Starting phenix.real_space_refine on Sat Jul 26 04:26:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2w_27152/07_2025/8d2w_27152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2w_27152/07_2025/8d2w_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2025/8d2w_27152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2025/8d2w_27152.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2025/8d2w_27152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2w_27152/07_2025/8d2w_27152.cif" } 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= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} 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: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 4, '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: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 4, '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: 179 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: 179 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: 8.48, per 1000 atoms: 1.24 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: 1.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.66 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: 1.95 Time building geometry restraints manager: 2.28 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: 4151 29.54 - 59.08: 248 59.08 - 88.62: 93 88.62 - 118.15: 137 118.15 - 147.69: 5 Dihedral angle restraints: 4634 sinusoidal: 2166 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=" C5B LMT C 301 " pdb=" C1B LMT C 301 " pdb=" O5B LMT C 301 " pdb=" O1B LMT C 301 " ideal model delta sinusoidal sigma weight residual 295.61 173.64 121.97 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C2B LMT C 301 " pdb=" C1B LMT C 301 " pdb=" O5B LMT C 301 " pdb=" C5B LMT C 301 " ideal model delta sinusoidal sigma weight residual -57.12 64.84 -121.96 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 4631 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 24.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 : 29.930 147.692 3050 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.85 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 (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: -1.42 (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 TRP 0.015 0.002 TRP C 33 HIS 0.001 0.000 HIS A 156 PHE 0.025 0.002 PHE B 89 TYR 0.013 0.001 TYR A 251 ARG 0.002 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.09925 ( 371) hydrogen bonds : angle 5.81154 ( 1088) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.72782 ( 8) covalent geometry : bond 0.01232 ( 7037) covalent geometry : angle 1.38684 ( 9582) *********************** 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 : 0.680 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: 0.8602 (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: 0.6738 (t-90) REVERT: A 296 MET cc_start: 0.6886 (mmt) cc_final: 0.6637 (mmp) REVERT: A 413 GLN cc_start: 0.8528 (mm110) cc_final: 0.8012 (mt0) outliers start: 5 outliers final: 0 residues processed: 135 average time/residue: 0.1952 time to fit residues: 34.8474 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 : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 152 GLN A 319 ASN A 413 GLN B 190 ASN C 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.170508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136682 restraints weight = 37604.942| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 6.41 r_work (final): 0.3588 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 7041 Z= 0.195 Angle : 0.894 9.925 9590 Z= 0.382 Chirality : 0.052 0.304 1156 Planarity : 0.005 0.057 1130 Dihedral : 19.396 156.216 1869 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.43 % Favored : 93.46 % Rotamer: Outliers : 2.18 % Allowed : 14.60 % Favored : 83.22 % 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: -0.82 (0.28), residues: 868 helix: 1.38 (0.25), residues: 381 sheet: -1.12 (0.41), residues: 175 loop : -2.72 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 140 HIS 0.002 0.001 HIS A 156 PHE 0.024 0.002 PHE A 367 TYR 0.013 0.002 TYR A 291 ARG 0.005 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 371) hydrogen bonds : angle 4.63800 ( 1088) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.76633 ( 8) covalent geometry : bond 0.00463 ( 7037) covalent geometry : angle 0.89436 ( 9582) *********************** 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 115 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7533 (ttm-80) REVERT: A 164 MET cc_start: 0.8260 (mmt) cc_final: 0.7999 (mmm) REVERT: A 172 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7942 (mt-10) REVERT: B 110 GLN cc_start: 0.7175 (tt0) cc_final: 0.6916 (mt0) REVERT: B 196 PHE cc_start: 0.8023 (m-80) cc_final: 0.7745 (m-80) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.3049 time to fit residues: 46.2701 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 : 1.057 ------------------------------------------------------------------------------- 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 439 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 VAL 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 