Starting phenix.real_space_refine on Fri Feb 16 19:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ne3_9356/02_2024/6ne3_9356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ne3_9356/02_2024/6ne3_9356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ne3_9356/02_2024/6ne3_9356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ne3_9356/02_2024/6ne3_9356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ne3_9356/02_2024/6ne3_9356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ne3_9356/02_2024/6ne3_9356_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 313 5.49 5 S 36 5.16 5 C 9321 2.51 5 N 3024 2.21 5 O 3642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "W ARG 272": "NH1" <-> "NH2" Residue "W ASP 273": "OD1" <-> "OD2" Residue "W TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 309": "OE1" <-> "OE2" Residue "W ASP 363": "OD1" <-> "OD2" Residue "W ASP 364": "OD1" <-> "OD2" Residue "W ASP 399": "OD1" <-> "OD2" Residue "W ARG 421": "NH1" <-> "NH2" Residue "W ARG 426": "NH1" <-> "NH2" Residue "W ASP 431": "OD1" <-> "OD2" Residue "W ASP 464": "OD1" <-> "OD2" Residue "W ASP 513": "OD1" <-> "OD2" Residue "W GLU 525": "OE1" <-> "OE2" Residue "W ASP 578": "OD1" <-> "OD2" Residue "W ARG 603": "NH1" <-> "NH2" Residue "W PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 620": "NH1" <-> "NH2" Residue "W GLU 622": "OE1" <-> "OE2" Residue "W ARG 626": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16336 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 780 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3178 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "I" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3215 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "W" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3764 Unusual residues: {'ADP': 1} Classifications: {'peptide': 461, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 441, None: 1} Not linked: pdbres="GLN W 634 " pdbres="ADP W 801 " Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ALA B 15 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 15 " occ=0.00 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N GLY C 8 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 8 " occ=0.00 residue: pdb=" N LYS C 9 " occ=0.00 ... (3 atoms not shown) pdb=" CB LYS C 9 " occ=0.00 residue: pdb=" N LYS C 13 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 13 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N GLU C 121 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU C 121 " occ=0.00 residue: pdb=" N ARG G 11 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 11 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 8.81, per 1000 atoms: 0.54 Number of scatterers: 16336 At special positions: 0 Unit cell: (96.0324, 145.872, 154.381, 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 36 16.00 P 313 15.00 O 3642 8.00 N 3024 7.00 C 9321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16331 O3A ADP W 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.58 Conformation dependent library (CDL) restraints added in 1.9 seconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 3 sheets defined 54.1% alpha, 3.1% beta 154 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 8.82 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.815A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 113 Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 87 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.759A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 75 removed outlier: 3.898A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.879A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 54 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'W' and resid 182 through 197 Processing helix chain 'W' and resid 211 through 225 removed outlier: 3.624A pdb=" N HIS W 224 " --> pdb=" O GLY W 220 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 250 removed outlier: 3.819A pdb=" N LEU W 241 " --> pdb=" O LYS W 238 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS W 242 " --> pdb=" O SER W 239 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 274 Processing helix chain 'W' and resid 287 through 292 Processing helix chain 'W' and resid 294 through 299 removed outlier: 4.321A pdb=" N LYS W 299 " --> pdb=" O SER W 295 " (cutoff:3.500A) Processing helix chain 'W' and resid 319 through 325 Processing helix chain 'W' and resid 345 through 354 Processing helix chain 'W' and resid 356 through 358 No H-bonds generated for 'chain 'W' and resid 356 through 358' Processing helix chain 'W' and resid 362 through 368 Processing helix chain 'W' and resid 379 through 391 Proline residue: W 390 - end of helix Processing helix chain 'W' and resid 397 through 400 No H-bonds generated for 'chain 'W' and resid 397 through 400' Processing helix chain 'W' and resid 418 through 429 Processing helix chain 'W' and resid 449 through 458 Processing helix chain 'W' and resid 460 through 462 No H-bonds generated for 'chain 'W' and resid 460 through 462' Processing helix chain 'W' and resid 483 through 498 Proline residue: W 493 - end of helix Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 535 through 537 No H-bonds generated for 'chain 'W' and resid 535 through 537' Processing helix