Starting phenix.real_space_refine on Sun Dec 10 10:55:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/12_2023/7wvf_32852_updated.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 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 90 5.49 5 S 38 5.16 5 C 8738 2.51 5 N 2408 2.21 5 O 2975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14249 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 917 Classifications: {'RNA': 46} Modifications used: {'5*END': 1, 'rna3p_pyr': 46} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1009 Classifications: {'RNA': 46} Modifications used: {'5*END': 1, 'rna3p': 46} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 45 Chain: "C" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1755 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Time building chain proxies: 7.77, per 1000 atoms: 0.55 Number of scatterers: 14249 At special positions: 0 Unit cell: (96.6985, 95.612, 203.176, 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 38 16.00 P 90 15.00 O 2975 8.00 N 2408 7.00 C 8738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 677 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 232 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 2.6 seconds 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 8.7% alpha, 12.6% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 6.65 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.503A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.674A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.960A pdb=" N TRP A 273 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 4.516A pdb=" N SER A 403 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 671 through 674 No H-bonds generated for 'chain 'A' and resid 671 through 674' Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.503A pdb=" N LYS B 97 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.674A pdb=" N ILE B 193 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.959A pdb=" N TRP B 273 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 4.516A pdb=" N SER B 403 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 627 through 630 No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 671 through 674 No H-bonds generated for 'chain 'B' and resid 671 through 674' Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.409A pdb=" N VAL A 55 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER A 79 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 103 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU A 127 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR A 151 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU A 175 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.365A pdb=" N ASN A 252 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR A 302 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 326 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.137A pdb=" N ILE A 411 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 435 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU A 460 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG A 484 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 510 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 534 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 566 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 590 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER A 614 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU A 639 " --> pdb=" O LEU A 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.405A pdb=" N TYR A 468 " --> pdb=" O GLN A 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.409A pdb=" N VAL B 55 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER B 79 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 103 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU B 127 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B 151 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B 175 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.364A pdb=" N ASN B 252 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET B 278 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR B 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR B 326 " --> pdb=" O PHE B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 383 through 385 removed outlier: 6.136A pdb=" N ILE B 411 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 435 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU B 460 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 534 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 566 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 590 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER B 614 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU B 639 " --> pdb=" O LEU B 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 444 through 446 removed outlier: 6.405A pdb=" N TYR B 468 " --> pdb=" O GLN B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 6 through 11 Processing sheet with id= J, first strand: chain 'C' and resid 119 through 121 removed outlier: 6.804A pdb=" N ALA C 37 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS C 58 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG C 43 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TRP