Starting phenix.real_space_refine on Thu Feb 15 14:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/02_2024/7v1y_31630_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/02_2024/7v1y_31630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/02_2024/7v1y_31630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/02_2024/7v1y_31630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/02_2024/7v1y_31630_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/02_2024/7v1y_31630_updated.pdb" } resolution = 2.82 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= 0.005 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 8032 2.51 5 N 2104 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D ARG 545": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 2} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 2} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 2} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 2} Time building chain proxies: 6.84, per 1000 atoms: 0.55 Number of scatterers: 12524 At special positions: 0 Unit cell: (117.284, 80.7, 153.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2324 8.00 N 2104 7.00 C 8032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 2.3 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B3S E 3 " pdb=" CB B3S F 3 " pdb=" CB B3S G 3 " pdb=" CB B3S H 3 " Number of C-beta restraints generated: 2936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 8 sheets defined 34.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 164 through 180 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 301 through 307 removed outlier: 4.065A pdb=" N ARG A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 395 through 398 No H-bonds generated for 'chain 'A' and resid 395 through 398' Processing helix chain 'A' and resid 404 through 423 removed outlier: 5.025A pdb=" N GLY A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 531 through 544 Processing helix chain 'C' and resid 105 through 122 Processing helix chain 'C' and resid 164 through 180 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 301 through 307 removed outlier: 4.065A pdb=" N ARG C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 395 through 398 No H-bonds generated for 'chain 'C' and resid 395 through 398' Processing helix chain 'C' and resid 404 through 423 removed outlier: 5.024A pdb=" N GLY C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 531 through 544 Processing helix chain 'B' and resid 105 through 122 Processing helix chain 'B' and resid 164 through 180 Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 301 through 307 removed outlier: 4.065A pdb=" N ARG B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 395 through 398 No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'B' and resid 404 through 423 removed outlier: 5.024A pdb=" N GLY B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 531 through 544 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'D' and resid 164 through 180 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 301 through 307 removed outlier: 4.064A pdb=" N ARG D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 395 through 398 No H-bonds generated for 'chain 'D' and resid 395 through 398' Processing helix chain 'D' and resid 404 through 423 removed outlier: 5.025A pdb=" N GLY D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU D 422 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 505 through 510 Processing helix chain 'D' and resid 531 through 544 Processing sheet with id= A, first strand: chain 'A' and resid 465 through 467 removed outlier: 6.341A pdb=" N VAL A 133 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 375 through 377 Processing sheet with id= C, first strand: chain 'C' and resid 465 through 467 removed outlier: 6.340A pdb=" N VAL C 133 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 375 through 377 Processing sheet with id= E, first strand: chain 'B' and resid 465 through 467 removed outlier: 6.341A pdb=" N VAL B 133 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 375 through 377 Processing sheet with id= G, first strand: chain 'D' and resid 465 through 467 removed outlier: 6.341A pdb=" N VAL D 133 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 375 through 377 452 hydrogen bonds defined for protein. 