Starting phenix.real_space_refine on Sun Feb 18 13:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avd_15679/02_2024/8avd_15679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avd_15679/02_2024/8avd_15679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avd_15679/02_2024/8avd_15679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avd_15679/02_2024/8avd_15679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avd_15679/02_2024/8avd_15679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avd_15679/02_2024/8avd_15679.pdb" } resolution = 4.42 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9439 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ni 3 6.56 5 S 60 5.16 5 C 8127 2.51 5 N 2154 2.21 5 O 2433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 76": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 482": "OE1" <-> "OE2" 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: 12777 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3181 Classifications: {'peptide': 399} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372} Chain: "C" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3181 Classifications: {'peptide': 399} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372} Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3181 Classifications: {'peptide': 399} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.07, per 1000 atoms: 0.55 Number of scatterers: 12777 At special positions: 0 Unit cell: (132.64, 144.246, 126.008, 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) Ni 3 28.00 S 60 16.00 O 2433 8.00 N 2154 7.00 C 8127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.04 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.02 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.06 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 410 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 434 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 486 " - pdb=" SG CYS D 496 " distance=2.02 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 167 " distance=2.04 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.04 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 496 " distance=2.08 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: 4.74 Conformation dependent library (CDL) restraints added in 2.3 seconds 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 21.2% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 23 through 44 Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.029A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.979A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.691A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.936A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 45 Processing helix chain 'C' and resid 45 through 50 removed outlier: 4.090A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.930A pdb=" N SER C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.518A pdb=" N VAL C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.936A pdb=" N VAL D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 45 Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.917A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 removed outlier: 3.892A pdb=" N SER E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 116 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.920A pdb=" N VAL F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246 removed outlier: 6.086A pdb=" N GLY B 241 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP B 257 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.546A pdb=" N ILE B 338 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417 removed outlier: 7.128A pdb=" N CYS B 416 " --> pdb=" O THR C 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 436 Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.264A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.264A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545 removed outlier: 5.344A pdb=" N ASN B 