54 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135218 restraints weight = 38160.362| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 6.56 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7041 Z= 0.177 Angle : 0.743 9.617 9590 Z= 0.337 Chirality : 0.045 0.325 1156 Planarity : 0.005 0.056 1130 Dihedral : 14.289 150.947 1869 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.19 % Favored : 93.69 % Rotamer: Outliers : 2.68 % Allowed : 15.10 % Favored : 82.21 % 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: -0.63 (0.29), residues: 868 helix: 1.65 (0.26), residues: 379 sheet: -1.16 (0.41), residues: 175 loop : -2.65 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.002 0.001 HIS A 156 PHE 0.022 0.002 PHE B 89 TYR 0.012 0.001 TYR A 291 ARG 0.004 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 371) hydrogen bonds : angle 4.51355 ( 1088) SS BOND : bond 0.00324 ( 4) SS BOND : angle 0.65793 ( 8) covalent geometry : bond 0.00414 ( 7037) covalent geometry : angle 0.74287 ( 9582) *********************** 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 116 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7463 (ttm-80) REVERT: A 173 ARG cc_start: 0.7279 (mtt180) cc_final: 0.7059 (mtt-85) REVERT: A 288 HIS cc_start: 0.6439 (t-170) cc_final: 0.5147 (t-170) REVERT: A 291 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.6400 (t80) REVERT: A 296 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6614 (tpp) REVERT: A 319 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: B 110 GLN cc_start: 0.7156 (tt0) cc_final: 0.6927 (mt0) REVERT: B 196 PHE cc_start: 0.8045 (m-80) cc_final: 0.7737 (m-80) outliers start: 16 outliers final: 7 residues processed: 108 average time/residue: 0.1908 time to fit residues: 27.7630 Evaluate side-chains 107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 319 ASN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135294 restraints weight = 34388.427| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 6.10 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7041 Z= 0.161 Angle : 0.686 10.327 9590 Z= 0.317 Chirality : 0.042 0.294 1156 Planarity : 0.005 0.055 1130 Dihedral : 12.643 148.408 1869 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 1.68 % Allowed : 15.94 % 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 (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: -0.47 (0.29), residues: 868 helix: 1.81 (0.26), residues: 379 sheet: -1.14 (0.42), residues: 173 loop : -2.55 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 95 HIS 0.002 0.001 HIS A 288 PHE 0.026 0.002 PHE A 367 TYR 0.012 0.001 TYR A 358 ARG 0.004 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 371) hydrogen bonds : angle 4.48334 ( 1088) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.57447 ( 8) covalent geometry : bond 0.00379 ( 7037) covalent geometry : angle 0.68568 ( 9582) *********************** 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 108 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7356 (ttm-80) REVERT: A 296 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6418 (tpp) REVERT: B 196 PHE cc_start: 0.7964 (m-80) cc_final: 0.7713 (m-80) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.1988 time to fit residues: 27.4467 Evaluate side-chains 102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 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 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 0.0060 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3970 r_free = 0.3970 target = 0.170350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138088 restraints weight = 39589.827| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 5.94 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2443 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= 0.143 Angle : 0.662 10.374 9590 Z= 0.306 Chirality : 0.041 0.290 1156 Planarity : 0.005 0.051 1130 Dihedral : 12.021 149.613 1869 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.51 % Allowed : 16.44 % 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 (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: -0.33 (0.29), residues: 868 helix: 1.95 (0.26), residues: 379 sheet: -1.09 (0.41), residues: 174 loop : -2.52 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 103 HIS 0.002 0.001 HIS A 288 PHE 0.019 0.001 PHE B 89 TYR 0.010 0.001 TYR B 48 ARG 0.009 0.001 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 371) hydrogen bonds : angle 4.35952 ( 1088) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.50488 ( 8) covalent geometry : bond 0.00334 ( 7037) covalent geometry : angle 0.66255 ( 9582) *********************** 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 105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.627 Fit side-chains REVERT: A 100 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7454 (ttm-80) REVERT: A 291 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6328 (t80) REVERT: A 296 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6331 (tpp) outliers start: 9 outliers final: 6 residues processed: 100 average time/residue: 0.1992 time to fit residues: 26.8289 Evaluate side-chains 