1152 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: 3.45 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2064 1.31 - 1.43: 3305 1.43 - 1.56: 7315 1.56 - 1.68: 4 1.68 - 1.81: 108 Bond restraints: 12796 Sorted by residual: bond pdb=" C ALA G 2 " pdb=" N B3S G 3 " ideal model delta sigma weight residual 1.329 1.450 -0.121 1.40e-02 5.10e+03 7.48e+01 bond pdb=" C ALA H 2 " pdb=" N B3S H 3 " ideal model delta sigma weight residual 1.329 1.450 -0.121 1.40e-02 5.10e+03 7.48e+01 bond pdb=" C ALA E 2 " pdb=" N B3S E 3 " ideal model delta sigma weight residual 1.329 1.450 -0.121 1.40e-02 5.10e+03 7.43e+01 bond pdb=" C ALA F 2 " pdb=" N B3S F 3 " ideal model delta sigma weight residual 1.329 1.449 -0.120 1.40e-02 5.10e+03 7.37e+01 bond pdb=" C ALA H 1 " pdb=" N ALA H 2 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.40e-02 5.10e+03 7.24e+01 ... (remaining 12791 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.61: 392 106.61 - 113.49: 6803 113.49 - 120.36: 4894 120.36 - 127.24: 5073 127.24 - 134.11: 134 Bond angle restraints: 17296 Sorted by residual: angle pdb=" N ILE D 165 " pdb=" CA ILE D 165 " pdb=" C ILE D 165 " ideal model delta sigma weight residual 113.00 104.01 8.99 1.30e+00 5.92e-01 4.78e+01 angle pdb=" N ILE C 165 " pdb=" CA ILE C 165 " pdb=" C ILE C 165 " ideal model delta sigma weight residual 113.00 104.04 8.96 1.30e+00 5.92e-01 4.75e+01 angle pdb=" N ILE A 165 " pdb=" CA ILE A 165 " pdb=" C ILE A 165 " ideal model delta sigma weight residual 113.00 104.05 8.95 1.30e+00 5.92e-01 4.74e+01 angle pdb=" N ILE B 165 " pdb=" CA ILE B 165 " pdb=" C ILE B 165 " ideal model delta sigma weight residual 113.00 104.07 8.93 1.30e+00 5.92e-01 4.72e+01 angle pdb=" N ILE D 162 " pdb=" CA ILE D 162 " pdb=" C ILE D 162 " ideal model delta sigma weight residual 109.30 101.32 7.98 1.25e+00 6.40e-01 4.07e+01 ... (remaining 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 6805 15.55 - 31.10: 681 31.10 - 46.66: 152 46.66 - 62.21: 22 62.21 - 77.76: 12 Dihedral angle restraints: 7672 sinusoidal: 3080 harmonic: 4592 Sorted by residual: dihedral pdb=" CA ALA G 2 " pdb=" C ALA G 2 " pdb=" N B3S G 3 " pdb=" CA B3S G 3 " ideal model delta harmonic sigma weight residual 180.00 137.43 42.57 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA ALA F 2 " pdb=" C ALA F 2 " pdb=" N B3S F 3 " pdb=" CA B3S F 3 " ideal model delta harmonic sigma weight residual 180.00 137.44 42.56 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA ALA H 2 " pdb=" C ALA H 2 " pdb=" N B3S H 3 " pdb=" CA B3S H 3 " ideal model delta harmonic sigma weight residual 180.00 137.44 42.56 0 5.00e+00 4.00e-02 7.24e+01 ... (remaining 7669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1692 0.100 - 0.200: 169 0.200 - 0.301: 34 0.301 - 0.401: 0 0.401 - 0.501: 5 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CA ALA F 2 " pdb=" N ALA F 2 " pdb=" C ALA F 2 " pdb=" CB ALA F 2 " both_signs ideal model delta sigma weight residual False 2.48 1.98 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA ALA G 2 " pdb=" N ALA G 2 " pdb=" C ALA G 2 " pdb=" CB ALA G 2 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CA ALA E 2 " pdb=" N ALA E 2 " pdb=" C ALA E 2 " pdb=" CB ALA E 2 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.22e+00 ... (remaining 1897 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 108 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ILE D 108 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE D 108 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU D 109 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 108 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE A 108 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 108 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 109 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 108 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C ILE C 108 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE C 108 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU C 109 " -0.009 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2692 2.78 - 3.31: 10947 3.31 - 3.84: 20011 3.84 - 4.37: 24805 4.37 - 4.90: 42124 Nonbonded interactions: 100579 Sorted by model distance: nonbonded pdb=" OG1 THR B 358 " pdb=" OD2 ASP B 406 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR A 358 " pdb=" OD2 ASP A 406 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR C 358 " pdb=" OD2 ASP C 406 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR D 358 " pdb=" OD2 ASP D 406 " model vdw 2.254 2.440 nonbonded pdb=" O VAL C 447 " pdb=" OG1 THR C 450 " model vdw 2.263 2.440 ... (remaining 100574 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' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.140 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.450 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.006 0.167 12796 Z= 0.410 Angle : 0.783 9.065 17296 Z= 0.498 Chirality : 0.065 0.501 1900 Planarity : 0.003 0.033 2200 Dihedral : 13.037 77.760 4736 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.15 % Allowed : 0.75 % Favored : 99.10 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.48 (0.21), residues: 1560 helix: 2.59 (0.22), residues: 544 sheet: 1.18 (0.50), residues: 116 loop : -0.03 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.002 0.001 HIS B 191 PHE 0.009 0.001 PHE B 298 TYR 0.012 0.001 TYR C 328 ARG 0.004 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7459 (tp30) cc_final: 0.7232 (tp30) REVERT: A 440 MET cc_start: 0.8819 (mmm) cc_final: 0.8502 (mmm) REVERT: C 355 ASP cc_start: 0.7517 (t0) cc_final: 0.7238 (t0) REVERT: C 525 MET cc_start: 0.8836 (tpt) cc_final: 0.8416 (tpp) REVERT: B 227 ILE cc_start: 0.8332 (mt) cc_final: 0.8011 (tt) REVERT: D 471 GLN cc_start: 0.8201 (tt0) cc_final: 0.7982 (tt0) REVERT: D 477 ARG cc_start: 0.7666 (ttt90) cc_final: 0.6039 (mpp-170) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 1.6308 time to fit residues: 389.7199 Evaluate side-chains 121 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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: 5.