540 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 557 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AB3, first strand: chain 'D' and resid 240 through 246 removed outlier: 5.959A pdb=" N GLY D 241 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP D 257 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 279 through 286 Processing sheet with id=AB5, first strand: chain 'D' and resid 331 through 334 Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 341 Processing sheet with id=AB7, first strand: chain 'D' and resid 416 through 417 removed outlier: 7.020A pdb=" N CYS D 416 " --> pdb=" O THR E 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AB9, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.759A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.759A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 539 through 545 removed outlier: 5.262A pdb=" N ASN D 540 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU D 557 " --> pdb=" O ASN D 540 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 582 through 586 Processing sheet with id=AC4, first strand: chain 'F' and resid 240 through 246 removed outlier: 6.008A pdb=" N GLY F 241 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP F 257 " --> pdb=" O GLY F 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 279 through 286 Processing sheet with id=AC6, first strand: chain 'F' and resid 331 through 334 Processing sheet with id=AC7, first strand: chain 'F' and resid 337 through 341 removed outlier: 3.670A pdb=" N ILE F 338 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 432 through 436 Processing sheet with id=AC9, first strand: chain 'F' and resid 482 through 483 Processing sheet with id=AD1, first strand: chain 'F' and resid 482 through 483 Processing sheet with id=AD2, first strand: chain 'F' and resid 539 through 545 removed outlier: 5.427A pdb=" N ASN F 540 " --> pdb=" O GLU F 557 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU F 557 " --> pdb=" O ASN F 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 582 through 586 615 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 2092 1.30 - 1.46: 4085 1.46 - 1.61: 6810 1.61 - 1.76: 1 1.76 - 1.92: 77 Bond restraints: 13065 Sorted by residual: bond pdb=" CG ASN A 103 " pdb=" OD1 ASN A 103 " ideal model delta sigma weight residual 1.231 1.150 0.081 1.90e-02 2.77e+03 1.83e+01 bond pdb=" CG LYS E 74 " pdb=" CD LYS E 74 " ideal model delta sigma weight residual 1.520 1.404 0.116 3.00e-02 1.11e+03 1.50e+01 bond pdb=" CG ASN A 103 " pdb=" ND2 ASN A 103 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.48e+01 bond pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " ideal model delta sigma weight residual 1.808 1.917 -0.109 3.30e-02 9.18e+02 1.10e+01 bond pdb=" CB THR C 58 " pdb=" CG2 THR C 58 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.85e+00 ... (remaining 13060 not shown) Histogram of bond angle deviations from ideal: 95.52 - 105.27: 311 105.27 - 115.03: 8080 115.03 - 124.78: 9077 124.78 - 134.53: 337 134.53 - 144.29: 3 Bond angle restraints: 17808 Sorted by residual: angle pdb=" CA CYS F 486 " pdb=" CB CYS F 486 " pdb=" SG CYS F 486 " ideal model delta sigma weight residual 114.40 144.29 -29.89 2.30e+00 1.89e-01 1.69e+02 angle pdb=" CA CYS F 496 " pdb=" CB CYS F 496 " pdb=" SG CYS F 496 " ideal model delta sigma weight residual 114.40 134.97 -20.57 2.30e+00 1.89e-01 8.00e+01 angle pdb=" C CYS F 496 " pdb=" CA CYS F 496 " pdb=" CB CYS F 496 " ideal model delta sigma weight residual 110.16 122.15 -11.99 1.66e+00 3.63e-01 5.22e+01 angle pdb=" CG LYS E 74 " pdb=" CD LYS E 74 " pdb=" CE LYS E 74 " ideal model delta sigma weight residual 111.30 95.52 15.78 2.30e+00 1.89e-01 4.71e+01 angle pdb=" C CYS F 486 " pdb=" CA CYS F 486 " pdb=" CB CYS F 486 " ideal model delta sigma weight residual 109.37 121.89 -12.52 1.83e+00 2.99e-01 4.68e+01 ... (remaining 17803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7333 17.65 - 35.30: 511 35.30 - 52.95: 78 