chain 'W' and resid 539 through 545 Processing helix chain 'W' and resid 559 through 563 Processing helix chain 'W' and resid 583 through 591 Processing helix chain 'W' and resid 614 through 632 removed outlier: 4.223A pdb=" N VAL W 631 " --> pdb=" O LEU W 627 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 201 through 203 removed outlier: 3.581A pdb=" N LEU W 334 " --> pdb=" O GLY W 201 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N MET W 233 " --> pdb=" O TYR W 304 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS W 283 " --> pdb=" O HIS W 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL W 284 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU W 260 " --> pdb=" O VAL W 284 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER W 286 " --> pdb=" O LEU W 260 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'W' and resid 408 through 413 removed outlier: 3.887A pdb=" N ARG W 606 " --> pdb=" O VAL W 410 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'W' and resid 573 through 576 464 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 393 hydrogen bonds 782 hydrogen bond angles 0 basepair planarities 154 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 8.45 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3095 1.33 - 1.45: 5471 1.45 - 1.57: 8024 1.57 - 1.69: 624 1.69 - 1.81: 64 Bond restraints: 17278 Sorted by residual: bond pdb=" C GLN C 24 " pdb=" N PHE C 25 " ideal model delta sigma weight residual 1.331 1.284 0.048 1.59e-02 3.96e+03 8.99e+00 bond pdb=" C GLN G 24 " pdb=" N PHE G 25 " ideal model delta sigma weight residual 1.331 1.259 0.072 2.83e-02 1.25e+03 6.46e+00 bond pdb=" C3' DG J 2 " pdb=" O3' DG J 2 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.96e+00 bond pdb=" C3' DC J 118 " pdb=" O3' DC J 118 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.93e+00 bond pdb=" CG1 ILE H 91 " pdb=" CD1 ILE H 91 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.78e+00 ... (remaining 17273 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.88: 1423 104.88 - 112.68: 9737 112.68 - 120.48: 7777 120.48 - 128.29: 5330 128.29 - 136.09: 425 Bond angle restraints: 24692 Sorted by residual: angle pdb=" N VAL W 602 " pdb=" CA VAL W 602 " pdb=" C VAL W 602 " ideal model delta sigma weight residual 106.21 112.15 -5.94 1.07e+00 8.73e-01 3.09e+01 angle pdb=" C GLN E 85 " pdb=" N SER E 86 " pdb=" CA SER E 86 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLN A 85 " pdb=" N SER A 86 " pdb=" CA SER A 86 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C3' DG J 2 " pdb=" O3' DG J 2 " pdb=" P DG J 3 " ideal model delta sigma weight residual 120.20 125.97 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" CA LEU F 62 " pdb=" CB LEU F 62 " pdb=" CG LEU F 62 " ideal model delta sigma weight residual 116.30 129.50 -13.20 3.50e+00 8.16e-02 1.42e+01 ... (remaining 24687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 7814 35.08 - 70.17: 1733 70.17 - 105.25: 58 105.25 - 140.34: 5 140.34 - 175.42: 2 Dihedral angle restraints: 9612 sinusoidal: 5983 harmonic: 3629 Sorted by residual: dihedral pdb=" CA PRO W 470 " pdb=" C PRO W 470 " pdb=" N PRO W 471 " pdb=" CA PRO W 471 " ideal model delta harmonic sigma weight residual 180.00 142.62 37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA GLY W 469 " pdb=" C GLY W 469 " pdb=" N PRO W 470 " pdb=" CA PRO W 470 " ideal model delta harmonic sigma weight residual 180.00 -144.13 -35.87 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" C5' ADP W 801 " pdb=" O5' ADP W 801 " pdb=" PA ADP W 801 " pdb=" O2A ADP W 801 " ideal model delta sinusoidal sigma weight residual -60.00 69.52 -129.52 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 9609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2483 0.080 - 0.159: 296 0.159 - 0.239: 17 0.239 - 0.319: 0 0.319 - 0.399: 1 Chirality restraints: 2797 Sorted by residual: chirality pdb=" CB ILE W 202 " pdb=" CA ILE W 202 " pdb=" CG1 ILE W 202 " pdb=" CG2 ILE W 202 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CB ILE W 608 " pdb=" CA ILE W 608 " pdb=" CG1 ILE W 608 " pdb=" CG2 ILE W 608 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE W 504 " pdb=" CA ILE W 504 " pdb=" CG1 ILE W 504 " pdb=" CG2 ILE W 504 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2794 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 20 " 0.052 2.00e-02 2.50e+03 2.09e-02 1.31e+01 pdb=" N9 DG J 20 " -0.043 2.00e-02 2.50e+03 pdb=" C8 DG J 20 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG J 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG J 20 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG J 20 " 0.008 2.00e-02 2.50e+03 pdb=" O6 DG J 20 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DG J 20 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DG J 20 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG J 20 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 20 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DG J 20 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 21 " 0.046 2.00e-02 2.50e+03 1.92e-02 1.11e+01 pdb=" N9 DG J 21 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DG J 21 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG J 21 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG J 21 