Starting phenix.real_space_refine on Wed Feb 14 02:53:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2w_27152/02_2024/8d2w_27152_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.74, per 1000 atoms: 1.13 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 2.6 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... running ksdssp... Secondary structure from input PDB file: 18 helices and 10 sheets defined 41.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 37 through 66 removed outlier: 3.696A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix 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 73 through 99 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 110 through 127 Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 137 through 164 Proline residue: A 158 - end of helix removed outlier: 4.197A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 199 Processing helix chain 'A' and resid 233 through 261 Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 326 through 351 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 353 through 372 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 removed outlier: 4.013A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 413 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 420 through 450 removed outlier: 3.542A pdb=" N TYR A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.574A pdb=" N LEU A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 493 through 506 removed outlier: 4.034A pdb=" N ARG A 496 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY A 498 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 18 through 22 Processing sheet with id= B, first strand: chain 'B' and resid 83 through 88 removed outlier: 5.793A pdb=" N ASN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU B 45 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'B' and resid 140 through 144 Processing sheet with id= E, 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= F, first strand: chain 'C' and resid 33 through 35 Processing sheet with id= G, first strand: chain 'C' and resid 89 through 91 Processing sheet with id= H, 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= I, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.676A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 185 through 187 342 hydrogen bonds defined for protein. 950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 3.08 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: 99.49 - 110.00: 1493 110.00 - 120.52: 5487 120.52 - 131.04: 2568 131.04 - 141.56: 31 141.56 - 152.08: 3 Bond angle restraints: 9582 Sorted by residual: angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 109.50 129.66 -20.16 3.00e+00 1.11e-01 4.51e+01 angle pdb=" CA GLU A 274 " pdb=" C GLU A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 120.77 116.95 3.82 9.70e-01 1.06e+00 1.55e+01 angle pdb=" C TRP B 49 " pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C SER B 66 " pdb=" N THR B 67 " pdb=" CA THR B 67 " ideal model delta sigma weight residual 122.61 127.82 -5.21 1.56e+00 4.11e-01 1.11e+01 angle pdb=" C GLY A 456 " pdb=" N CYS A 457 " pdb=" CA CYS A 457 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 ... (remaining 9577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 4060 24.60 - 49.21: 279 49.21 - 73.81: 98 73.81 - 98.41: 77 98.41 - 123.01: 106 Dihedral angle restraints: 4620 sinusoidal: 2152 harmonic: 2468 Sorted by residual: dihedral pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " pdb=" C09 ZGS A 601 " ideal model delta sinusoidal sigma weight residual 77.11 -159.88 -123.01 1 3.00e+01 1.11e-03 1.65e+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 4617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 850 0.050 - 0.100: 224 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: 1762 2.80 - 3.33: 6120 3.33 - 3.85: 11599 3.85 - 4.38: 12744 4.38 - 4.90: 22843 Nonbonded interactions: 55068 Sorted by model distance: nonbonded pdb=" O TYR A 43 " pdb=" OH TYR A 159 " model vdw 2.277 2.440 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR A 425 " pdb=" O HOH A 701 " model vdw 2.314 2.440 nonbonded pdb=" O TYR A 452 " pdb=" ND2 ASN C 99 " model vdw 2.322 2.520 nonbonded pdb=" O3' LMT A 607 " pdb=" O6'BLMT A 610 " model vdw 2.329 2.440 ... (remaining 55063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 11.560 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 29.200 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- 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 7037 Z= 0.761 Angle : 1.274 20.155 9582 Z= 0.515 Chirality : 0.053 0.250 1156 Planarity : 0.006 0.058 1130 Dihedral : 29.859 123.011 3036 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.717 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: 0.2013 time to fit residues: 36.0184 Evaluate side-chains 97 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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: 