52.95 - 70.59: 37 70.59 - 88.24: 12 Dihedral angle restraints: 7971 sinusoidal: 3198 harmonic: 4773 Sorted by residual: dihedral pdb=" CB CYS F 486 " pdb=" SG CYS F 486 " pdb=" SG CYS F 496 " pdb=" CB CYS F 496 " ideal model delta sinusoidal sigma weight residual -86.00 -16.56 -69.44 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 31.72 61.28 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" C CYS F 486 " pdb=" N CYS F 486 " pdb=" CA CYS F 486 " pdb=" CB CYS F 486 " ideal model delta harmonic sigma weight residual -122.60 -139.14 16.54 0 2.50e+00 1.60e-01 4.38e+01 ... (remaining 7968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1979 0.127 - 0.253: 76 0.253 - 0.380: 4 0.380 - 0.507: 1 0.507 - 0.633: 4 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CB THR C 58 " pdb=" CA THR C 58 " pdb=" OG1 THR C 58 " pdb=" CG2 THR C 58 " both_signs ideal model delta sigma weight residual False 2.55 1.92 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB ILE E 69 " pdb=" CA ILE E 69 " pdb=" CG1 ILE E 69 " pdb=" CG2 ILE E 69 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" CA CYS F 486 " pdb=" N CYS F 486 " pdb=" C CYS F 486 " pdb=" CB CYS F 486 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.77e+00 ... (remaining 2061 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 63 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A 64 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " 0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" CG ASN A 103 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 63 " 0.059 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO E 64 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.047 5.00e-02 4.00e+02 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 39 2.40 - 3.03: 7364 3.03 - 3.65: 19511 3.65 - 4.28: 28279 4.28 - 4.90: 46720 Nonbonded interactions: 101913 Sorted by model distance: nonbonded pdb=" NH2 ARG E 41 " pdb=" O TYR F 439 " model vdw 1.776 2.520 nonbonded pdb=" ND2 ASN A 103 " pdb=" N LEU B 504 " model vdw 1.888 3.200 nonbonded pdb=" OH TYR B 409 " pdb=" CB SER C 141 " model vdw 1.972 3.440 nonbonded pdb=" NH1 ARG B 512 " pdb=" OD1 ASN B 514 " model vdw 2.071 2.520 nonbonded pdb=" OE1 GLU B 274 " pdb=" NH1 ARG B 280 " model vdw 2.129 2.520 ... (remaining 101908 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 3.220 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 35.560 Find NCS groups from input model: 0.750 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.005 0.116 13065 Z= 0.307 Angle : 1.094 29.888 17808 Z= 0.584 Chirality : 0.064 0.633 2064 Planarity : 0.006 0.108 2259 Dihedral : 13.218 88.242 4815 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.25 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 9.38 % 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: -0.68 (0.19), residues: 1599 helix: -0.38 (0.26), residues: 300 sheet: 0.20 (0.19), residues: 546 loop : -0.90 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 447 HIS 0.007 0.001 HIS C 47 PHE 0.029 0.002 PHE B 502 TYR 0.031 0.003 TYR B 470 ARG 0.029 0.002 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9656 (mm) cc_final: 0.9434 (mp) REVERT: A 110 LEU cc_start: 0.8700 (mm) cc_final: 0.8374 (mm) REVERT: A 143 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8797 (tm-30) REVERT: C 30 ASP cc_start: 0.8730 (m-30) cc_final: 0.8506 (m-30) REVERT: C 106 ASP cc_start: 0.8934 (m-30) cc_final: 0.8654 (m-30) REVERT: C 156 ASP cc_start: 0.9073 (m-30) cc_final: 0.8829 (m-30) REVERT: D 584 HIS cc_start: 0.9178 (t70) cc_final: 0.8862 (t-170) REVERT: E 69 ILE cc_start: 0.8398 (tp) cc_final: 0.8122 (pt) REVERT: F 302 TYR cc_start: 0.8494 (m-80) cc_final: 0.8049 (m-80) REVERT: F 366 TRP cc_start: 0.7657 (m100) cc_final: 0.7429 (m100) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2149 time to fit residues: 47.6608 Evaluate side-chains 92 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 124 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 