Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 14:15:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/04_2023/7v1y_31630_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/04_2023/7v1y_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_31630/04_2023/7v1y_31630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/04_2023/7v1y_31630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/04_2023/7v1y_31630_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/04_2023/7v1y_31630_updated.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 6.80, per 1000 atoms: 0.54 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: 4.63 Conformation dependent library (CDL) restraints added in 2.0 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: 1.16 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: 3.37 Time building geometry restraints manager: 5.01 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: 1.070 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: 5.620 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.110 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 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:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.558 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 1.7331 time to fit residues: 413.9507 Evaluate side-chains 119 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1559 ------------------------------------------------------------------------------- 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 222 HIS D 289 GLN D 471 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 12796 Z= 0.155 Angle : 0.505 7.366 17296 Z= 0.272 Chirality : 0.041 0.129 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.152 28.436 1732 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 2.02 % 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: 1.53 (0.21), residues: 1560 helix: 2.37 (0.22), residues: 544 sheet: 1.00 (0.47), residues: 148 loop : 0.20 (0.21), residues: 868 *********************** 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 156 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.502 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 148 average time/residue: 1.6581 time to fit residues: 263.1982 Evaluate side-chains 128 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 5 average time/residue: 1.0533 time to fit residues: 7.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 12796 Z= 0.385 Angle : 0.646 7.849 17296 Z= 0.347 Chirality : 0.047 0.134 1900 Planarity : 0.005 0.039 2200 Dihedral : 4.637 39.178 1732 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 2.47 % 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: 0.85 (0.20), residues: 1560 helix: 1.81 (0.22), residues: 544 sheet: 0.83 (0.46), residues: 116 loop : -0.23 (0.20), residues: 900 *********************** 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 168 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.522 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 161 average time/residue: 1.6650 time to fit residues: 286.9630 Evaluate side-chains 138 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.7106 time to fit residues: 3.8421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8485 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12796 Z= 0.218 Angle : 0.531 6.710 17296 Z= 0.284 Chirality : 0.042 0.132 1900 Planarity : 0.004 0.039 2200 Dihedral : 4.393 42.764 1732 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.25 % 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: 0.81 (0.20), residues: 1560 helix: 1.62 (0.22), residues: 568 sheet: 0.80 (0.44), residues: 116 loop : -0.19 (0.20), residues: 876 *********************** 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 157 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.500 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 149 average time/residue: 1.6067 time to fit residues: 256.8825 Evaluate side-chains 133 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.3642 time to fit residues: 4.9851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.4980 chunk 85 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12796 Z= 0.148 Angle : 0.482 5.414 17296 Z= 0.257 Chirality : 0.041 0.131 1900 Planarity : 0.003 0.038 2200 Dihedral : 4.122 42.796 1732 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.32 % 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: 0.92 (0.21), residues: 1560 helix: 1.65 (0.22), residues: 568 sheet: 0.88 (0.45), residues: 116 loop : -0.08 (0.20), residues: 876 *********************** 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 162 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.529 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 153 average time/residue: 1.6372 time to fit residues: 268.8090 Evaluate side-chains 139 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.9788 time to fit residues: 5.4000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.0020 chunk 49 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7050 ------------------------------------------------------------------------------- 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: 0.8450 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12796 Z= 0.149 Angle : 0.479 5.837 17296 Z= 0.255 Chirality : 0.040 0.130 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.028 41.922 1732 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.87 % 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: 1.06 (0.21), residues: 1560 helix: 1.70 (0.22), residues: 568 sheet: 0.60 (0.44), residues: 148 loop : 0.10 (0.21), residues: 844 *********************** 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 145 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.542 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 140 average time/residue: 1.5845 time to fit residues: 238.3061 Evaluate side-chains 130 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1339 time to fit residues: 2.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.0770 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 91 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 222 HIS B 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 12796 Z= 0.134 Angle : 0.463 6.176 17296 Z= 0.245 Chirality : 0.040 0.130 1900 Planarity : 0.003 0.037 2200 Dihedral : 3.897 40.585 1732 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.50 % 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: 1.70 (0.22), residues: 568 sheet: 0.02 (0.38), residues: 188 loop : 0.24 (0.22), residues: 804 *********************** 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 145 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.394 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 1.5741 time to fit residues: 240.0781 Evaluate side-chains 136 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 2.1466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 222 HIS C 510 ASN B 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2547 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= 0.231 Angle : 0.527 6.134 17296 Z= 0.279 Chirality : 0.042 0.131 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.137 41.113 1732 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.72 % 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: 0.87 (0.21), residues: 1560 helix: 1.65 (0.22), residues: 568 sheet: 0.06 (0.38), residues: 156 loop : -0.00 (0.21), residues: 836 *********************** 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 149 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.405 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 144 average time/residue: 1.5404 time to fit residues: 238.9165 Evaluate side-chains 135 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.2328 time to fit residues: 2.7382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 509 ASN B 191 HIS D 222 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 12796 Z= 0.149 Angle : 0.485 6.985 17296 Z= 0.257 Chirality : 0.040 0.131 1900 Planarity : 0.003 0.037 2200 Dihedral : 3.980 40.178 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 : 1.05 % 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: 1.76 (0.22), residues: 564 sheet: -0.04 (0.38), residues: 188 loop : 0.22 (0.22), residues: 808 *********************** 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 140 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.505 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 138 average time/residue: 1.5706 time to fit residues: 233.2086 Evaluate side-chains 134 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 2.0708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 0.0170 chunk 155 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN B 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2586 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= 0.138 Angle : 0.475 6.043 17296 Z= 0.251 Chirality : 0.040 0.130 1900 Planarity : 0.003 0.036 2200 Dihedral : 3.856 38.070 1732 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.05 % 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: 1.11 (0.21), residues: 1560 helix: 1.74 (0.22), residues: 568 sheet: -0.01 (0.38), residues: 188 loop : 0.31 (0.22), residues: 804 ********************** 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 143 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.535 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 1.6007 time to fit residues: 242.7533 Evaluate side-chains 133 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 2.1290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 0.0010 chunk 127 optimal weight: 0.0970 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.0070 chunk 108 optimal weight: 0.0980 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN B 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.099055 restraints weight = 15508.314| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.68 r_work: 0.2947 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2660 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= 0.117 Angle : 0.456 7.795 17296 Z= 0.240 Chirality : 0.039 0.131 1900 Planarity : 0.003 0.036 2200 Dihedral : 3.628 34.657 1732 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.05 % 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: 1.20 (0.21), residues: 1560 helix: 1.77 (0.22), residues: 568 sheet: 0.01 (0.39), residues: 188 loop : 0.40 (0.22), residues: 804 =============================================================================== Job complete usr+sys time: 4568.84 seconds wall clock time: 81 minutes 50.43 seconds (4910.43 seconds total)