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 289 GLN C 479 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN D 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12796 Z= 0.155 Angle : 0.499 7.537 17296 Z= 0.269 Chirality : 0.041 0.129 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.146 29.214 1732 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.95 % Allowed : 10.10 % Favored : 87.95 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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 (0.21), residues: 1560 helix: 2.36 (0.22), residues: 544 sheet: 0.93 (0.46), residues: 148 loop : 0.20 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 454 HIS 0.003 0.001 HIS B 191 PHE 0.010 0.001 PHE B 374 TYR 0.013 0.001 TYR C 328 ARG 0.002 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.555 Fit side-chains REVERT: A 121 GLU cc_start: 0.7474 (tp30) cc_final: 0.7192 (tp30) REVERT: C 136 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7716 (tptm) REVERT: C 157 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: C 355 ASP cc_start: 0.7561 (t0) cc_final: 0.7306 (t0) REVERT: C 451 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: C 525 MET cc_start: 0.8854 (tpt) cc_final: 0.8558 (tpp) REVERT: B 227 ILE cc_start: 0.8338 (mt) cc_final: 0.7937 (tt) REVERT: B 361 GLN cc_start: 0.8816 (pm20) cc_final: 0.8599 (pm20) REVERT: B 468 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6821 (mm-30) outliers start: 26 outliers final: 11 residues processed: 151 average time/residue: 1.4687 time to fit residues: 239.3316 Evaluate side-chains 132 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS C 222 HIS C 479 GLN B 191 HIS B 222 HIS D 222 HIS D 471 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12796 Z= 0.275 Angle : 0.570 7.202 17296 Z= 0.307 Chirality : 0.044 0.149 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.360 38.584 1732 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.62 % Allowed : 10.70 % Favored : 86.68 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.05 (0.21), residues: 1560 helix: 1.99 (0.22), residues: 544 sheet: 0.93 (0.46), residues: 116 loop : -0.10 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 464 HIS 0.004 0.001 HIS A 222 PHE 0.012 0.001 PHE A 374 TYR 0.019 0.002 TYR C 328 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7551 (tp30) cc_final: 0.7214 (tp30) REVERT: A 443 MET cc_start: 0.8129 (mtp) cc_final: 0.7693 (ttm) REVERT: C 171 MET cc_start: 0.8266 (tpp) cc_final: 0.7949 (tpt) REVERT: C 355 ASP cc_start: 0.7581 (t0) cc_final: 0.7291 (t0) REVERT: C 451 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: B 468 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: D 121 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6482 (tt0) outliers start: 35 outliers final: 17 residues processed: 159 average time/residue: 1.5451 time to fit residues: 263.4884 Evaluate side-chains 141 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN B 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12796 Z= 0.183 Angle : 0.503 6.474 17296 Z= 0.268 Chirality : 0.041 0.130 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.209 42.230 1732 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.02 % Allowed : 12.28 % Favored : 85.70 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.02 (0.21), residues: 1560 helix: 1.93 (0.22), residues: 544 sheet: 0.90 (0.46), residues: 116 loop : -0.09 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS B 216 PHE 0.011 0.001 PHE D 374 TYR 0.013 0.001 TYR C 328 ARG 0.003 0.000 ARG C 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.542 Fit side-chains REVERT: A 121 GLU cc_start: 0.7496 (tp30) cc_final: 0.7217 (tp30) REVERT: A 365 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: A 443 MET cc_start: 0.8102 (mtp) cc_final: 0.7690 (ttm) REVERT: C 171 MET cc_start: 0.8272 (tpp) cc_final: 0.8027 (tpt) REVERT: C 355 ASP cc_start: 0.7554 (t0) cc_final: 0.7281 (t0) REVERT: C 451 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: D 109 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6653 (pp20) REVERT: D 121 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6400 (tt0) REVERT: D 336 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7639 (tm-30) REVERT: D 362 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7338 (mm-30) outliers start: 27 outliers final: 13 residues processed: 149 average time/residue: 1.5768 time to fit residues: 252.2658 Evaluate side-chains 133 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN B 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12796 Z= 0.188 Angle : 0.506 6.117 17296 Z= 0.269 Chirality : 0.042 0.130 