C 52 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 154 through 157 removed outlier: 6.052A pdb=" N LYS C 248 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 157 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N THR C 250 " --> pdb=" O VAL C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 163 through 168 Processing sheet with id= M, first strand: chain 'C' and resid 240 through 243 removed outlier: 6.138A pdb=" N GLN C 181 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU C 190 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.172A pdb=" N TYR C 114 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER C 106 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE C 112 " --> pdb=" O SER C 106 " (cutoff:3.500A) 89 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4296 1.34 - 1.46: 3499 1.46 - 1.58: 6717 1.58 - 1.70: 180 1.70 - 1.81: 54 Bond restraints: 14746 Sorted by residual: bond pdb=" C2 I F 22 " pdb=" N3 I F 22 " ideal model delta sigma weight residual 1.462 1.312 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C2 I F 42 " pdb=" N3 I F 42 " ideal model delta sigma weight residual 1.462 1.313 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C2 I F 21 " pdb=" N3 I F 21 " ideal model delta sigma weight residual 1.462 1.313 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C2 I F 4 " pdb=" N3 I F 4 " ideal model delta sigma weight residual 1.462 1.314 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C2 I F 31 " pdb=" N3 I F 31 " ideal model delta sigma weight residual 1.462 1.314 0.148 2.00e-02 2.50e+03 5.50e+01 ... (remaining 14741 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.74: 808 106.74 - 113.55: 8499 113.55 - 120.36: 5143 120.36 - 127.18: 5669 127.18 - 133.99: 333 Bond angle restraints: 20452 Sorted by residual: angle pdb=" C1' I F 37 " pdb=" N9 I F 37 " pdb=" C4 I F 37 " ideal model delta sigma weight residual 106.08 123.87 -17.79 3.00e+00 1.11e-01 3.51e+01 angle pdb=" C1' I F 43 " pdb=" N9 I F 43 " pdb=" C4 I F 43 " ideal model delta sigma weight residual 106.08 123.85 -17.77 3.00e+00 1.11e-01 3.51e+01 angle pdb=" C1' I F 26 " pdb=" N9 I F 26 " pdb=" C4 I F 26 " ideal model delta sigma weight residual 106.08 123.75 -17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C1' I F 27 " pdb=" N9 I F 27 " pdb=" C4 I F 27 " ideal model delta sigma weight residual 106.08 123.75 -17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C1' I F 19 " pdb=" N9 I F 19 " pdb=" C4 I F 19 " ideal model delta sigma weight residual 106.08 123.73 -17.65 3.00e+00 1.11e-01 3.46e+01 ... (remaining 20447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8004 17.98 - 35.97: 404 35.97 - 53.95: 184 53.95 - 71.93: 125 71.93 - 89.92: 142 Dihedral angle restraints: 8859 sinusoidal: 4326 harmonic: 4533 Sorted by residual: dihedral pdb=" CB CYS C 25 " pdb=" SG CYS C 25 " pdb=" SG CYS C 102 " pdb=" CB CYS C 102 " ideal model delta sinusoidal sigma weight residual 93.00 63.18 29.82 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CA TYR C 101 " pdb=" C TYR C 101 " pdb=" N CYS C 102 " pdb=" CA CYS C 102 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA SER C 60 " pdb=" C SER C 60 " pdb=" N LYS C 61 " pdb=" CA LYS C 61 " ideal model delta harmonic sigma weight residual 180.00 164.33 15.67 0 5.00e+00 4.00e-02 9.82e+00 ... (remaining 8856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1343 0.031 - 0.061: 581 0.061 - 0.092: 174 0.092 - 0.123: 86 0.123 - 0.154: 14 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CA ILE A 577 " pdb=" N ILE A 577 " pdb=" C ILE A 577 " pdb=" CB ILE A 577 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE B 577 " pdb=" N ILE B 577 " pdb=" C ILE B 577 " pdb=" CB ILE B 577 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 138 " pdb=" N ILE A 138 " pdb=" C ILE A 138 " pdb=" CB ILE A 138 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 2195 not shown) Planarity restraints: 2335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I F 19 " -0.218 2.00e-02 2.50e+03 5.95e-01 7.97e+03 pdb=" C2' I F 19 " 0.194 2.00e-02 2.50e+03 pdb=" C3' I F 19 " 0.597 2.00e-02 2.50e+03 pdb=" C4' I F 19 " -0.439 2.00e-02 2.50e+03 pdb=" C5' I F 19 " -0.051 2.00e-02 2.50e+03 pdb=" N9 I F 19 " 0.914 2.00e-02 2.50e+03 pdb=" O2' I F 19 " -0.951 2.00e-02 2.50e+03 pdb=" O3' I F 19 " 0.614 2.00e-02 2.50e+03 pdb=" O4' I F 19 " -0.660 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 2 " 0.214 2.00e-02 2.50e+03 5.92e-01 7.89e+03 pdb=" C2' I F 2 " -0.208 2.00e-02 2.50e+03 pdb=" C3' I F 2 " -0.591 2.00e-02 2.50e+03 pdb=" C4' I F 2 " 0.445 2.00e-02 2.50e+03 pdb=" C5' I F 2 " 0.040 2.00e-02 2.50e+03 pdb=" N9 I F 2 " -0.917 2.00e-02 2.50e+03 pdb=" O2' I F 2 " 0.924 2.00e-02 2.50e+03 pdb=" O3' I F 2 " -0.594 2.00e-02 2.50e+03 pdb=" O4' I F 2 " 0.688 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 15 " -0.217 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C2' I F 15 " 0.204 2.00e-02 2.50e+03 pdb=" C3' I F 15 " 0.592 2.00e-02 2.50e+03 pdb=" C4' I F 15 " -0.443 2.00e-02 2.50e+03 pdb=" C5' I F 15 " -0.044 2.00e-02 2.50e+03 pdb=" N9 I F 15 " 0.912 2.00e-02 2.50e+03 pdb=" O2' I F 15 " -0.930 2.00e-02 2.50e+03 pdb=" O3' I F 15 " 0.597 2.00e-02 2.50e+03 pdb=" O4' I F 15 " -0.673 2.00e-02 2.50e+03 ... (remaining 2332 