0.0870 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 103 ASN E 103 ASN E 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 13065 Z= 0.201 Angle : 0.665 13.554 17808 Z= 0.339 Chirality : 0.046 0.362 2064 Planarity : 0.004 0.050 2259 Dihedral : 5.309 62.214 1740 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.60 (0.20), residues: 1599 helix: 1.37 (0.29), residues: 306 sheet: 0.64 (0.19), residues: 552 loop : -0.11 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 367 HIS 0.011 0.001 HIS E 67 PHE 0.011 0.001 PHE B 502 TYR 0.016 0.001 TYR B 470 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8700 (mm-30) REVERT: A 110 LEU cc_start: 0.8952 (mm) cc_final: 0.8719 (mm) REVERT: A 143 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8877 (tm-30) REVERT: B 509 MET cc_start: 0.9270 (mpp) cc_final: 0.9039 (mpp) REVERT: C 30 ASP cc_start: 0.8735 (m-30) cc_final: 0.8489 (m-30) REVERT: C 37 THR cc_start: 0.9482 (m) cc_final: 0.9114 (m) REVERT: C 106 ASP cc_start: 0.8961 (m-30) cc_final: 0.8692 (m-30) REVERT: C 156 ASP cc_start: 0.9068 (m-30) cc_final: 0.8826 (m-30) REVERT: D 252 LEU cc_start: 0.9001 (tt) cc_final: 0.8715 (tt) REVERT: D 584 HIS cc_start: 0.9137 (t70) cc_final: 0.8803 (t-170) REVERT: E 35 ILE cc_start: 0.9647 (mt) cc_final: 0.9244 (tt) REVERT: E 89 LEU cc_start: 0.9480 (tt) cc_final: 0.9267 (tt) REVERT: E 104 LEU cc_start: 0.9667 (tt) cc_final: 0.9445 (pp) REVERT: F 302 TYR cc_start: 0.8533 (m-80) cc_final: 0.8031 (m-80) REVERT: F 366 TRP cc_start: 0.7763 (m100) cc_final: 0.7260 (m100) outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.2023 time to fit residues: 42.4672 Evaluate side-chains 86 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 120 optimal weight: 0.0020 chunk 98 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 143 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13065 Z= 0.194 Angle : 0.597 11.577 17808 Z= 0.309 Chirality : 0.043 0.242 2064 Planarity : 0.003 0.027 2259 Dihedral : 5.171 63.871 1740 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.13 (0.21), residues: 1599 helix: 1.76 (0.30), residues: 306 sheet: 0.85 (0.19), residues: 593 loop : 0.33 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 556 HIS 0.004 0.001 HIS A 47 PHE 0.007 0.001 PHE D 403 TYR 0.014 0.001 TYR B 470 ARG 0.005 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9220 (m-30) cc_final: 0.8941 (m-30) REVERT: A 102 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8641 (mm-30) REVERT: A 110 LEU cc_start: 0.8944 (mm) cc_final: 0.8707 (mm) REVERT: A 143 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8826 (tm-30) REVERT: B 461 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8667 (pp30) REVERT: C 30 ASP cc_start: 0.8736 (m-30) cc_final: 0.8483 (m-30) REVERT: C 37 THR cc_start: 0.9564 (m) cc_final: 0.9227 (m) REVERT: C 106 ASP cc_start: 0.8975 (m-30) cc_final: 0.8708 (m-30) REVERT: C 132 ASP cc_start: 0.7962 (p0) cc_final: 0.7455 (p0) REVERT: C 156 ASP cc_start: 0.9059 (m-30) cc_final: 0.8772 (m-30) REVERT: D 584 HIS cc_start: 0.9181 (t70) cc_final: 0.8869 (t-170) REVERT: E 35 ILE cc_start: 0.9697 (mt) cc_final: 0.9414 (tt) REVERT: E 76 ASP cc_start: 0.8650 (t0) cc_final: 0.8375 (t0) REVERT: F 302 TYR cc_start: 0.8706 (m-80) cc_final: 0.8281 (m-80) REVERT: F 366 TRP cc_start: 0.7843 (m100) cc_final: 0.7372 (m100) outliers start: 3 outliers final: 0 residues processed: 123 average time/residue: 0.2225 time to fit residues: 41.9384 Evaluate side-chains 85 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 40.0000 chunk 97 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 103 ASN D 461 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 GLN F 478 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13065 Z= 0.381 Angle : 0.775 14.340 17808 Z= 0.400 Chirality : 0.046 0.244 2064 Planarity : 0.005 0.040 2259 Dihedral : 5.897 73.612 1740 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.89 (0.21), residues: 1599 helix: 1.05 (0.29), residues: 306 