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.150 42.756 1732 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.47 % Allowed : 12.20 % Favored : 85.33 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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 (0.20), residues: 1560 helix: 1.85 (0.22), residues: 544 sheet: 0.87 (0.45), residues: 116 loop : -0.08 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 178 HIS 0.002 0.001 HIS A 191 PHE 0.011 0.001 PHE D 374 TYR 0.013 0.001 TYR C 328 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.515 Fit side-chains REVERT: A 121 GLU cc_start: 0.7504 (tp30) cc_final: 0.7230 (tp30) REVERT: A 365 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 443 MET cc_start: 0.8127 (mtp) cc_final: 0.7733 (ttm) REVERT: C 171 MET cc_start: 0.8231 (tpp) cc_final: 0.7926 (tpt) REVERT: C 355 ASP cc_start: 0.7567 (t0) cc_final: 0.7275 (t0) REVERT: C 451 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: B 468 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: D 121 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: D 362 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: D 543 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8042 (mtmm) outliers start: 33 outliers final: 15 residues processed: 149 average time/residue: 1.4852 time to fit residues: 238.1507 Evaluate side-chains 140 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 ASN B 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12796 Z= 0.143 Angle : 0.470 5.557 17296 Z= 0.250 Chirality : 0.040 0.131 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.011 42.540 1732 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.57 % Allowed : 13.47 % Favored : 84.96 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.05 (0.21), residues: 1560 helix: 1.73 (0.22), residues: 568 sheet: 0.03 (0.38), residues: 188 loop : 0.21 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 178 HIS 0.002 0.001 HIS A 191 PHE 0.010 0.001 PHE D 374 TYR 0.011 0.001 TYR B 328 ARG 0.002 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.445 Fit side-chains REVERT: A 121 GLU cc_start: 0.7480 (tp30) cc_final: 0.7223 (tp30) REVERT: A 365 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: A 443 MET cc_start: 0.8108 (mtp) cc_final: 0.7731 (ttm) REVERT: C 171 MET cc_start: 0.8226 (tpp) cc_final: 0.7939 (tpt) REVERT: C 355 ASP cc_start: 0.7538 (t0) cc_final: 0.7264 (t0) REVERT: C 451 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: D 362 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: D 543 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8009 (mtmm) outliers start: 21 outliers final: 9 residues processed: 134 average time/residue: 1.4272 time to fit residues: 206.3006 Evaluate side-chains 128 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN B 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12796 Z= 0.196 Angle : 0.502 5.703 17296 Z= 0.266 Chirality : 0.041 0.130 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.105 42.370 1732 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.87 % Allowed : 12.95 % Favored : 85.18 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1560 helix: 1.71 (0.22), residues: 568 sheet: 0.85 (0.45), residues: 116 loop : -0.05 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 178 HIS 0.002 0.001 HIS B 222 PHE 0.011 0.001 PHE D 374 TYR 0.012 0.001 TYR C 328 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.516 Fit side-chains REVERT: A 121 GLU cc_start: 0.7518 (tp30) cc_final: 0.7233 (tp30) REVERT: A 365 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: A 443 MET cc_start: 0.8148 (mtp) cc_final: 0.7745 (ttm) REVERT: C 171 MET cc_start: 0.8244 (tpp) cc_final: 0.7997 (tpt) REVERT: C 355 ASP cc_start: 0.7562 (t0) cc_final: 0.7265 (t0) REVERT: C 451 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: B 469 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7362 (ptp90) REVERT: D 121 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6425 (tt0) REVERT: D 362 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: D 543 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8016 (mtmm) outliers start: 25 outliers final: 15 residues processed: 141 average time/residue: 1.5179 time to fit residues: 229.9239 Evaluate side-chains 140 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12796 Z= 0.255 Angle : 0.539 6.241 17296 Z= 0.286 Chirality : 0.043 0.131 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.276 43.243 1732 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.32 % Allowed : 13.17 % Favored : 84.51 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 0.86 (0.20), residues: 1560 helix: 1.62 (0.22), residues: 568 sheet: 0.80 (0.44), residues: 116 loop : -0.12 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 178 HIS 0.009 0.001 HIS C 481 PHE 0.013 0.001 PHE D 374 TYR 0.013 0.001 TYR C 328 ARG 0.007 0.000 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.493 Fit side-chains REVERT: A 121 GLU cc_start: 0.7528 (tp30) cc_final: 0.7224 (tp30) REVERT: A 