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DG J 21 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 21 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DG J 21 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 21 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG J 21 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG J 21 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 102 " 0.042 2.00e-02 2.50e+03 1.84e-02 9.33e+00 pdb=" N9 DA J 102 " -0.033 2.00e-02 2.50e+03 pdb=" C8 DA J 102 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J 102 " -0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 102 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA J 102 " 0.008 2.00e-02 2.50e+03 pdb=" N6 DA J 102 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA J 102 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA J 102 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA J 102 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA J 102 " -0.005 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4260 2.81 - 3.33: 14940 3.33 - 3.85: 33473 3.85 - 4.38: 36710 4.38 - 4.90: 53164 Nonbonded interactions: 142547 Sorted by model distance: nonbonded pdb=" O ARG W 538 " pdb=" OG SER W 541 " model vdw 2.287 2.440 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.296 2.440 nonbonded pdb=" O2 DC J 94 " pdb=" N2 DG I 113 " model vdw 2.302 2.496 nonbonded pdb=" OG SER W 500 " pdb=" OD1 ASP W 572 " model vdw 2.307 2.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.310 2.440 ... (remaining 142542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and (resid 37 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 102)) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 117 or (resid 118 through 119 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.850 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 55.110 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 17278 Z= 0.471 Angle : 0.951 13.198 24692 Z= 0.543 Chirality : 0.052 0.399 2797 Planarity : 0.007 0.070 2042 Dihedral : 28.201 175.419 7264 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.48 % Allowed : 10.51 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 4.65 % 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: -3.61 (0.19), residues: 1225 helix: -1.82 (0.15), residues: 726 sheet: -3.25 (0.57), residues: 71 loop : -3.04 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP W 348 HIS 0.011 0.002 HIS B 75 PHE 0.034 0.003 PHE W 391 TYR 0.015 0.002 TYR B 72 ARG 0.005 0.001 ARG W 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7481 (tp40) REVERT: B 84 MET cc_start: 0.7237 (mmm) cc_final: 0.6958 (mmm) REVERT: C 36 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7348 (mmtt) REVERT: C 56 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 92 GLU cc_start: 0.7172 (mp0) cc_final: 0.6786 (mp0) REVERT: C 99 ARG cc_start: 0.8023 (mmt180) cc_final: 0.7797 (mmm160) REVERT: C 104 GLN cc_start: 0.7812 (mm110) cc_final: 0.6941 (tt0) REVERT: D 31 LYS cc_start: 0.8163 (tptm) cc_final: 0.7858 (tppt) REVERT: D 48 ASP cc_start: 0.8699 (t70) cc_final: 0.8179 (p0) REVERT: D 65 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7086 (t0) REVERT: D 68 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7464 (tm-30) REVERT: D 90 GLU cc_start: 0.7219 (mp0) cc_final: 0.6178 (mp0) REVERT: D 110 GLU cc_start: 0.7006 (tp30) cc_final: 0.6802 (tp30) REVERT: E 61 LEU cc_start: 0.7567 (mt) cc_final: 0.7267 (mt) REVERT: E 76 GLN cc_start: 0.7679 (tp40) cc_final: 0.7344 (mm-40) REVERT: E 107 THR cc_start: 0.7707 (m) cc_final: 0.7416 (t) REVERT: E 110 CYS cc_start: 0.8543 (t) cc_final: 0.7630 (t) REVERT: E 123 ASP cc_start: 0.7592 (m-30) cc_final: 0.7201 (m-30) REVERT: F 59 LYS cc_start: 0.7451 (ttpt) cc_final: 0.7111 (ttpp) REVERT: F 77 LYS cc_start: 0.8305 (mttt) cc_final: 0.8076 (mmtp) REVERT: G 36 LYS cc_start: 0.8179 (mmtp) cc_final: 0.7670 (mmmm) REVERT: G 64 GLU cc_start: 0.7540 (tt0) cc_final: 0.7202 (pt0) REVERT: G 90 ASP cc_start: 0.6967 (t70) cc_final: 0.6210 (t70) REVERT: G 95 LYS cc_start: 0.8488 (tttp) cc_final: 0.7825 (tptp) REVERT: G 104 GLN cc_start: 0.8217 (tp40) cc_final: 0.7972 (tp40) REVERT: G 110 ASN cc_start: 0.8306 (t0) cc_final: 0.7912 (p0) REVERT: H 33 SER cc_start: 0.7967 (t) cc_final: 0.7430 (p) REVERT: H 73 GLU cc_start: 0.7605 (tp30) cc_final: 0.7116 (tp30) REVERT: H 117 LYS cc_start: 0.7047 (tptm) cc_final: 0.6795 (tptt) REVERT: W 174 TYR cc_start: 0.5134 (p90) cc_final: 0.4638 (p90) REVERT: W 233 MET cc_start: 0.7294 (ptp) cc_final: 0.6930 (ptp) REVERT: W 289 MET cc_start: 0.8810 (mmt) cc_final: 0.8603 (mmm) REVERT: W 309 GLU cc_start: 0.7672 (tp30) cc_final: 0.7244 (tp30) REVERT: W 322 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7995 (mm-30) REVERT: W 389 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7179 (mmm-85) REVERT: W 419 MET cc_start: 0.8346 (ttm) cc_final: 0.8056 (ttm) REVERT: W 590 MET cc_start: 0.8209 (tpp) cc_final: 0.7843 (tpp) REVERT: W 616 ARG cc_start: 0.8709 (mmp-170) cc_final: 0.8307 (ttp80) REVERT: W 623 MET cc_start: 0.5508 (mtm) cc_final: 0.5257 (mtp) REVERT: W 626 ARG cc_start: 0.8031 (tpt170) cc_final: 0.7616 (ttp-110) outliers start: 5 outliers final: 1 residues processed: 242 average time/residue: 0.3717 time to fit residues: 123.1729 