0.3980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 149 GLN A 152 GLN A 413 GLN A 414 ASN B 134 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7037 Z= 0.262 Angle : 0.865 9.421 9582 Z= 0.364 Chirality : 0.050 0.307 1156 Planarity : 0.005 0.056 1130 Dihedral : 18.348 108.512 1855 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.66 % Favored : 93.11 % Rotamer: Outliers : 2.35 % Allowed : 15.27 % 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: -0.97 (0.28), residues: 868 helix: 1.18 (0.25), residues: 380 sheet: -1.12 (0.40), residues: 175 loop : -2.70 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 140 HIS 0.001 0.001 HIS A 156 PHE 0.020 0.002 PHE B 89 TYR 0.013 0.001 TYR A 291 ARG 0.006 0.001 ARG B 104 *********************** 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 111 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7485 (mmm-85) cc_final: 0.7093 (ttm-80) REVERT: A 172 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7777 (mt-10) REVERT: A 173 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6774 (mtt-85) REVERT: A 199 VAL cc_start: 0.8861 (t) cc_final: 0.8551 (m) REVERT: A 286 MET cc_start: 0.7581 (mmp) cc_final: 0.7283 (mmp) REVERT: A 288 HIS cc_start: 0.7629 (t-90) cc_final: 0.6774 (t70) REVERT: A 413 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7767 (mt0) REVERT: B 110 GLN cc_start: 0.6967 (tt0) cc_final: 0.6698 (mt0) REVERT: B 196 PHE cc_start: 0.8003 (m-80) cc_final: 0.7601 (m-80) outliers start: 14 outliers final: 10 residues processed: 106 average time/residue: 0.1775 time to fit residues: 25.6460 Evaluate side-chains 105 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 480 ILE 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 Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 319 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7037 Z= 0.248 Angle : 0.697 7.510 9582 Z= 0.315 Chirality : 0.043 0.311 1156 Planarity : 0.005 0.056 1130 Dihedral : 12.733 114.968 1855 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.28 % Rotamer: Outliers : 1.85 % Allowed : 16.11 % 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: -0.84 (0.28), residues: 868 helix: 1.42 (0.26), residues: 378 sheet: -1.19 (0.40), residues: 176 loop : -2.73 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 95 HIS 0.001 0.001 HIS A 156 PHE 0.023 0.002 PHE B 89 TYR 0.011 0.001 TYR A 251 ARG 0.002 0.000 ARG C 31 *********************** 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 112 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7086 (ttm-80) REVERT: A 173 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6766 (mtt-85) REVERT: A 288 HIS cc_start: 0.7634 (t-90) cc_final: 0.7167 (t-90) REVERT: A 413 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7870 (mt0) REVERT: A 448 ASP cc_start: 0.8116 (t0) cc_final: 0.7859 (t0) REVERT: B 110 GLN cc_start: 0.6971 (tt0) cc_final: 0.6745 (mt0) REVERT: B 196 PHE cc_start: 0.8043 (m-80) cc_final: 0.7661 (m-80) outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.2150 time to fit residues: 31.4969 Evaluate side-chains 101 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7037 Z= 0.188 Angle : 0.636 7.820 9582 Z= 0.289 Chirality : 0.041 0.291 1156 Planarity : 0.004 0.053 1130 Dihedral : 11.287 113.620 1855 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 1.68 % Allowed : 18.12 % Favored : 80.20 % 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: -0.55 (0.29), residues: 868 helix: 1.59 (0.26), residues: 384 sheet: -1.07 (0.41), residues: 174 loop : -2.52 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.000 0.000 HIS A 156 PHE 0.017 0.001 PHE A 367 TYR 0.009 0.001 TYR A 251 ARG 0.005 0.000 ARG B 104 *********************** 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 105 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7500 (mmm-85) cc_final: 0.6807 (ttm-80) REVERT: A 164 MET cc_start: 0.8106 (mmt) cc_final: 0.7875 (mmt) REVERT: A 172 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7751 (mt-10) REVERT: A 173 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6723 (mtt-85) REVERT: A 199 VAL cc_start: 0.8849 (t) cc_final: 0.8533 (m) REVERT: A 288 HIS cc_start: 0.7603 (t-90) cc_final: 0.7053 (t-90) REVERT: A 291 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6379 (t80) REVERT: A 413 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7912 (mt0) REVERT: A 448 ASP cc_start: 0.8079 (t0) cc_final: 0.7826 (t0) REVERT: B 110 GLN cc_start: 0.6956 (tt0) cc_final: 0.6711 (mt0) outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.1931 time to fit residues: 25.7613 Evaluate side-chains 99 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 480 ILE 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 Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 135 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7037 Z= 0.272 Angle : 0.662 7.534 9582 Z= 