 1.41 (0.17), residues: 886 sheet: None (None), residues: 0 loop : -1.65 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.004 0.001 HIS B 545 PHE 0.015 0.002 PHE A 119 TYR 0.010 0.001 TYR A 274 ARG 0.005 0.001 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.898 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 108 average time/residue: 0.1673 time to fit residues: 27.9751 Evaluate side-chains 106 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 104 optimal weight: 40.0000 chunk 69 optimal weight: 0.0470 chunk 123 optimal weight: 40.0000 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9528 Z= 0.168 Angle : 0.484 7.256 12960 Z= 0.253 Chirality : 0.040 0.175 1572 Planarity : 0.004 0.050 1620 Dihedral : 6.495 66.651 1454 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.00 % Allowed : 14.59 % Favored : 83.42 % 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: 1.17 (0.24), residues: 1284 helix: 1.65 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -1.42 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 386 HIS 0.002 0.000 HIS B 545 PHE 0.012 0.001 PHE B 382 TYR 0.008 0.001 TYR B 274 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.951 Fit side-chains REVERT: A 346 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7018 (mm-30) REVERT: B 346 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6998 (mm-30) outliers start: 16 outliers final: 16 residues processed: 108 average time/residue: 0.1522 time to fit residues: 25.9450 Evaluate side-chains 114 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9528 Z= 0.245 Angle : 0.517 7.891 12960 Z= 0.268 Chirality : 0.041 0.204 1572 Planarity : 0.004 0.051 1620 Dihedral : 6.813 66.711 1454 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.37 % Allowed : 14.96 % Favored : 82.67 % 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: 1.10 (0.24), residues: 1284 helix: 1.61 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.44 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 386 HIS 0.003 0.001 HIS B 545 PHE 0.015 0.001 PHE B 119 TYR 0.010 0.001 TYR A 274 ARG 0.004 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.993 Fit side-chains REVERT: B 125 ILE cc_start: 0.8694 (tt) cc_final: 0.8446 (tt) outliers start: 19 outliers final: 16 residues processed: 108 average time/residue: 0.1584 time to fit residues: 26.8972 Evaluate side-chains 116 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 0.0980 chunk 103 optimal weight: 50.0000 chunk 108 optimal weight: 50.0000 chunk 75 optimal weight: 0.5980 chunk 121 optimal weight: 50.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 9528 Z= 0.572 Angle : 0.701 10.387 12960 Z= 0.359 Chirality : 0.050 0.273 1572 Planarity : 0.005 0.053 1620 Dihedral : 8.163 67.176 1454 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.24 % Allowed : 15.34 % Favored : 82.42 % 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: 0.11 (0.23), residues: 1284 helix: 0.91 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.91 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 386 HIS 0.007 0.001 HIS B 545 PHE 0.021 0.002 PHE A 119 TYR 0.014 0.002 TYR B 283 ARG 0.009 0.001 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.927 Fit side-chains REVERT: B 421 CYS cc_start: 0.7816 (m) cc_final: 0.7471 (m) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.1608 time to fit residues: 24.4252 Evaluate side-chains 106 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 127 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9528 Z= 0.157 Angle : 0.489 8.096 12960 Z= 0.255 Chirality : 0.040 0.179 1572 Planarity : 0.004 0.051 1620 Dihedral : 6.536 66.343 1454 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.50 % Allowed : 16.96 % Favored : 81.55 % 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 (0.24), residues: 1284 helix: 1.55 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 409 HIS 0.002 0.000 HIS A 544 PHE 0.011 0.001 PHE A 382 TYR 0.007 0.001 TYR B 274 ARG 0.005 0.001 ARG A 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.954 Fit side-chains REVERT: B 279 GLU cc_start: 0.7768 (tt0) cc_final: 0.7478 (tt0) outliers start: 12 outliers final: 11 residues processed: 104 average time/residue: 0.1559 time to fit residues: 25.5861 Evaluate side-chains 105 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 40.0000 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.0060 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 104 optimal weight: 50.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.192451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.177827 restraints weight = 8768.208| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 0.65 r_work: 0.3679 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9528 Z= 0.230 Angle : 0.517 8.618 12960 Z= 0.269 Chirality : 0.042 0.207 1572 Planarity : 0.004 0.051 1620 Dihedral : 6.782 65.167 1454 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.75 % Allowed : 17.58 % Favored : 80.67 % 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: 1.11 (0.24), residues: 1284 helix: 1.66 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -1.55 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 386 HIS 0.003 0.001 HIS B 545 PHE 0.014 0.001 PHE A 119 TYR 0.009 0.001 TYR A 274 ARG 0.004 0.001 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.12 seconds wall clock time: 33 minutes 33.21 seconds (2013.21 seconds total)