Starting phenix.real_space_refine on Thu Jul 2 10:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.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 { model { file = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2026/8d2w_27152.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1622 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 34 5.16 5 C 4501 2.51 5 N 1026 2.21 5 O 1296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6858 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3442 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3417 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 6, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 115 Conformer: "B" Number of residues, atoms: 460, 3417 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 6, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 115 bond proxies already assigned to first conformer: 3476 Chain: "B" Number of atoms: 1404 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 201, 1393 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Conformer: "B" Number of residues, atoms: 201, 1393 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 bond proxies already assigned to first conformer: 1419 Chain: "C" Number of atoms: 1419 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1408 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 203, 1408 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 1436 Chain: "A" Number of atoms: 553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 15, 448 Unusual residues: {'LMT': 14, 'ZGS': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 35 Conformer: "B" Number of residues, atoms: 15, 448 Unusual residues: {'LMT': 14, 'ZGS': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 35 bond proxies already assigned to first conformer: 346 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N ATRP A 346 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 346 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" N AARG B 191 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 191 " occ=0.50 residue: pdb=" N AARG C 13 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 13 " occ=0.50 residue: pdb=" C1 ALMT A 602 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 602 " occ=0.50 residue: pdb=" C1 ALMT A 603 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 603 " occ=0.50 residue: pdb=" C1 ALMT A 610 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 610 " occ=0.50 Time building chain proxies: 2.32, per 1000 atoms: 0.34 Number of scatterers: 6858 At special positions: 0 Unit cell: (69.208, 73.428, 141.792, 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 34 16.00 P 1 15.00 O 1296 8.00 N 1026 7.00 C 4501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " 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 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 472.0 milliseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 10 sheets defined 45.5% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 47 through 67 removed outlier: 3.998A pdb=" N GLN A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 100 removed outlier: 4.021A pdb=" N ALA A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 109 through 128 Proline residue: A 118 - end of helix removed outlier: 3.715A pdb=" N TRP A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 169 through 200 Processing helix chain 'A' and resid 232 through 262 removed outlier: 3.512A pdb=" N VAL A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 288 through 311 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 325 through 352 Proline residue: A 342 - end of helix removed outlier: 3.770A pdb=" N THR A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.664A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'A' and resid 377 through 414 removed outlier: 3.535A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 419 through 451 removed outlier: 3.542A pdb=" N TYR A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.574A pdb=" N LEU A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.570A pdb=" N SER A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.644A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'C' and resid 28 through 31 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 5.976A pdb=" N LYS B 11 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR B 48 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.858A pdb=" N ALA B 127 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE B 174 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL B 129 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 172 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE B 131 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA B 170 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET B 168 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.658A pdb=" N TRP B 143 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.646A pdb=" N GLU C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.886A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.886A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 187 384 hydrogen bonds defined for protein. 