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3062 2.78 - 3.31: 12790 3.31 - 3.84: 24964 3.84 - 4.37: 30666 4.37 - 4.90: 48954 Nonbonded interactions: 120436 Sorted by model distance: nonbonded pdb=" OE1 GLN C 57 " pdb=" OH TYR C 107 " model vdw 2.252 2.440 nonbonded pdb=" OD2 ASP A 192 " pdb=" OH TYR C 63 " model vdw 2.309 2.440 nonbonded pdb=" OG SER A 115 " pdb=" OG1 THR A 118 " model vdw 2.329 2.440 nonbonded pdb=" OG SER B 115 " pdb=" OG1 THR B 118 " model vdw 2.329 2.440 nonbonded pdb=" OD1 ASN A 507 " pdb=" NZ LYS A 531 " model vdw 2.346 2.520 ... (remaining 120431 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' selection = chain 'B' } 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=1.00 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.510 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 44.900 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 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 : 0.014 0.150 14746 Z= 0.909 Angle : 1.429 17.786 20452 Z= 0.521 Chirality : 0.041 0.154 2198 Planarity : 0.081 0.595 2335 Dihedral : 19.246 89.919 5889 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 0.07 % Allowed : 0.63 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1538 helix: -1.04 (0.66), residues: 74 sheet: -1.43 (0.30), residues: 340 loop : -0.32 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 115 HIS 0.003 0.001 HIS A 548 PHE 0.016 0.001 PHE C 85 TYR 0.015 0.001 TYR C 63 ARG 0.006 0.001 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.2775 time to fit residues: 190.4077 Evaluate side-chains 226 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN B 62 GLN B 174 GLN B 316 HIS B 441 ASN B 466 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 596 ASN B 674 HIS B 678 ASN C 9 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14746 Z= 0.388 Angle : 1.927 17.036 20452 Z= 1.184 Chirality : 0.046 0.174 2198 Planarity : 0.016 0.118 2335 Dihedral : 23.237 98.876 2899 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.52 % Allowed : 13.01 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1538 helix: -1.46 (0.57), residues: 82 sheet: -1.29 (0.32), residues: 312 loop : -0.60 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 115 HIS 0.006 0.001 HIS B 548 PHE 0.022 0.002 PHE A 304 TYR 0.025 0.002 TYR A 302 ARG 0.004 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 269 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 31 residues processed: 306 average time/residue: 0.2625 time to fit residues: 120.4447 Evaluate side-chains 215 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1409 time to fit residues: 10.2261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14746 Z= 0.401 Angle : 1.843 15.746 20452 Z= 1.127 Chirality : 0.047 0.177 2198 Planarity : 0.016 0.120 2335 Dihedral : 23.933 100.369 2899 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.81 % Allowed : 16.39 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.22), residues: 1538 helix: -1.86 (0.58), residues: 68 sheet: -1.29 (0.32), residues: 303 loop : -1.00 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 179 HIS 0.008 0.001 HIS A 682 PHE 0.025 0.003 PHE B 212 TYR 0.029 0.002 TYR A 302 ARG 0.003 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 239 average time/residue: 0.2256 time to fit residues: 82.6234 Evaluate side-chains 192 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1335 time to fit residues: 7.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 323 ASN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14746 Z= 0.258 Angle : 1.769 15.448 20452 Z= 1.103 Chirality : 0.044 0.250 2198 Planarity : 0.016 0.121 2335 Dihedral : 23.927 103.581 2899 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.48 % Allowed : 17.51 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1538 helix: -1.53 (0.56), residues: 82 sheet: -1.33 (0.31), residues: 305 loop : -0.97 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 41 HIS 0.004 0.001 HIS B 539 PHE 0.018 0.002 PHE A 647 TYR 0.017 0.002 TYR A 302 ARG 0.011 0.001 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 212 average time/residue: 0.2397 time to fit residues: 78.3453 Evaluate side-chains 177 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1866 time to fit residues: 5.0967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 229 ASN ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14746 Z= 0.276 Angle : 1.730 15.566 20452 Z= 1.089 Chirality : 0.044 0.248 2198 Planarity : 0.016 0.121 2335 Dihedral : 24.189 103.586 2899 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.55 % Allowed : 19.76 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.22), residues: 1538 helix: -0.82 (0.67), residues: 68 sheet: -1.35 (0.31), residues: 315 loop : -0.97 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 41 HIS 0.004 0.001 HIS B 539 PHE 0.027 0.002 PHE B 212 TYR 0.019 0.002 TYR A 302 ARG 0.006 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 204 average time/residue: 0.2481 time to fit residues: 77.3980 Evaluate side-chains 184 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 175 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1402 time to fit residues: 4.