0.307 Chirality : 0.042 0.305 1156 Planarity : 0.005 0.055 1130 Dihedral : 11.094 111.844 1855 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 1.51 % Allowed : 17.95 % Favored : 80.54 % 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: -0.69 (0.29), residues: 868 helix: 1.47 (0.26), residues: 383 sheet: -1.15 (0.41), residues: 174 loop : -2.57 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 95 HIS 0.001 0.001 HIS A 156 PHE 0.026 0.002 PHE B 89 TYR 0.012 0.001 TYR B 48 ARG 0.002 0.000 ARG A 34 *********************** 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 103 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7456 (ttt180) REVERT: A 164 MET cc_start: 0.8141 (mmt) cc_final: 0.7898 (mmt) REVERT: A 173 ARG cc_start: 0.7343 (mtt180) cc_final: 0.6803 (mtt-85) REVERT: A 291 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6475 (t80) REVERT: B 110 GLN cc_start: 0.6966 (tt0) cc_final: 0.6728 (mt0) outliers start: 9 outliers final: 7 residues processed: 100 average time/residue: 0.1975 time to fit residues: 26.4986 Evaluate side-chains 101 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 135 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7037 Z= 0.212 Angle : 0.625 7.623 9582 Z= 0.290 Chirality : 0.040 0.295 1156 Planarity : 0.005 0.052 1130 Dihedral : 10.672 106.904 1855 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Rotamer: Outliers : 1.85 % Allowed : 18.29 % Favored : 79.87 % 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: -0.57 (0.29), residues: 868 helix: 1.61 (0.26), residues: 382 sheet: -1.10 (0.41), residues: 174 loop : -2.55 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 95 HIS 0.008 0.003 HIS A 288 PHE 0.025 0.001 PHE A 367 TYR 0.010 0.001 TYR A 251 ARG 0.004 0.000 ARG A 100 *********************** 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 104 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8116 (mmt) cc_final: 0.7910 (mmt) REVERT: A 172 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7733 (mt-10) REVERT: A 173 ARG cc_start: 0.7286 (mtt180) cc_final: 0.6710 (mtt-85) REVERT: A 199 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8497 (m) REVERT: A 288 HIS cc_start: 0.7369 (t70) cc_final: 0.6527 (t-170) REVERT: A 291 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6543 (t80) REVERT: A 448 ASP cc_start: 0.8030 (t0) cc_final: 0.7800 (t0) REVERT: B 110 GLN cc_start: 0.6899 (tt0) cc_final: 0.6652 (mt0) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.1821 time to fit residues: 24.2755 Evaluate side-chains 102 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 0.0170 chunk 46 optimal weight: 0.0770 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7037 Z= 0.153 Angle : 0.596 7.876 9582 Z= 0.276 Chirality : 0.039 0.287 1156 Planarity : 0.005 0.047 1130 Dihedral : 10.138 103.582 1855 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.37 % Favored : 94.51 % Rotamer: Outliers : 1.68 % Allowed : 18.29 % 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: -0.40 (0.29), residues: 868 helix: 1.67 (0.26), residues: 389 sheet: -1.07 (0.41), residues: 174 loop : -2.38 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 103 HIS 0.007 0.002 HIS A 288 PHE 0.014 0.001 PHE B 89 TYR 0.009 0.001 TYR B 48 ARG 0.004 0.000 ARG A 100 *********************** 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 fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8087 (mmt) cc_final: 0.7851 (mmt) REVERT: A 172 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7724 (mt-10) REVERT: A 173 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6641 (mtt-85) REVERT: A 199 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8529 (m) REVERT: A 291 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6251 (t80) REVERT: A 448 ASP cc_start: 0.8077 (t0) cc_final: 0.7868 (t0) REVERT: B 110 GLN cc_start: 0.6795 (tt0) cc_final: 0.6549 (mt0) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1995 time to fit residues: 27.3490 Evaluate side-chains 104 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.0060 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7037 Z= 0.244 Angle : 0.647 8.082 9582 Z= 0.303 Chirality : 0.041 0.298 1156 Planarity : 0.005 0.049 1130 Dihedral : 10.109 99.595 1855 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.43 % Favored : 93.46 % Rotamer: Outliers : 1.85 % Allowed : 18.62 % Favored : 79.53 % 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: -0.54 (0.29), residues: 868 helix: 1.51 (0.26), residues: 389 sheet: -1.10 (0.42), residues: 169 loop : -2.40 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 103 HIS 0.002 0.001 HIS A 288 PHE 0.027 0.002 PHE A 367 TYR 0.012 0.001 TYR B 48 ARG 0.004 0.001 ARG A 100 *********************** 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 112 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.747 Fit side-chains REVERT: A 164 MET cc_start: 0.8090 (mmt) cc_final: 0.7864 (mmt) REVERT: A 172 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7724 (mt-10) REVERT: A 173 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6710 (mtt-85) REVERT: A 199 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8470 (m) REVERT: A 286 MET cc_start: 0.6999 (mmp) cc_final: 0.6772 (mmp) REVERT: A 291 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6388 (t80) REVERT: A 448 ASP cc_start: 0.8108 (t0) cc_final: 0.7849 (t0) REVERT: B 110 GLN cc_start: 0.6855 (tt0) cc_final: 0.6597 (mt0) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 0.1889 time to fit residues: 27.0902 Evaluate side-chains 102 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 4 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 Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7037 Z= 0.180 Angle : 0.609 7.732 9582 Z= 0.284 Chirality : 0.040 0.291 1156 Planarity : 0.005 0.047 1130 Dihedral : 9.735 93.601 1855 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.85 % Allowed : 18.62 % Favored : 79.53 % 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: -0.44 (0.29), residues: 868 helix: 1.65 (0.26), residues: 387 sheet: -1.05 (0.42), residues: 169 loop : -2.41 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 103 HIS 0.005 0.002 HIS A 288 PHE 0.016 0.001 PHE B 89 TYR 0.010 0.001 TYR B 48 ARG 0.004 0.000 ARG A 100 *********************** 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 fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7740 (mt-10) REVERT: A 173 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6960 (mtt-85) REVERT: A 199 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8512 (m) REVERT: A 286 MET cc_start: 0.6981 (mmp) cc_final: 0.6778 (mmp) REVERT: A 291 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6503 (t80) REVERT: B 110 GLN cc_start: 0.6818 (tt0) cc_final: 0.6552 (mt0) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2237 time to fit residues: 29.6541 Evaluate side-chains 105 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 4 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 Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 0.0060 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 0.0070 chunk 7 optimal weight: 0.0570 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.0170 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.0170 chunk 20 optimal weight: 0.6980 overall best weight: 0.0208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7037 Z= 0.134 Angle : 0.573 8.279 9582 Z= 0.266 Chirality : 0.038 0.275 1156 Planarity : 0.004 0.045 1130 Dihedral : 9.079 85.712 1855 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.67 % Favored : 95.21 % Rotamer: Outliers : 1.17 % Allowed : 20.13 % Favored : 78.69 % 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: -0.06 (0.30), residues: 868 helix: 1.88 (0.27), residues: 388 sheet: -0.83 (0.41), residues: 186 loop : -2.18 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 103 HIS 0.003 0.001 HIS A 288 PHE 0.017 0.001 PHE A 367 TYR 0.008 0.001 TYR B 48 ARG 0.005 0.001 ARG A 323 ********************** 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 102 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8021 (ptt-90) REVERT: A 115 LEU cc_start: 0.8193 (mp) cc_final: 0.7712 (pt) REVERT: A 172 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7686 (mt-10) REVERT: A 173 ARG cc_start: 0.7149 (mtt180) cc_final: 0.6544 (mtt-85) REVERT: A 199 VAL cc_start: 0.8813 (t) cc_final: 0.8593 (m) REVERT: A 291 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.6128 (t80) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 0.2039 time to fit residues: 26.8821 Evaluate side-chains 98 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 291 TYR 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 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** 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 = 0.3990 r_free = 0.3990 target = 0.172579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136800 restraints weight = 30180.124| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 6.42 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 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 = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7037 Z= 0.179 Angle : 0.607 8.074 9582 Z= 0.279 Chirality : 0.039 0.286 1156 Planarity : 0.004 0.043 1130 Dihedral : 8.975 79.056 1855 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 0.84 % Allowed : 20.64 % Favored : 78.52 % 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: -0.13 (0.29), residues: 868 helix: 1.90 (0.26), residues: 387 sheet: -0.93 (0.43), residues: 163 loop : -2.20 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 103 HIS 0.004 0.002 HIS A 288 PHE 0.016 0.001 PHE B 89 TYR 0.010 0.001 TYR B 48 ARG 0.004 0.000 ARG A 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.03 seconds wall clock time: 35 minutes 16.33 seconds (2116.33 seconds total)