Evaluate side-chains 177 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain W residue 574 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 116 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 85 GLN C 68 ASN C 84 GLN C 104 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN G 31 HIS H 79 HIS ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 242 HIS W 243 ASN W 331 ASN W 523 ASN ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17278 Z= 0.283 Angle : 0.679 10.435 24692 Z= 0.384 Chirality : 0.040 0.177 2797 Planarity : 0.005 0.059 2042 Dihedral : 31.346 179.927 4810 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.67 % Allowed : 16.43 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -1.67 (0.23), residues: 1225 helix: -0.04 (0.18), residues: 731 sheet: -2.68 (0.67), residues: 57 loop : -2.73 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 280 HIS 0.004 0.001 HIS F 75 PHE 0.012 0.001 PHE W 605 TYR 0.015 0.002 TYR W 413 ARG 0.005 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6597 (mt-10) REVERT: B 27 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7126 (tm-30) REVERT: C 36 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7401 (mmtt) REVERT: C 92 GLU cc_start: 0.7157 (mp0) cc_final: 0.6859 (mp0) REVERT: C 99 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7565 (mmm160) REVERT: C 104 GLN cc_start: 0.7756 (mm-40) cc_final: 0.6977 (tt0) REVERT: D 48 ASP cc_start: 0.8675 (t70) cc_final: 0.8093 (p0) REVERT: D 73 GLU cc_start: 0.7931 (tp30) cc_final: 0.7572 (tp30) REVERT: E 73 GLU cc_start: 0.7234 (tt0) cc_final: 0.6959 (tt0) REVERT: F 59 LYS cc_start: 0.7277 (ttpt) cc_final: 0.7043 (ttpp) REVERT: F 77 LYS cc_start: 0.8420 (mttt) cc_final: 0.8130 (mmtp) REVERT: G 36 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7675 (mmmm) REVERT: G 64 GLU cc_start: 0.7535 (tt0) cc_final: 0.7116 (mt-10) REVERT: G 90 ASP cc_start: 0.7126 (t70) cc_final: 0.6630 (t70) REVERT: G 91 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6779 (tm-30) REVERT: G 95 LYS cc_start: 0.8503 (tttp) cc_final: 0.8147 (mtpp) REVERT: G 110 ASN cc_start: 0.8294 (t0) cc_final: 0.7865 (p0) REVERT: H 33 SER cc_start: 0.8089 (t) cc_final: 0.7600 (p) REVERT: H 65 ASP cc_start: 0.7756 (t70) cc_final: 0.7539 (t0) REVERT: H 117 LYS cc_start: 0.7211 (tptm) cc_final: 0.6885 (tptt) REVERT: W 174 TYR cc_start: 0.4927 (p90) cc_final: 0.4571 (p90) REVERT: W 289 MET cc_start: 0.8854 (mmt) cc_final: 0.8622 (mmm) REVERT: W 309 GLU cc_start: 0.7635 (tp30) cc_final: 0.7154 (tp30) REVERT: W 389 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7248 (mmm-85) REVERT: W 419 MET cc_start: 0.8344 (ttm) cc_final: 0.8081 (ttm) REVERT: W 429 MET cc_start: 0.8036 (mpp) cc_final: 0.7588 (mpp) REVERT: W 451 MET cc_start: 0.8081 (ptm) cc_final: 0.7572 (ppp) REVERT: W 590 MET cc_start: 0.8242 (tpp) cc_final: 0.7921 (tpp) REVERT: W 616 ARG cc_start: 0.8705 (mmp-170) cc_final: 0.8274 (ttp80) outliers start: 28 outliers final: 17 residues processed: 204 average time/residue: 0.3290 time to fit residues: 95.6179 Evaluate side-chains 183 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 0.0770 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17278 Z= 0.220 Angle : 0.630 12.327 24692 Z= 0.357 Chirality : 0.037 0.168 2797 Planarity : 0.004 0.042 2042 Dihedral : 30.957 178.183 4808 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.06 % Allowed : 19.39 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.88 (0.24), residues: 1225 helix: 0.64 (0.19), residues: 732 sheet: -2.64 (0.67), residues: 59 loop : -2.44 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 280 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE W 605 TYR 0.013 0.001 TYR W 413 ARG 0.005 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6655 (tt0) REVERT: B 27 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7866 (tp-100) REVERT: C 36 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7415 (mmtt) REVERT: C 99 ARG cc_start: 0.7913 (mmt180) cc_final: 0.7544 (mmm160) REVERT: C 104 GLN cc_start: 0.7661 (mm-40) cc_final: 0.6945 (tt0) REVERT: D 33 SER cc_start: 0.8121 (p) cc_final: 0.7844 (p) REVERT: D 48 ASP cc_start: 0.8634 (t70) cc_final: 0.8092 (p0) REVERT: D 76 ARG cc_start: 0.7041 (mtm180) cc_final: 0.6386 (mtm-85) REVERT: E 73 GLU cc_start: 0.7347 (tt0) cc_final: 0.7019 (tt0) REVERT: E 107 THR cc_start: 0.7290 (t) cc_final: 0.7002 (m) REVERT: F 59 LYS cc_start: 0.7230 (ttpt) cc_final: 0.7012 (ttpp) REVERT: F 77 LYS cc_start: 0.8496 (mttt) cc_final: 0.8195 (mmtp) REVERT: G 36 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7614 (mmmm) REVERT: G 64 GLU cc_start: 0.7508 (tt0) cc_final: 0.7084 (mt-10) REVERT: G 91 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6725 (tm-30) REVERT: G 95 LYS cc_start: 0.8504 (tttp) cc_final: 0.8217 (mtpp) REVERT: G 110 ASN cc_start: 0.8309 (t0) cc_final: 0.7844 (p0) REVERT: G 115 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7797 (mp) REVERT: H 32 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7117 (tp30) REVERT: H 33 SER cc_start: 0.8089 (t) cc_final: 0.7698 (p) REVERT: H 117 LYS cc_start: 0.7023 (tptm) cc_final: 0.6757 (tptt) REVERT: W 174 TYR cc_start: 0.5096 (p90) cc_final: 0.4711 (p90) REVERT: W 222 MET cc_start: 0.6762 (mmp) cc_final: 0.6344 (mmm) REVERT: W 289 MET cc_start: 0.8920 (mmt) cc_final: 0.8661 (mmm) REVERT: W 309 GLU cc_start: 0.7355 (tp30) cc_final: 0.6963 (tp30) REVERT: W 389 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7268 (mmm-85) REVERT: W 419 MET cc_start: 0.8363 (ttm) cc_final: 0.8122 (ttm) REVERT: W 429 MET cc_start: 0.8216 (mpp) cc_final: 0.7832 (mpp) REVERT: W 451 MET cc_start: 0.8123 (ptm) cc_final: 0.7635 (ppp) REVERT: W 616 ARG cc_start: 0.8702 (mmp-170) cc_final: 0.8257 (ttp80) outliers start: 32 outliers final: 19 residues processed: 201 average time/residue: 0.3481 time to fit residues: 101.7237 Evaluate side-chains 188 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 0.0170 chunk 101 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 0.0070 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17278 Z= 0.198 Angle : 0.615 11.163 24692 Z= 0.347 Chirality : 0.036 0.142 2797 Planarity : 0.004 0.039 2042 Dihedral : 30.657 177.788 4808 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.63 % Allowed : 20.44 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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 (0.24), residues: 1225 helix: 1.03 (0.19), residues: 724 sheet: -2.54 (0.68), residues: 58 loop : -2.18 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 251 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 84 TYR 0.013 0.001 TYR W 518 ARG 0.004 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6656 (tt0) REVERT: B 27 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7955 (tp-100) REVERT: C 36 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7377 (mmtt) REVERT: C 104 GLN cc_start: 0.7651 (mm-40) cc_final: 0.6985 (tt0) REVERT: D 33 SER cc_start: 0.8104 (p) cc_final: 0.7826 (p) REVERT: D 48 ASP cc_start: 0.8685 (t70) cc_final: 0.8080 (p0) REVERT: D 76 ARG cc_start: 0.6992 (mtm180) cc_final: 0.6328 (mtm-85) REVERT: D 102 GLU cc_start: 0.7922 (pm20) cc_final: 0.7627 (pp20) REVERT: E 73 GLU cc_start: 0.7423 (tt0) cc_final: 0.7058 (tt0) REVERT: E 76 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7942 (mm-40) REVERT: E 120 MET cc_start: 0.7052 (mtp) cc_final: 0.6618 (mtp) REVERT: F 59 LYS cc_start: 0.7233 (ttpt) cc_final: 0.7025 (ttpp) REVERT: F 77 LYS cc_start: 0.8625 (mttt) cc_final: 0.8311 (mmtp) REVERT: G 36 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7612 (mmmm) REVERT: G 64 GLU cc_start: 0.7591 (tt0) cc_final: 0.7234 (pt0) REVERT: G 91 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6793 (tm-30) REVERT: G 95 LYS cc_start: 0.8556 (tttp) cc_final: 0.8203 (mtpp) REVERT: G 110 ASN cc_start: 0.8312 (t0) cc_final: 0.7861 (p0) REVERT: G 115 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7759 (mp) REVERT: H 32 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6795 (mm-30) REVERT: H 33 SER cc_start: 0.8060 (t) cc_final: 0.7209 (p) REVERT: H 73 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6707 (tp30) REVERT: H 117 LYS cc_start: 0.6985 (tptm) cc_final: 0.6707 (tptt) REVERT: W 174 TYR cc_start: 0.4818 (p90) cc_final: 0.4445 (p90) REVERT: W 289 MET cc_start: 0.8938 (mmt) cc_final: 0.8664 (mmm) REVERT: W 309 GLU cc_start: 0.7337 (tp30) cc_final: 0.6973 (tp30) REVERT: W 389 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7250 (mmm-85) REVERT: W 419 MET cc_start: 0.8344 (ttm) cc_final: 0.8121 (ttm) REVERT: W 516 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: W 556 MET cc_start: 0.6197 (mtm) cc_final: 0.5802 (ptp) REVERT: W 590 MET cc_start: 0.8246 (tpp) cc_final: 0.8009 (tpp) REVERT: W 616 ARG cc_start: 0.8686 (mmp-170) cc_final: 0.8283 (ttp80) outliers start: 38 outliers final: 26 residues processed: 200 average time/residue: 0.3091 time to fit residues: 90.0993 Evaluate side-chains 191 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 213 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 129 optimal weight: 40.0000 chunk 36 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 266 GLN ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.008 0.077 17278 Z= 0.487 Angle : 0.771 14.311 24692 Z= 0.430 Chirality : 0.045 0.202 2797 Planarity : 0.005 0.057 2042 Dihedral : 31.131 174.652 4808 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.06 % Allowed : 20.82 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.24), residues: 1225 helix: 0.52 (0.19), residues: 719 sheet: -2.54 (0.64), residues: 64 loop : -2.36 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP W 521 HIS 0.006 0.002 HIS C 31 PHE 0.016 0.002 PHE G 25 TYR 0.018 0.002 TYR D 118 ARG 0.005 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 172 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7299 (mm) REVERT: A 81 ASP cc_start: 0.7443 (t0) cc_final: 0.7175 (t70) REVERT: A 94 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 105 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6686 (mt-10) REVERT: B 27 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7761 (tp40) REVERT: C 104 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7127 (tt0) REVERT: C 110 ASN cc_start: 0.7837 (t0) cc_final: 0.6939 (p0) REVERT: D 48 ASP cc_start: 0.8755 (t70) cc_final: 0.8161 (p0) REVERT: F 59 LYS cc_start: 0.7355 (ttpt) cc_final: 0.7115 (tttm) REVERT: G 36 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7609 (mmmm) REVERT: G 64 GLU cc_start: 0.7369 (tt0) cc_final: 