sheet: 0.96 (0.20), residues: 571 loop : 0.19 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 366 HIS 0.008 0.002 HIS D 418 PHE 0.018 0.002 PHE D 403 TYR 0.020 0.003 TYR F 619 ARG 0.006 0.001 ARG D 467 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ASP cc_start: 0.8752 (m-30) cc_final: 0.8515 (m-30) REVERT: C 36 LYS cc_start: 0.9036 (pptt) cc_final: 0.8815 (pptt) REVERT: C 37 THR cc_start: 0.9544 (m) cc_final: 0.9156 (m) REVERT: C 106 ASP cc_start: 0.9135 (m-30) cc_final: 0.8860 (m-30) REVERT: C 156 ASP cc_start: 0.9002 (m-30) cc_final: 0.8638 (m-30) REVERT: D 320 TRP cc_start: 0.8184 (m100) cc_final: 0.7924 (m100) REVERT: D 584 HIS cc_start: 0.9349 (t70) cc_final: 0.9001 (t-170) REVERT: E 61 ASP cc_start: 0.8699 (p0) cc_final: 0.8468 (p0) REVERT: F 366 TRP cc_start: 0.8588 (m100) cc_final: 0.8266 (m100) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2107 time to fit residues: 35.2836 Evaluate side-chains 74 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.0370 chunk 2 optimal weight: 0.1980 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 83 GLN E 103 ASN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13065 Z= 0.173 Angle : 0.603 10.433 17808 Z= 0.310 Chirality : 0.044 0.327 2064 Planarity : 0.004 0.073 2259 Dihedral : 5.430 58.381 1740 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.13 % Allowed : 1.28 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.21), residues: 1599 helix: 1.60 (0.30), residues: 306 sheet: 0.91 (0.19), residues: 610 loop : 0.48 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 367 HIS 0.004 0.001 HIS C 109 PHE 0.012 0.001 PHE F 334 TYR 0.018 0.001 TYR D 424 ARG 0.006 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8886 (pt) cc_final: 0.8527 (pt) REVERT: A 100 ASP cc_start: 0.9278 (m-30) cc_final: 0.8922 (m-30) REVERT: B 384 ASP cc_start: 0.8770 (m-30) cc_final: 0.8464 (p0) REVERT: B 461 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8647 (pp30) REVERT: B 632 MET cc_start: 0.5379 (ptt) cc_final: 0.5114 (ptt) REVERT: C 30 ASP cc_start: 0.8694 (m-30) cc_final: 0.8442 (m-30) REVERT: C 37 THR cc_start: 0.9549 (m) cc_final: 0.9176 (m) REVERT: C 106 ASP cc_start: 0.9122 (m-30) cc_final: 0.8865 (m-30) REVERT: C 156 ASP cc_start: 0.8935 (m-30) cc_final: 0.8597 (m-30) REVERT: D 320 TRP cc_start: 0.8161 (m100) cc_final: 0.7876 (m100) REVERT: E 61 ASP cc_start: 0.8581 (p0) cc_final: 0.8326 (p0) REVERT: F 366 TRP cc_start: 0.8093 (m100) cc_final: 0.7828 (m100) REVERT: F 423 LEU cc_start: 0.9394 (tp) cc_final: 0.8991 (pp) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.2170 time to fit residues: 38.9533 Evaluate side-chains 83 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 103 ASN E 160 GLN F 363 GLN F 567 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13065 Z= 0.276 Angle : 0.651 8.775 17808 Z= 0.340 Chirality : 0.044 0.245 2064 Planarity : 0.005 0.056 2259 Dihedral : 5.545 60.064 1740 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.13 % Allowed : 2.76 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.21), residues: 1599 helix: 1.59 (0.30), residues: 306 sheet: 0.74 (0.20), residues: 577 loop : 0.31 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 366 HIS 0.008 0.002 HIS B 478 PHE 0.016 0.002 PHE F 334 TYR 0.016 0.002 TYR F 619 ARG 0.004 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: B 384 ASP cc_start: 0.9069 (m-30) cc_final: 0.8757 (p0) REVERT: B 632 MET cc_start: 0.6198 (ptt) cc_final: 0.5681 (ptt) REVERT: C 30 ASP cc_start: 0.8770 (m-30) cc_final: 0.8532 (m-30) REVERT: C 36 LYS cc_start: 0.8956 (pptt) cc_final: 0.8681 (pptt) REVERT: C 106 ASP cc_start: 0.9090 (m-30) cc_final: 0.8816 (m-30) REVERT: C 156 ASP cc_start: 0.9123 (m-30) cc_final: 0.8818 (m-30) REVERT: D 320 TRP cc_start: 0.8237 (m100) cc_final: 0.7878 (m100) REVERT: D 584 HIS cc_start: 0.9502 (t70) cc_final: 0.9299 (t70) REVERT: E 61 ASP cc_start: 0.8835 (p0) cc_final: 0.8565 (p0) REVERT: F 366 TRP cc_start: 0.8590 (m100) cc_final: 0.8348 (m100) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.2310 time to fit residues: 36.2978 Evaluate side-chains 71 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13065 Z= 0.237 Angle : 0.629 11.659 17808 Z= 0.328 Chirality : 0.044 0.220 2064 Planarity : 0.004 0.052 2259 Dihedral : 5.478 54.583 1740 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.07 % Allowed : 1.41 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.01 (0.22), residues: 1599 helix: 1.56 (0.30), residues: 306 sheet: 0.69 (0.21), residues: 588 loop : 0.40 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 366 HIS 0.005 0.001 HIS B 478 PHE 0.011 0.001 PHE F 334 TYR 0.035 0.002 TYR C 82 ARG 0.007 0.001 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: B 384 ASP cc_start: 0.9072 (m-30) cc_final: 0.8760 (p0) REVERT: B 632 MET cc_start: 0.6469 (ptt) cc_final: 0.5953 (ptt) REVERT: C 30 ASP cc_start: 0.8757 (m-30) cc_final: 0.8540 (m-30) REVERT: C 36 LYS cc_start: 0.8939 (pptt) cc_final: 0.8638 (pptt) REVERT: C 37 THR cc_start: 0.9550 (m) cc_final: 0.9176 (m) REVERT: C 106 ASP cc_start: 0.9075 (m-30) cc_final: 0.8807 (m-30) REVERT: C 156 ASP cc_start: 0.9108 (m-30) cc_final: 0.8756 (m-30) REVERT: E 61 ASP cc_start: 0.8842 (p0) cc_final: 0.8549 (p0) REVERT: F 366 TRP cc_start: 0.8301 (m100) cc_final: 0.7970 (m100) REVERT: F 509 MET cc_start: 0.9048 (mpp) cc_final: 0.8638 (mpp) REVERT: F 632 MET cc_start: 0.2087 (ttp) cc_final: 0.1766 (ttp) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2091 time to fit residues: 35.4829 Evaluate side-chains 69 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 75 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 120 optimal weight: 0.0010 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN D 349 HIS E 103 ASN F 349 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13065 Z= 0.151 Angle : 0.591 11.821 17808 Z= 0.303 Chirality : 0.044 0.202 2064 Planarity : 0.004 0.045 2259 Dihedral : 5.144 50.449 1740 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.20 % Allowed : 0.81 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.20 (0.22), residues: 1599 helix: 1.83 (0.30), residues: 303 sheet: 0.75 (0.20), residues: 599 loop : 0.52 (0.26), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 366 HIS 0.004 0.001 HIS B 349 PHE 0.017 0.001 PHE F 334 TYR 0.027 0.001 TYR C 82 ARG 0.007 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9330 (m-30) cc_final: 0.9083 (m-30) REVERT: A 102 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8553 (mm-30) REVERT: B 384 ASP cc_start: 0.8987 (m-30) cc_final: 0.8719 (p0) REVERT: B 461 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8564 (pp30) REVERT: B 632 MET cc_start: 0.6334 (ptt) cc_final: 0.5676 (ptt) REVERT: C 30 ASP cc_start: 0.8992 (m-30) cc_final: 0.8653 (m-30) REVERT: C 36 LYS cc_start: 0.8985 (pptt) cc_final: 0.8723 (pptt) REVERT: C 37 THR cc_start: 0.9541 (m) cc_final: 0.9165 (m) REVERT: C 156 ASP cc_start: 0.9088 (m-30) cc_final: 0.8730 (m-30) REVERT: E 61 ASP cc_start: 0.8759 (p0) cc_final: 0.8428 (p0) REVERT: E 75 MET cc_start: 0.8356 (ptp) cc_final: 0.8010 (ptp) REVERT: F 366 TRP cc_start: 0.8246 (m100) cc_final: 0.7961 (m100) REVERT: F 632 MET cc_start: 0.1884 (ttp) cc_final: 0.1576 (ttp) outliers start: 3 outliers final: 0 residues processed: 109 average time/residue: 0.2102 time to fit residues: 36.2007 Evaluate side-chains 76 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.8980 chunk 142 optimal weight: 0.0870 chunk 146 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13065 Z= 0.150 Angle : 0.583 11.484 17808 Z= 0.299 Chirality : 0.044 0.203 2064 Planarity : 0.004 0.043 2259 Dihedral : 5.060 49.662 1740 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.29 (0.22), residues: 1599 helix: 1.89 (0.30), residues: 303 sheet: 0.83 (0.20), residues: 595 loop : 0.57 (0.26), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 447 HIS 0.003 0.001 HIS B 349 PHE 0.013 0.001 PHE F 334 TYR 0.013 0.001 TYR C 82 ARG 0.006 