103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 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 = 0.3949 r_free = 0.3949 target = 0.168938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145221 restraints weight = 36129.213| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.53 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2556 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= 0.167 Angle : 0.680 10.170 9590 Z= 0.315 Chirality : 0.042 0.292 1156 Planarity : 0.005 0.052 1130 Dihedral : 11.792 151.089 1869 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.19 % Favored : 93.69 % Rotamer: Outliers : 1.68 % Allowed : 15.94 % 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 (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: -0.38 (0.29), residues: 868 helix: 1.79 (0.26), residues: 386 sheet: -1.18 (0.41), residues: 173 loop : -2.42 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 103 HIS 0.002 0.001 HIS A 156 PHE 0.028 0.002 PHE A 367 TYR 0.011 0.001 TYR A 358 ARG 0.002 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 371) hydrogen bonds : angle 4.39780 ( 1088) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.54990 ( 8) covalent geometry : bond 0.00394 ( 7037) covalent geometry : angle 0.68012 ( 9582) *********************** 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 106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7175 (ttm-80) REVERT: A 291 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.6345 (t80) REVERT: A 296 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6055 (tpp) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.1960 time to fit residues: 26.5270 Evaluate side-chains 102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 70 optimal weight: 0.0970 chunk 45 optimal weight: 30.0000 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 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 = 0.3976 r_free = 0.3976 target = 0.171384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141953 restraints weight = 40213.900| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 6.45 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2679 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= 0.137 Angle : 0.646 10.440 9590 Z= 0.300 Chirality : 0.040 0.284 1156 Planarity : 0.005 0.053 1130 Dihedral : 11.393 152.255 1869 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.37 % Favored : 94.51 % Rotamer: Outliers : 1.68 % Allowed : 16.61 % 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 (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: -0.25 (0.29), residues: 868 helix: 1.91 (0.26), residues: 386 sheet: -1.14 (0.41), residues: 169 loop : -2.33 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 103 HIS 0.002 0.001 HIS A 156 PHE 0.017 0.001 PHE B 89 TYR 0.010 0.001 TYR B 48 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 371) hydrogen bonds : angle 4.29553 ( 1088) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.46026 ( 8) covalent geometry : bond 0.00319 ( 7037) covalent geometry : angle 0.64574 ( 9582) *********************** 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 108 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7653 (ttm-80) REVERT: A 291 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.6258 (t80) REVERT: A 296 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6485 (tpp) REVERT: A 354 LYS cc_start: 0.7599 (ttpp) cc_final: 0.7233 (ttmt) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.1889 time to fit residues: 25.8702 Evaluate side-chains 101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG 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 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 141 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143690 restraints weight = 34435.337| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 5.54 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2732 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= 0.130 Angle : 0.639 10.583 9590 Z= 0.296 Chirality : 0.040 0.281 1156 Planarity : 0.005 0.053 1130 Dihedral : 11.081 153.716 1869 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.68 % Allowed : 16.95 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.29), residues: 868 helix: 1.95 (0.26), residues: 387 sheet: -1.12 (0.41), residues: 169 loop : -2.28 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 103 HIS 0.004 0.002 HIS A 288 PHE 0.018 0.001 PHE A 367 TYR 0.009 0.001 TYR B 48 ARG 0.007 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 371) hydrogen bonds : angle 4.23804 ( 1088) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.45168 ( 8) covalent geometry : bond 0.00301 ( 7037) covalent geometry : angle 0.63940 ( 9582) *********************** 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 105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7592 (ttm-80) REVERT: A 291 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6353 (t80) REVERT: A 296 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6349 (tpp) REVERT: A 354 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7155 (ttmt) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.1915 time to fit residues: 25.3408 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 : 0.617 ------------------------------------------------------------------------------- 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 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.0020 chunk 82 optimal weight: 0.0970 chunk 48 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 0.0470 chunk 61 optimal weight: 0.9980 overall best weight: 0.