0.6968 (pt0) REVERT: G 91 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6583 (tm-30) REVERT: G 95 LYS cc_start: 0.8562 (tttp) cc_final: 0.8254 (mtpp) REVERT: G 110 ASN cc_start: 0.8298 (t0) cc_final: 0.7723 (p0) REVERT: H 32 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7011 (mm-30) REVERT: H 33 SER cc_start: 0.7918 (t) cc_final: 0.7450 (p) REVERT: H 90 GLU cc_start: 0.6044 (mp0) cc_final: 0.5637 (mp0) REVERT: W 174 TYR cc_start: 0.5056 (p90) cc_final: 0.4557 (p90) REVERT: W 309 GLU cc_start: 0.7373 (tp30) cc_final: 0.6827 (tm-30) REVERT: W 389 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7230 (mmm-85) REVERT: W 444 MET cc_start: 0.7683 (mtt) cc_final: 0.7475 (mtp) REVERT: W 590 MET cc_start: 0.8390 (tpp) cc_final: 0.8099 (tpp) REVERT: W 616 ARG cc_start: 0.8696 (mmp-170) cc_final: 0.8334 (ttp-170) outliers start: 53 outliers final: 37 residues processed: 216 average time/residue: 0.3140 time to fit residues: 99.8301 Evaluate side-chains 196 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 158 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 427 ILE Chi-restraints excluded: chain W residue 453 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 564 LEU Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17278 Z= 0.227 Angle : 0.647 11.616 24692 Z= 0.364 Chirality : 0.038 0.158 2797 Planarity : 0.004 0.044 2042 Dihedral : 30.762 175.808 4808 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.92 % Allowed : 23.11 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.45 (0.24), residues: 1225 helix: 0.92 (0.19), residues: 726 sheet: -2.43 (0.68), residues: 59 loop : -2.09 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 348 HIS 0.006 0.001 HIS W 232 PHE 0.009 0.001 PHE W 605 TYR 0.018 0.001 TYR F 88 ARG 0.009 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6594 (tt0) REVERT: C 36 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7467 (mmtt) REVERT: C 104 GLN cc_start: 0.7615 (mm-40) cc_final: 0.6990 (tt0) REVERT: C 110 ASN cc_start: 0.7828 (t0) cc_final: 0.6915 (p0) REVERT: D 33 SER cc_start: 0.8216 (p) cc_final: 0.7922 (p) REVERT: D 48 ASP cc_start: 0.8694 (t70) cc_final: 0.8076 (p0) REVERT: D 76 ARG cc_start: 0.6904 (mtm180) cc_final: 0.6056 (mtm-85) REVERT: E 73 GLU cc_start: 0.7028 (tt0) cc_final: 0.6749 (tt0) REVERT: E 120 MET cc_start: 0.7193 (mtp) cc_final: 0.6677 (mtp) REVERT: G 36 LYS cc_start: 0.8059 (mmtp) cc_final: 0.7593 (mmmm) REVERT: G 64 GLU cc_start: 0.7632 (tt0) cc_final: 0.7227 (pt0) REVERT: G 91 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6598 (tm-30) REVERT: G 95 LYS cc_start: 0.8557 (tttp) cc_final: 0.8259 (mtpp) REVERT: G 110 ASN cc_start: 0.8242 (t0) cc_final: 0.7679 (p0) REVERT: H 33 SER cc_start: 0.7923 (t) cc_final: 0.7507 (p) REVERT: W 240 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7601 (t) REVERT: W 309 GLU cc_start: 0.7308 (tp30) cc_final: 0.6896 (tm-30) REVERT: W 327 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.4696 (t80) REVERT: W 389 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7229 (mmm-85) REVERT: W 429 MET cc_start: 0.8310 (mpp) cc_final: 0.8077 (mpp) REVERT: W 444 MET cc_start: 0.7459 (mtt) cc_final: 0.6964 (mtp) REVERT: W 476 MET cc_start: 0.8389 (tpp) cc_final: 0.7878 (tpp) REVERT: W 616 ARG cc_start: 0.8696 (mmp-170) cc_final: 0.8395 (ttp-170) outliers start: 41 outliers final: 33 residues processed: 200 average time/residue: 0.3155 time to fit residues: 93.9813 Evaluate side-chains 191 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 240 THR Chi-restraints excluded: chain W residue 286 SER Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 327 PHE Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17278 Z= 0.347 Angle : 0.697 12.572 24692 Z= 0.389 Chirality : 0.041 0.215 2797 Planarity : 0.004 0.034 2042 Dihedral : 30.794 174.999 4808 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.25 % Allowed : 22.83 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.61 (0.24), residues: 1225 helix: 0.80 (0.19), residues: 723 sheet: -2.49 (0.63), residues: 64 loop : -2.14 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 521 HIS 0.005 0.001 HIS W 232 PHE 0.013 0.002 PHE G 25 TYR 0.018 0.002 TYR F 88 ARG 0.012 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 162 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6615 (mt-10) REVERT: B 27 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8004 (tp-100) REVERT: C 36 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7563 (mmtt) REVERT: C 104 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7057 (tt0) REVERT: C 110 ASN cc_start: 0.7819 (t0) cc_final: 0.6924 (p0) REVERT: D 48 ASP cc_start: 0.8731 (t70) cc_final: 0.8116 (p0) REVERT: D 76 ARG cc_start: 0.6928 (mtm180) cc_final: 0.6069 (mtm-85) REVERT: D 90 GLU cc_start: 0.6999 (mp0) cc_final: 0.6717 (mp0) REVERT: E 73 GLU cc_start: 0.7075 (tt0) cc_final: 0.6804 (tt0) REVERT: G 36 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7643 (mmmm) REVERT: G 64 GLU cc_start: 0.7433 (tt0) cc_final: 0.7010 (pt0) REVERT: G 91 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6658 (tm-30) REVERT: G 95 LYS cc_start: 0.8552 (tttp) cc_final: 0.8242 (mtpp) REVERT: G 110 ASN cc_start: 0.8298 (t0) cc_final: 0.7697 (p0) REVERT: H 33 SER cc_start: 0.7621 (t) cc_final: 