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8894 (pt) cc_final: 0.8683 (pt) REVERT: A 100 ASP cc_start: 0.9286 (m-30) cc_final: 0.9067 (m-30) REVERT: A 102 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8532 (mm-30) REVERT: A 156 ASP cc_start: 0.9357 (m-30) cc_final: 0.9157 (m-30) REVERT: B 384 ASP cc_start: 0.8978 (m-30) cc_final: 0.8728 (p0) REVERT: C 30 ASP cc_start: 0.9000 (m-30) cc_final: 0.8710 (m-30) REVERT: C 36 LYS cc_start: 0.8986 (pptt) cc_final: 0.8658 (pptt) REVERT: C 37 THR cc_start: 0.9537 (m) cc_final: 0.9214 (m) REVERT: C 106 ASP cc_start: 0.8749 (m-30) cc_final: 0.8436 (m-30) REVERT: C 156 ASP cc_start: 0.9071 (m-30) cc_final: 0.8706 (m-30) REVERT: D 584 HIS cc_start: 0.9525 (t70) cc_final: 0.9323 (t70) REVERT: E 61 ASP cc_start: 0.8721 (p0) cc_final: 0.8386 (p0) REVERT: E 75 MET cc_start: 0.8358 (ptp) cc_final: 0.7974 (ptp) REVERT: F 366 TRP cc_start: 0.8219 (m100) cc_final: 0.7940 (m100) REVERT: F 452 ILE cc_start: 0.9451 (mm) cc_final: 0.9226 (tt) REVERT: F 632 MET cc_start: 0.2146 (ttp) cc_final: 0.1935 (ttp) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.2185 time to fit residues: 35.8418 Evaluate side-chains 79 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 0.2980 chunk 145 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13065 Z= 0.152 Angle : 0.581 11.295 17808 Z= 0.299 Chirality : 0.044 0.203 2064 Planarity : 0.004 0.049 2259 Dihedral : 4.931 49.747 1740 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.13 % Allowed : 0.27 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.33 (0.22), residues: 1599 helix: 1.77 (0.30), residues: 303 sheet: 0.93 (0.20), residues: 587 loop : 0.59 (0.26), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 447 HIS 0.003 0.001 HIS B 349 PHE 0.013 0.001 PHE F 334 TYR 0.011 0.001 TYR F 424 ARG 0.006 0.000 ARG E 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9233 (m-30) cc_final: 0.8854 (m-30) REVERT: A 102 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8532 (mm-30) REVERT: B 384 ASP cc_start: 0.8984 (m-30) cc_final: 0.8729 (p0) REVERT: C 30 ASP cc_start: 0.8802 (m-30) cc_final: 0.8583 (m-30) REVERT: C 36 LYS cc_start: 0.8983 (pptt) cc_final: 0.8650 (pptt) REVERT: C 37 THR cc_start: 0.9535 (m) cc_final: 0.9202 (m) REVERT: C 106 ASP cc_start: 0.8772 (m-30) cc_final: 0.8455 (m-30) REVERT: C 156 ASP cc_start: 0.9101 (m-30) cc_final: 0.8751 (m-30) REVERT: D 584 HIS cc_start: 0.9527 (t70) cc_final: 0.9326 (t70) REVERT: E 61 ASP cc_start: 0.8706 (p0) cc_final: 0.8372 (p0) REVERT: E 75 MET cc_start: 0.8452 (ptp) cc_final: 0.8225 (ptp) REVERT: F 366 TRP cc_start: 0.8220 (m100) cc_final: 0.7937 (m100) REVERT: F 452 ILE cc_start: 0.9440 (mm) cc_final: 0.9196 (tt) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.2291 time to fit residues: 37.4838 Evaluate side-chains 74 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 126 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 43 ASN E 103 ASN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.068358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.052947 restraints weight = 75205.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.053614 restraints weight = 51160.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.054334 restraints weight = 27023.747| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13065 Z= 0.245 Angle : 0.614 10.637 17808 Z= 0.321 Chirality : 0.044 0.224 2064 Planarity : 0.004 0.048 2259 Dihedral : 5.108 49.508 1740 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.20 % Allowed : 0.13 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.19 (0.22), residues: 1599 helix: 1.66 (0.30), residues: 300 sheet: 0.84 (0.20), residues: 578 loop : 0.52 (0.26), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 447 HIS 0.006 0.001 HIS C 109 PHE 0.010 0.002 PHE F 334 TYR 0.013 0.002 TYR C 82 ARG 0.005 0.001 ARG E 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.40 seconds wall clock time: 42 minutes 57.30 seconds (2577.30 seconds total)