171 MET cc_start: 0.8306 (tpp) cc_final: 0.8095 (tpt) REVERT: A 365 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 443 MET cc_start: 0.8166 (mtp) cc_final: 0.7719 (ttm) REVERT: C 171 MET cc_start: 0.8269 (tpp) cc_final: 0.8005 (tpt) REVERT: C 355 ASP cc_start: 0.7569 (t0) cc_final: 0.7276 (t0) REVERT: C 451 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: B 469 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7392 (ptp90) REVERT: D 121 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: D 362 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: D 543 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8031 (mtmm) outliers start: 31 outliers final: 19 residues processed: 144 average time/residue: 1.4746 time to fit residues: 228.3355 Evaluate side-chains 141 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 126 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 HIS C 479 GLN B 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12796 Z= 0.137 Angle : 0.472 6.432 17296 Z= 0.250 Chirality : 0.040 0.131 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.018 42.157 1732 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.87 % Allowed : 13.77 % Favored : 84.36 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.04 (0.21), residues: 1560 helix: 1.72 (0.22), residues: 564 sheet: 0.00 (0.37), residues: 188 loop : 0.23 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 178 HIS 0.002 0.001 HIS A 191 PHE 0.011 0.001 PHE D 374 TYR 0.011 0.001 TYR B 328 ARG 0.001 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.494 Fit side-chains REVERT: A 121 GLU cc_start: 0.7492 (tp30) cc_final: 0.7223 (tp30) REVERT: A 365 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: A 443 MET cc_start: 0.8120 (mtp) cc_final: 0.7734 (ttm) REVERT: C 171 MET cc_start: 0.8221 (tpp) cc_final: 0.7968 (tpt) REVERT: C 355 ASP cc_start: 0.7518 (t0) cc_final: 0.7256 (t0) REVERT: C 540 GLU cc_start: 0.7003 (tt0) cc_final: 0.6795 (tt0) REVERT: B 469 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7380 (ptp90) REVERT: D 121 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: D 543 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7948 (mtmm) outliers start: 25 outliers final: 17 residues processed: 140 average time/residue: 1.5290 time to fit residues: 230.5021 Evaluate side-chains 142 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 0.0270 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 HIS C 479 GLN B 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12796 Z= 0.149 Angle : 0.479 6.574 17296 Z= 0.254 Chirality : 0.040 0.131 1900 Planarity : 0.003 0.036 2200 Dihedral : 3.959 40.418 1732 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.80 % Allowed : 14.15 % Favored : 84.06 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.07 (0.21), residues: 1560 helix: 1.76 (0.22), residues: 564 sheet: -0.00 (0.38), residues: 188 loop : 0.23 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 178 HIS 0.002 0.001 HIS A 191 PHE 0.012 0.001 PHE D 374 TYR 0.011 0.001 TYR B 328 ARG 0.001 0.000 ARG B 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.477 Fit side-chains REVERT: A 121 GLU cc_start: 0.7500 (tp30) cc_final: 0.7232 (tp30) REVERT: A 365 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: A 443 MET cc_start: 0.8135 (mtp) cc_final: 0.7763 (ttm) REVERT: A 462 MET cc_start: 0.8470 (mtt) cc_final: 0.8257 (mtt) REVERT: C 171 MET cc_start: 0.8239 (tpp) cc_final: 0.7975 (tpt) REVERT: C 355 ASP cc_start: 0.7516 (t0) cc_final: 0.7256 (t0) REVERT: C 540 GLU cc_start: 0.7069 (tt0) cc_final: 0.6864 (tt0) REVERT: B 469 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7375 (ptp90) REVERT: D 121 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: D 543 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7942 (mtmm) outliers start: 24 outliers final: 18 residues processed: 139 average time/residue: 1.4854 time to fit residues: 222.2888 Evaluate side-chains 145 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.0000 chunk 108 optimal weight: 0.0770 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 HIS C 479 GLN B 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.093262 restraints weight = 15496.285| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.69 r_work: 0.2857 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12796 Z= 0.172 Angle : 0.491 5.807 17296 Z= 0.259 Chirality : 0.041 0.131 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.024 39.268 1732 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.80 % Allowed : 14.22 % Favored : 83.98 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 0.94 (0.21), residues: 1560 helix: 1.67 (0.22), residues: 572 sheet: 0.11 (0.38), residues: 156 loop : 0.07 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 178 HIS 0.002 0.001 HIS B 222 PHE 0.012 0.001 PHE D 374 TYR 0.012 0.001 TYR C 328 ARG 0.001 0.000 ARG B 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4574.61 seconds wall clock time: 82 minutes 9.66 seconds (4929.66 seconds total)