0.7170 (p) REVERT: H 90 GLU cc_start: 0.6110 (mp0) cc_final: 0.5701 (mp0) REVERT: W 240 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7708 (t) REVERT: W 327 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.4649 (t80) REVERT: W 389 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7223 (mmm-85) REVERT: W 429 MET cc_start: 0.8325 (mpp) cc_final: 0.8023 (mpp) REVERT: W 444 MET cc_start: 0.7508 (mtt) cc_final: 0.6986 (mtp) REVERT: W 476 MET cc_start: 0.8455 (tpp) cc_final: 0.7938 (tpp) REVERT: W 590 MET cc_start: 0.8222 (tpp) cc_final: 0.7898 (tpp) REVERT: W 616 ARG cc_start: 0.8662 (mmp-170) cc_final: 0.8336 (ttp-170) outliers start: 55 outliers final: 45 residues processed: 207 average time/residue: 0.2884 time to fit residues: 89.2879 Evaluate side-chains 206 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 240 THR Chi-restraints excluded: chain W residue 286 SER Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 327 PHE Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 453 LEU Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 31 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 594 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17278 Z= 0.249 Angle : 0.654 11.498 24692 Z= 0.366 Chirality : 0.038 0.227 2797 Planarity : 0.004 0.035 2042 Dihedral : 30.608 175.223 4808 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.25 % Allowed : 23.21 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.30 (0.25), residues: 1225 helix: 1.04 (0.19), residues: 723 sheet: -2.32 (0.67), residues: 59 loop : -2.01 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 251 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE C 25 TYR 0.019 0.001 TYR F 88 ARG 0.012 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6589 (tt0) REVERT: B 27 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8080 (tp-100) REVERT: C 36 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7439 (mmtt) REVERT: C 104 GLN cc_start: 0.7551 (mm-40) cc_final: 0.6999 (tt0) REVERT: C 110 ASN cc_start: 0.7840 (t0) cc_final: 0.6931 (p0) REVERT: D 33 SER cc_start: 0.8220 (p) cc_final: 0.7934 (p) REVERT: D 48 ASP cc_start: 0.8694 (t70) cc_final: 0.8079 (p0) REVERT: D 76 ARG cc_start: 0.6869 (mtm180) cc_final: 0.6035 (mtm-85) REVERT: D 90 GLU cc_start: 0.7025 (mp0) cc_final: 0.6747 (mp0) REVERT: E 73 GLU cc_start: 0.7028 (tt0) cc_final: 0.6764 (tt0) REVERT: E 133 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6563 (mt-10) REVERT: G 36 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7599 (mmmm) REVERT: G 64 GLU cc_start: 0.7407 (tt0) cc_final: 0.6990 (pt0) REVERT: G 91 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6855 (tm-30) REVERT: G 95 LYS cc_start: 0.8564 (tttp) cc_final: 0.8264 (mtpp) REVERT: G 110 ASN cc_start: 0.8302 (t0) cc_final: 0.7693 (p0) REVERT: H 33 SER cc_start: 0.7462 (t) cc_final: 0.7112 (p) REVERT: H 73 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6788 (mm-30) REVERT: H 90 GLU cc_start: 0.5972 (mp0) cc_final: 0.5576 (mp0) REVERT: W 233 MET cc_start: 0.7103 (ptp) cc_final: 0.6134 (ptp) REVERT: W 240 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7630 (t) REVERT: W 389 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7232 (mmm-85) REVERT: W 429 MET cc_start: 0.8291 (mpp) cc_final: 0.8016 (mpp) REVERT: W 476 MET cc_start: 0.8494 (tpp) cc_final: 0.7974 (tpp) REVERT: W 590 MET cc_start: 0.8317 (tpp) cc_final: 0.7957 (tpp) REVERT: W 616 ARG cc_start: 0.8674 (mmp-170) cc_final: 0.8311 (ttp-170) outliers start: 55 outliers final: 47 residues processed: 211 average time/residue: 0.2736 time to fit residues: 85.7829 Evaluate side-chains 206 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 240 THR Chi-restraints excluded: chain W residue 286 SER Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 564 LEU Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17278 Z= 0.373 Angle : 0.714 13.421 24692 Z= 0.396 Chirality : 0.041 0.222 2797 Planarity : 0.004 0.034 2042 Dihedral : 30.754 174.195 4808 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.54 % Allowed : 22.73 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.58 (0.24), residues: 1225 helix: 0.81 (0.19), residues: 722 sheet: -2.33 (0.64), residues: 64 loop : -2.12 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 521 HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE C 25 TYR 0.021 0.002 TYR F 88 ARG 0.006 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 159 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7432 (t0) cc_final: 0.7123 (t70) REVERT: A 105 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6679 (mt-10) REVERT: C 36 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7544 (mmtt) REVERT: C 104 GLN cc_start: 0.7529 (mm-40) cc_final: 0.6998 (tt0) REVERT: C 110 ASN cc_start: 0.7811 (t0) cc_final: 0.6912 (p0) REVERT: D 48 ASP cc_start: 0.8734 (t70) cc_final: 0.8122 (p0) REVERT: D 76 ARG cc_start: 0.6918 (mtm180) cc_final: 0.6057 (mtm-85) REVERT: D 90 GLU cc_start: 0.6992 (mp0) cc_final: 0.6703 (mp0) REVERT: E 73 GLU cc_start: 0.7060 (tt0) cc_final: 0.6777 (tt0) REVERT: G 36 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7606 (mmmm) REVERT: G 64 GLU cc_start: 0.7441 (tt0) cc_final: 0.7007 (pt0) REVERT: G 91 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6759 (tm-30) REVERT: G 95 LYS cc_start: 0.8554 (tttp) cc_final: 0.8243 (mtpp) REVERT: G 110 ASN cc_start: 0.8306 (t0) cc_final: 0.7689 (p0) REVERT: H 90 GLU cc_start: 0.6018 (mp0) cc_final: 0.5631 (mp0) REVERT: W 327 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.4761 (t80) REVERT: W 389 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7223 (mmm-85) REVERT: W 429 MET cc_start: 0.8337 (mpp) cc_final: 0.7941 (mpp) REVERT: W 476 MET cc_start: 0.8558 (tpp) cc_final: 0.8046 (tpp) REVERT: W 590 MET cc_start: 0.8329 (tpp) cc_final: 0.7956 (tpp) REVERT: W 616 ARG cc_start: 0.8597 (mmp-170) cc_final: 0.8240 (ttp-170) outliers start: 58 outliers final: 50 residues processed: 207 average time/residue: 0.2876 time to fit residues: 88.8181 Evaluate side-chains 205 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 154 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 286 SER Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 327 PHE Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 453 LEU Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 516 GLU Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 564 LEU Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17278 Z= 0.265 Angle : 0.667 12.679 24692 Z= 0.371 Chirality : 0.039 0.229 2797 Planarity : 0.004 0.048 2042 Dihedral : 30.602 174.366 4808 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.68 % Allowed : 23.30 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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 (0.25), residues: 1225 helix: 0.99 (0.19), residues: 723 sheet: -2.06 (0.69), residues: 59 loop : -2.03 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 348 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE C 25 TYR 0.020 0.002 TYR F 88 ARG 0.006 0.000 ARG F 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 160 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6587 (tt0) REVERT: B 27 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8078 (tp-100) REVERT: C 36 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7453 (mmtt) REVERT: C 104 GLN cc_start: 0.7489 (mm-40) cc_final: 0.6999 (tt0) REVERT: C 110 ASN cc_start: 0.7827 (t0) cc_final: 0.6923 (p0) REVERT: D 33 SER cc_start: 0.8227 (p) cc_final: 0.7933 (p) REVERT: D 48 ASP cc_start: 0.8591 (t70) cc_final: 0.8094 (p0) REVERT: D 76 ARG cc_start: 0.6889 (mtm180) cc_final: 0.6044 (mtm-85) REVERT: D 90 GLU cc_start: 0.7012 (mp0) cc_final: 0.6730 (mp0) REVERT: E 73 GLU cc_start: 0.7005 (tt0) cc_final: 0.6718 (tt0) REVERT: E 133 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6555 (mt-10) REVERT: G 36 LYS cc_start: 0.8080 (mmtp) cc_final: 0.7597 (mmmm) REVERT: G 64 GLU cc_start: 0.7420 (tt0) cc_final: 0.6992 (pt0) REVERT: G 91 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6896 (tm-30) REVERT: G 95 LYS cc_start: 0.8554 (tttp) cc_final: 0.8260 (mtpp) REVERT: G 110 ASN cc_start: 0.8304 (t0) cc_final: 0.7678 (p0) REVERT: H 73 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6746 (mm-30) REVERT: H 90 GLU cc_start: 0.5957 (mp0) cc_final: 0.5562 (mp0) REVERT: W 389 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7229 (mmm-85) REVERT: W 429 MET cc_start: 0.8356 (mpp) cc_final: 0.7927 (mpp) REVERT: W 476 MET cc_start: 0.8563 (tpp) cc_final: 0.8056 (tpp) REVERT: W 616 ARG cc_start: 0.8642 (mmp-170) cc_final: 0.8253 (ttp-170) outliers start: 49 outliers final: 48 residues processed: 198 average time/residue: 0.3076 time to fit residues: 92.1906 Evaluate side-chains 208 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 199 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 286 SER Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 345 HIS Chi-restraints excluded: chain W residue 391 PHE Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 478 LEU Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 533 THR Chi-restraints excluded: chain W residue 564 LEU Chi-restraints excluded: chain W residue 574 VAL Chi-restraints excluded: chain W residue 586 ASP Chi-restraints excluded: chain W residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.0070 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 584 GLN ** 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 = 0.3729 r_free = 0.3729 target = 0.110546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083855 restraints weight = 40283.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083208 restraints weight = 39206.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083400 restraints weight = 38914.363| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17278 Z= 0.198 Angle : 0.632 11.649 24692 Z= 0.351 Chirality : 0.037 0.222 2797 Planarity : 0.004 0.046 2042 Dihedral : 30.365 174.922 4808 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.20 % Allowed : 23.50 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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 (0.25), residues: 1225 helix: 1.25 (0.19), residues: 724 sheet: -1.93 (0.69), residues: 58 loop : -1.94 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 302 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE B 100 TYR 0.027 0.001 TYR F 88 ARG 0.005 0.000 ARG F 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2763.51 seconds wall clock time: 51 minutes 24.20 seconds (3084.20 seconds total)