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14746 Z= 0.238 Angle : 1.703 15.517 20452 Z= 1.081 Chirality : 0.044 0.258 2198 Planarity : 0.016 0.119 2335 Dihedral : 24.313 103.634 2899 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.98 % Allowed : 20.60 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1538 helix: -0.65 (0.67), residues: 68 sheet: -1.47 (0.30), residues: 335 loop : -0.91 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 353 HIS 0.003 0.001 HIS B 548 PHE 0.025 0.002 PHE B 212 TYR 0.013 0.001 TYR A 302 ARG 0.005 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 203 average time/residue: 0.2412 time to fit residues: 74.4612 Evaluate side-chains 183 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1410 time to fit residues: 4.2125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 352 GLN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14746 Z= 0.198 Angle : 1.682 15.443 20452 Z= 1.074 Chirality : 0.043 0.270 2198 Planarity : 0.016 0.118 2335 Dihedral : 24.460 102.990 2899 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.84 % Allowed : 21.31 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1538 helix: -0.74 (0.67), residues: 68 sheet: -1.43 (0.30), residues: 333 loop : -0.90 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 353 HIS 0.003 0.001 HIS B 108 PHE 0.026 0.001 PHE B 212 TYR 0.010 0.001 TYR B 302 ARG 0.005 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 205 average time/residue: 0.2660 time to fit residues: 83.6755 Evaluate side-chains 183 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2152 time to fit residues: 4.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.0050 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 HIS B 323 ASN B 352 GLN ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14746 Z= 0.450 Angle : 1.738 15.368 20452 Z= 1.092 Chirality : 0.049 0.280 2198 Planarity : 0.017 0.122 2335 Dihedral : 24.780 102.054 2899 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 1.34 % Allowed : 21.87 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.21), residues: 1538 helix: -1.07 (0.63), residues: 68 sheet: -1.70 (0.29), residues: 333 loop : -1.18 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP B 353 HIS 0.006 0.001 HIS B 319 PHE 0.024 0.003 PHE A 304 TYR 0.032 0.002 TYR A 302 ARG 0.006 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 192 average time/residue: 0.2571 time to fit residues: 73.7598 Evaluate side-chains 167 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1789 time to fit residues: 5.5296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 140 optimal weight: 0.0970 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN B 61 ASN ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14746 Z= 0.210 Angle : 1.693 15.295 20452 Z= 1.077 Chirality : 0.044 0.292 2198 Planarity : 0.016 0.118 2335 Dihedral : 24.623 102.651 2899 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.28 % Allowed : 23.28 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.22), residues: 1538 helix: -0.98 (0.65), residues: 68 sheet: -1.51 (0.30), residues: 325 loop : -1.02 (0.19), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 353 HIS 0.005 0.001 HIS A 108 PHE 0.028 0.001 PHE A 606 TYR 0.012 0.001 TYR C 110 ARG 0.004 0.001 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.2290 time to fit residues: 66.4989 Evaluate side-chains 167 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.7989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14746 Z= 0.238 Angle : 1.685 15.258 20452 Z= 1.074 Chirality : 0.045 0.305 2198 Planarity : 0.016 0.119 2335 Dihedral : 24.720 102.086 2899 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.35 % Allowed : 23.42 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1538 helix: -0.59 (0.74), residues: 54 sheet: -1.56 (0.30), residues: 329 loop : -0.99 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 353 HIS 0.004 0.001 HIS A 108 PHE 0.025 0.002 PHE B 212 TYR 0.014 0.001 TYR A 302 ARG 0.004 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 176 average time/residue: 0.2310 time to fit residues: 62.8654 Evaluate side-chains 166 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1356 time to fit residues: 2.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 127 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.147312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118889 restraints weight = 31714.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.120359 restraints weight = 19003.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121142 restraints weight = 12977.347| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.8064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14746 Z= 0.228 Angle : 1.681 15.227 20452 Z= 1.073 Chirality : 0.044 0.297 2198 Planarity : 0.016 0.119 2335 Dihedral : 24.763 101.599 2899 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 24.12 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.22), residues: 1538 helix: -0.79 (0.74), residues: 54 sheet: -1.49 (0.30), residues: 329 loop : -0.98 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 353 HIS 0.004 0.001 HIS B 539 PHE 0.046 0.002 PHE B 375 TYR 0.015 0.001 TYR C 180 ARG 0.004 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2883.53 seconds wall clock time: 53 minutes 45.57 seconds (3225.57 seconds total)