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 36 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.175631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149637 restraints weight = 34225.270| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.98 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7041 Z= 0.105 Angle : 0.611 10.982 9590 Z= 0.284 Chirality : 0.039 0.268 1156 Planarity : 0.005 0.054 1130 Dihedral : 10.625 156.446 1869 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 1.17 % Allowed : 17.95 % Favored : 80.87 % 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: 0.00 (0.29), residues: 868 helix: 2.11 (0.26), residues: 388 sheet: -1.04 (0.41), residues: 167 loop : -2.19 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 103 HIS 0.004 0.002 HIS A 288 PHE 0.012 0.001 PHE B 89 TYR 0.008 0.001 TYR B 48 ARG 0.005 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 371) hydrogen bonds : angle 4.11829 ( 1088) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.42630 ( 8) covalent geometry : bond 0.00232 ( 7037) covalent geometry : angle 0.61091 ( 9582) *********************** 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 105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7529 (ttm-80) REVERT: A 291 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.6152 (t80) REVERT: A 296 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6177 (tpp) REVERT: A 354 LYS cc_start: 0.7439 (ttpp) cc_final: 0.7067 (ttmt) outliers start: 7 outliers final: 3 residues processed: 101 average time/residue: 0.1914 time to fit residues: 25.9992 Evaluate side-chains 98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 0.0980 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 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 = 0.3997 r_free = 0.3997 target = 0.173418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147818 restraints weight = 28817.287| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.21 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7041 Z= 0.125 Angle : 0.627 10.699 9590 Z= 0.290 Chirality : 0.040 0.273 1156 Planarity : 0.005 0.055 1130 Dihedral : 10.520 156.623 1869 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.01 % Allowed : 18.96 % Favored : 80.03 % 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: 0.03 (0.29), residues: 868 helix: 2.13 (0.26), residues: 386 sheet: -0.91 (0.41), residues: 169 loop : -2.22 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 103 HIS 0.005 0.002 HIS A 288 PHE 0.020 0.001 PHE A 367 TYR 0.009 0.001 TYR B 48 ARG 0.006 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 371) hydrogen bonds : angle 4.13670 ( 1088) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.47506 ( 8) covalent geometry : bond 0.00289 ( 7037) covalent geometry : angle 0.62754 ( 9582) ********************** 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 103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7478 (ttm-80) REVERT: A 291 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.6344 (t80) REVERT: A 296 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6268 (tpp) REVERT: A 354 LYS cc_start: 0.7371 (ttpp) cc_final: 0.7021 (ttmt) outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.1953 time to fit residues: 26.1166 Evaluate side-chains 100 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG 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 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 0.0070 chunk 31 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 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 = 0.3994 r_free = 0.3994 target = 0.173094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147697 restraints weight = 35031.008| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.10 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7041 Z= 0.128 Angle : 0.632 10.616 9590 Z= 0.294 Chirality : 0.040 0.273 1156 Planarity : 0.005 0.056 1130 Dihedral : 10.452 157.265 1869 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.02 % Favored : 94.86 % Rotamer: Outliers : 1.17 % Allowed : 18.46 % Favored : 80.37 % 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: 0.01 (0.29), residues: 868 helix: 2.07 (0.26), residues: 387 sheet: -0.90 (0.41), residues: 169 loop : -2.21 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 103 HIS 0.005 0.002 HIS A 288 PHE 0.017 0.001 PHE B 89 TYR 0.009 0.001 TYR A 251 ARG 0.006 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 371) hydrogen bonds : angle 4.14705 ( 1088) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.42723 ( 8) covalent geometry : bond 0.00294 ( 7037) covalent geometry : angle 0.63252 ( 9582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4521.93 seconds wall clock time: 81 minutes 40.95 seconds (4900.95 seconds total)