1088 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: 0.91 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 990 1.30 - 1.43: 1870 1.43 - 1.56: 4019 1.56 - 1.68: 110 1.68 - 1.81: 48 Bond restraints: 7037 Sorted by residual: bond pdb=" C1BALMT A 603 " pdb=" O5BALMT A 603 " ideal model delta sigma weight residual 1.393 1.519 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C1B LMT A 604 " pdb=" O5B LMT A 604 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C1BBLMT A 602 " pdb=" O5BBLMT A 602 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1B LMT A 605 " pdb=" O5B LMT A 605 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 7032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 9361 4.95 - 9.89: 212 9.89 - 14.84: 3 14.84 - 19.79: 3 19.79 - 24.74: 3 Bond angle restraints: 9582 Sorted by residual: angle pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " ideal model delta sigma weight residual 127.34 152.08 -24.74 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C09 ZGS A 601 " pdb=" C10 ZGS A 601 " pdb=" C11 ZGS A 601 " ideal model delta sigma weight residual 127.16 151.03 -23.87 3.00e+00 1.11e-01 6.33e+01 angle pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " ideal model delta sigma weight residual 127.52 151.32 -23.80 3.00e+00 1.11e-01 6.29e+01 angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 110.70 129.66 -18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C02 ZGS A 601 " pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " ideal model delta sigma weight residual 127.67 111.44 16.23 3.00e+00 1.11e-01 2.93e+01 ... (remaining 9577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 3766 29.54 - 59.08: 134 59.08 - 88.62: 8 88.62 - 118.15: 1 118.15 - 147.69: 1 Dihedral angle restraints: 3910 sinusoidal: 1442 harmonic: 2468 Sorted by residual: dihedral pdb=" C23 ZGS A 601 " pdb=" O24 ZGS A 601 " pdb=" P25 ZGS A 601 " pdb=" O26 ZGS A 601 " ideal model delta sinusoidal sigma weight residual 177.58 -34.73 -147.69 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C23 ZGS A 601 " pdb=" O24 ZGS A 601 " pdb=" P25 ZGS A 601 " pdb=" O27 ZGS A 601 " ideal model delta sinusoidal sigma weight residual -49.09 -152.68 103.59 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CA LEU B 132 " pdb=" C LEU B 132 " pdb=" N PRO B 133 " pdb=" CA PRO B 133 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 3907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 849 0.050 - 0.100: 225 0.100 - 0.150: 68 0.150 - 0.200: 9 0.200 - 0.250: 5 Chirality restraints: 1156 Sorted by residual: chirality pdb=" C1BALMT A 602 " pdb=" C2BALMT A 602 " pdb=" O1BALMT A 602 " pdb=" O5BALMT A 602 " both_signs ideal model delta sigma weight residual False -2.20 -2.45 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C1B LMT A 607 " pdb=" C2B LMT A 607 " pdb=" O1B LMT A 607 " pdb=" O5B LMT A 607 " both_signs ideal model delta sigma weight residual False -2.20 -2.43 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1B LMT A 608 " pdb=" C2B LMT A 608 " pdb=" O1B LMT A 608 " pdb=" O5B LMT A 608 " both_signs ideal model delta sigma weight residual False -2.20 -2.42 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1153 not shown) Planarity restraints: 1130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO C 47 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 76 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 374 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 375 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.025 5.00e-02 4.00e+02 ... (remaining 1127 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1748 2.80 - 3.33: 6113 3.33 - 3.85: 11558 3.85 - 4.38: 12697 4.38 - 4.90: 22836 Nonbonded interactions: 54952 Sorted by model distance: nonbonded pdb=" O TYR A 43 " pdb=" OH TYR A 159 " model vdw 2.277 3.040 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 425 " pdb=" O HOH A 701 " model vdw 2.314 3.040 nonbonded pdb=" O TYR A 452 " pdb=" ND2 ASN C 99 " model vdw 2.322 3.120 nonbonded pdb=" O3' LMT A 607 " pdb=" O6'BLMT A 610 " model vdw 2.329 3.040 ... (remaining 54947 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.012 0.126 7041 Z= 0.612 Angle : 1.386 24.737 9590 Z= 0.547 Chirality : 0.053 0.250 1156 Planarity : 0.006 0.058 1130 Dihedral : 14.662 147.692 2326 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 0.84 % Allowed : 7.55 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.27), residues: 868 helix: 0.47 (0.24), residues: 385 sheet: -0.76 (0.43), residues: 150 loop : -2.76 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 40 TYR 0.013 0.001 TYR A 251 PHE 0.025 0.002 PHE B 89 TRP 0.015 0.002 TRP C 33 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.01232 / 0.61 ( 7037) covalent geometry : angle 1.38684 / 0.55 ( 9582) SS BOND : bond 0.00219 / 0.11 ( 4) SS BOND : angle 0.72782 / 0.40 ( 8) hydrogen bonds : bond 0.09925 / 6.82 ( 371) hydrogen bonds : angle 5.81154 / 4.15 ( 1088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7242 (mmm-85) cc_final: 0.6932 (ttm-80) REVERT: A 159 TYR cc_start: 0.8601 (t80) cc_final: 0.8345 (t80) REVERT: A 173 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6781 (mtt-85) REVERT: A 199 VAL cc_start: 0.8805 (t) cc_final: 0.8386 (m) REVERT: A 288 HIS cc_start: 0.7354 (t-90) cc_final: 0.6739 (t-90) REVERT: A 296 MET cc_start: 0.6885 (mmt) cc_final: 0.6637 (mmp) REVERT: A 413 GLN cc_start: 0.8528 (mm110) cc_final: 0.8013 (mt0) outliers start: 5 outliers final: 0 residues processed: 135 average time/residue: 0.0719 time to fit residues: 12.9452 Evaluate side-chains 97 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN A 152 GLN A 170 GLN A 319 ASN A 413 GLN B 190 ASN C 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.172157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139545 restraints weight = 28555.170| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 5.12 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7041 Z= 0.167 Angle : 0.662 9.553 9590 Z= 0.317 Chirality : 0.044 0.311 1156 Planarity : 0.005 0.056 1130 Dihedral : 14.270 155.717 1145 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 1.85 % Allowed : 15.10 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.28), residues: 868 helix: 1.41 (0.26), residues: 382 sheet: -1.09 (0.40), residues: 175 loop : -2.66 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 34 TYR 0.014 0.001 TYR A 291 PHE 0.023 0.002 PHE A 367 TRP 0.014 0.002 TRP A 140 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 7037) covalent geometry : angle 0.66166 / 0.32 ( 9582) SS BOND : bond 0.00234 / 0.12 ( 4) SS BOND : angle 0.62790 / 0.33 ( 8) hydrogen bonds : bond 0.03924 / 2.65 ( 371) hydrogen bonds : angle 4.68128 / 3.41 ( 1088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.7378 (ttm-80) REVERT: A 173 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6934 (mtt-85) REVERT: B 110 GLN cc_start: 0.7202 (tt0) cc_final: 0.6946 (mt0) REVERT: B 196 PHE cc_start: 0.7793 (m-80) cc_final: 0.7568 (m-80) outliers start: 11 outliers final: 6 residues processed: 108 average time/residue: 0.0615 time to fit residues: 9.0670 Evaluate side-chains 104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.171782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138451 restraints weight = 32529.236| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 6.02 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7041 Z= 0.135 Angle : 0.636 10.262 9590 Z= 0.302 Chirality : 0.042 0.291 1156 Planarity : 0.005 0.054 1130 Dihedral : 13.274 153.418 1145 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.68 % Allowed : 15.44 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.29), residues: 868 helix: 1.86 (0.26), residues: 376 sheet: -1.13 (0.40), residues: 177 loop : -2.66 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 104 TYR 0.011 0.001 TYR A 291 PHE 0.019 0.001 PHE A 367 TRP 0.012 0.001 TRP A 140 HIS 0.007 0.003 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7037) covalent geometry : angle 0.63619 / 0.30 ( 9582) SS BOND : bond 0.00217 / 0.11 ( 4) SS BOND : angle 0.60772 / 0.32 ( 8) hydrogen bonds : bond 0.03691 / 2.48 ( 371) hydrogen bonds : angle 4.42265 / 3.23 ( 1088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7433 (ttm-80) REVERT: A 288 HIS cc_start: 0.6689 (t-90) cc_final: 0.6123 (t-170) REVERT: A 296 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6317 (tpp) REVERT: B 110 GLN cc_start: 0.7152 (tt0) cc_final: 0.6943 (mt0) REVERT: B 196 PHE cc_start: 0.7963 (m-80) cc_final: 0.7698 (m-80) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.0725 time to fit residues: 10.1073 Evaluate side-chains 101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain C residue 45 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 0.0020 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136292 restraints weight = 30926.925| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 5.99 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7041 Z= 0.166 Angle : 0.658 10.258 9590 Z= 0.311 Chirality : 0.043 0.292 1156 Planarity : 0.005 0.067 1130 Dihedral : 12.733 150.566 1145 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Rotamer: Outliers : 1.68 % Allowed : 16.28 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.29), residues: 868 helix: 1.84 (0.26), residues: 380 sheet: -1.10 (0.41), residues: 173 loop : -2.56 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 173 TYR 0.010 0.001 TYR A 251 PHE 0.022 0.002 PHE B 89 TRP 0.014 0.001 TRP C 95 HIS 0.005 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7037) covalent geometry : angle 0.65776 / 0.31 ( 9582) SS BOND : bond 0.00280 / 0.14 ( 4) SS BOND : angle 0.64652 / 0.34 ( 8) hydrogen bonds : bond 0.03797 / 2.55 ( 371) hydrogen bonds : angle 4.42837 / 3.23 ( 1088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7442 (ttm-80) REVERT: A 291 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6406 (t80) REVERT: A 296 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6338 (tpp) REVERT: B 196 PHE cc_start: 0.7938 (m-80) cc_final: 0.7710 (m-80) outliers start: 10 outliers final: 5 residues processed: 105 average time/residue: 0.0761 time to fit residues: 10.8204 Evaluate side-chains 104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 141 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.170798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138174 restraints weight = 33590.345| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 5.60 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7041 Z= 0.148 Angle : 0.643 10.517 9590 Z= 0.302 Chirality : 0.043 0.293 1156 Planarity : 0.005 0.053 1130 Dihedral : 12.408 149.249 1145 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.37 % Favored : 94.51 % Rotamer: Outliers : 1.85 % Allowed : 16.44 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.29), residues: 868 helix: 1.98 (0.26), residues: 379 sheet: -1.16 (0.41), residues: 173 loop : -2.54 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 104 TYR 0.010 0.001 TYR A 251 PHE 0.027 0.002 PHE A 367 TRP 0.015 0.001 TRP C 95 HIS 0.005 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7037) covalent geometry : angle 0.64356 / 0.30 ( 9582) SS BOND : bond 0.00245 / 0.13 ( 4) SS BOND : angle 0.56484 / 0.29 ( 8) hydrogen bonds : bond 0.03672 / 2.47 ( 371) hydrogen bonds : angle 4.36817 / 3.20 ( 1088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7372 (ttm-80) REVERT: A 291 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6565 (t80) REVERT: A 296 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6148 (tpp) REVERT: B 196 PHE cc_start: 0.7942 (m-80) cc_final: 0.7694 (m-80) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.0720 time to fit residues: 9.7330 Evaluate side-chains 107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141242 restraints weight = 38836.309| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 5.65 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7041 Z= 0.121 Angle : 0.628 10.653 9590 Z= 0.294 Chirality : 0.042 0.297 1156 Planarity : 0.005 0.050 1130 Dihedral : 12.064 150.236 1145 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.34 % Allowed : 16.28 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.30), residues: 868 helix: 2.16 (0.26), residues: 379 sheet: -1.18 (0.40), residues: 176 loop : -2.50 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 34 TYR 0.010 0.001 TYR A 251 PHE 0.015 0.001 PHE B 89 TRP 0.017 0.001 TRP A 103 HIS 0.005 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7037) covalent geometry : angle 0.62824 / 0.29 ( 9582) SS BOND : bond 0.00198 / 0.10 ( 4) SS BOND : angle 0.48282 / 0.25 ( 8) hydrogen bonds : bond 0.03462 / 2.32 ( 371) hydrogen bonds : angle 4.22702 / 3.09 ( 1088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.188 Fit side-chains REVERT: A 100 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7367 (ttm-80) REVERT: A 291 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6493 (t80) REVERT: A 296 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6136 (tpp) REVERT: A 414 ASN cc_start: 0.8360 (m-40) cc_final: 0.8047 (m-40) REVERT: B 196 PHE cc_start: 0.7892 (m-80) cc_final: 0.7664 (m-80) outliers start: 8 outliers final: 6 residues processed: 104 average time/residue: 0.0776 time to fit residues: 10.9157 Evaluate side-chains 106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 56 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139903 restraints weight = 32373.755| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 5.16 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7041 Z= 0.138 Angle : 0.630 10.498 9590 Z= 0.297 Chirality : 0.043 0.290 1156 Planarity : 0.005 0.049 1130 Dihedral : 11.984 151.688 1145 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 1.34 % Allowed : 16.61 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 868 helix: 2.03 (0.26), residues: 386 sheet: -1.09 (0.41), residues: 169 loop : -2.34 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.009 0.001 TYR B 48 PHE 0.019 0.001 PHE A 367 TRP 0.043 0.002 TRP A 103 HIS 0.005 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7037) covalent geometry : angle 0.63047 / 0.30 ( 9582) SS BOND : bond 0.00199 / 0.10 ( 4) SS BOND : angle 0.48560 / 0.25 ( 8) hydrogen bonds : bond 0.03573 / 2.39 ( 371) hydrogen bonds : angle 4.25920 / 3.12 ( 1088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7397 (ttm-80) REVERT: A 291 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 296 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6142 (tpp) REVERT: A 354 LYS cc_start: 0.7579 (ttpt) cc_final: 0.7330 (ttpp) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.0801 time to fit residues: 10.9823 Evaluate side-chains 104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136999 restraints weight = 31884.093| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 5.36 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7041 Z= 0.155 Angle : 0.660 10.607 9590 Z= 0.308 Chirality : 0.043 0.281 1156 Planarity : 0.005 0.051 1130 Dihedral : 11.980 152.970 1145 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.68 % Allowed : 16.28 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.29), residues: 868 helix: 2.00 (0.26), residues: 386 sheet: -1.10 (0.41), residues: 169 loop : -2.34 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.011 0.001 TYR A 358 PHE 0.021 0.001 PHE B 89 TRP 0.029 0.002 TRP A 103 HIS 0.005 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 7037) covalent geometry : angle 0.66037 / 0.31 ( 9582) SS BOND : bond 0.00219 / 0.11 ( 4) SS BOND : angle 0.45812 / 0.24 ( 8) hydrogen bonds : bond 0.03667 / 2.45 ( 371) hydrogen bonds : angle 4.31669 / 3.16 ( 1088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7420 (ttm-80) REVERT: A 288 HIS cc_start: 0.6743 (t-90) cc_final: 0.6482 (t-170) REVERT: A 291 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6442 (t80) REVERT: A 296 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6239 (tpp) REVERT: A 319 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7948 (m110) REVERT: A 354 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7348 (ttpp) outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.0687 time to fit residues: 9.8448 Evaluate side-chains 110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 0.0470 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.170061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137234 restraints weight = 31523.092| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 5.33 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7041 Z= 0.169 Angle : 1.028 59.199 9590 Z= 0.561 Chirality : 0.043 0.280 1156 Planarity : 0.005 0.051 1130 Dihedral : 11.971 152.803 1145 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.28 % Rotamer: Outliers : 1.68 % Allowed : 17.11 % Favored : 81.21 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.29), residues: 868 helix: 2.00 (0.26), residues: 386 sheet: -1.11 (0.41), residues: 169 loop : -2.33 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 34 TYR 0.020 0.001 TYR A 318 PHE 0.020 0.001 PHE B 89 TRP 0.053 0.002 TRP A 103 HIS 0.005 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 7037) covalent geometry : angle 1.02849 / 0.56 ( 9582) SS BOND : bond 0.00206 / 0.11 ( 4) SS BOND : angle 0.49516 / 0.26 ( 8) hydrogen bonds : bond 0.03688 / 2.48 ( 371) hydrogen bonds : angle 4.26648 / 3.15 ( 1088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7384 (ttm-80) REVERT: A 172 GLU cc_start: 0.7498 (tt0) cc_final: 0.7268 (tm-30) REVERT: A 286 MET cc_start: 0.6843 (mmp) cc_final: 0.6639 (mmp) REVERT: A 291 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6446 (t80) REVERT: A 296 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6237 (tpp) REVERT: A 319 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8087 (m110) REVERT: A 354 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7368 (ttpp) outliers start: 10 outliers final: 6 residues processed: 104 average time/residue: 0.0857 time to fit residues: 11.8983 Evaluate side-chains 109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 73 optimal weight: 0.2980 chunk 41 optimal weight: 0.0970 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 0.0070 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136255 restraints weight = 37807.366| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 6.42 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7041 Z= 0.171 Angle : 1.028 59.096 9590 Z= 0.561 Chirality : 0.043 0.280 1156 Planarity : 0.005 0.051 1130 Dihedral : 11.970 152.803 1145 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.28 % Rotamer: Outliers : 1.51 % Allowed : 17.45 % Favored : 81.04 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.29), residues: 868 helix: 2.00 (0.26), residues: 386 sheet: -1.11 (0.41), residues: 169 loop : -2.33 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.020 0.001 TYR A 318 PHE 0.020 0.001 PHE B 89 TRP 0.051 0.003 TRP A 103 HIS 0.005 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7037) covalent geometry : angle 1.02871 / 0.56 ( 9582) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 0.49522 / 0.26 ( 8) hydrogen bonds : bond 0.03687 / 2.48 ( 371) hydrogen bonds : angle 4.26762 / 3.15 ( 1088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7467 (ttm-80) REVERT: A 172 GLU cc_start: 0.7649 (tt0) cc_final: 0.7325 (tm-30) REVERT: A 291 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6414 (t80) REVERT: A 296 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6314 (tpp) REVERT: A 319 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8099 (m110) REVERT: A 354 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7358 (ttpp) outliers start: 9 outliers final: 6 residues processed: 104 average time/residue: 0.0716 time to fit residues: 10.0692 Evaluate side-chains 109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 56 optimal weight: 0.0370 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 30.0000 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136539 restraints weight = 35538.027| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 6.10 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.223 7041 Z= 0.267 Angle : 1.065 59.200 9590 Z= 0.578 Chirality : 0.044 0.285 1156 Planarity : 0.005 0.070 1130 Dihedral : 11.968 152.791 1145 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.28 % Rotamer: Outliers : 1.85 % Allowed : 17.28 % Favored : 80.87 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.29), residues: 868 helix: 2.00 (0.26), residues: 386 sheet: -1.11 (0.41), residues: 169 loop : -2.33 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.019 0.001 TYR A 318 PHE 0.020 0.002 PHE B 89 TRP 0.121 0.005 TRP A 103 HIS 0.006 0.003 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.27 ( 7037) covalent geometry : angle 1.06516 / 0.58 ( 9582) SS BOND : bond 0.00200 / 0.10 ( 4) SS BOND : angle 0.49164 / 0.26 ( 8) hydrogen bonds : bond 0.03677 / 2.47 ( 371) hydrogen bonds : angle 4.28096 / 3.16 ( 1088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1263.78 seconds wall clock time: 22 minutes 29.11 seconds (1349.11 seconds total)