Starting phenix.real_space_refine on Sat Jul 20 23:44:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/07_2024/7v1y_31630.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/07_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_31630/07_2024/7v1y_31630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/07_2024/7v1y_31630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/07_2024/7v1y_31630.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1y_31630/07_2024/7v1y_31630.cif" } 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-5388/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: 8.98, per 1000 atoms: 0.72 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: 4.67 Conformation dependent library (CDL) restraints added in 2.4 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... Secondary structure from input PDB file: 60 helices and 12 sheets defined 40.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 104 through 123 Processing helix chain 'A' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.716A pdb=" N LEU A 294 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.631A pdb=" N GLY A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.609A pdb=" N GLY A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 424 removed outlier: 3.675A pdb=" N LEU A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) 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 436 through 444 Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 530 through 545 Processing helix chain 'C' and resid 104 through 123 Processing helix chain 'C' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.717A pdb=" N LEU C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 340 removed outlier: 3.631A pdb=" N GLY C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 403 through 424 removed outlier: 3.674A pdb=" N LEU C 407 " --> pdb=" O THR C 403 " (cutoff:3.500A) 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 436 through 444 Processing helix chain 'C' and resid 504 through 511 Processing helix chain 'C' and resid 530 through 545 Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.626A pdb=" N LEU B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 226 through 235 Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.717A pdb=" N LEU B 294 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 325 through 340 removed outlier: 3.632A pdb=" N GLY B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 403 through 424 removed outlier: 3.676A pdb=" N LEU B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) 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 436 through 444 Processing helix chain 'B' and resid 504 through 511 Processing helix chain 'B' and resid 530 through 545 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'D' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 226 through 235 Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.717A pdb=" N LEU D 294 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 325 through 340 removed outlier: 3.631A pdb=" N GLY D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 403 through 424 removed outlier: 3.675A pdb=" N LEU D 407 " --> pdb=" O THR D 403 " (cutoff:3.500A) 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 436 through 444 Processing helix chain 'D' and resid 504 through 511 Processing helix chain 'D' and resid 530 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 5.211A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 133 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 5.212A pdb=" N GLU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 133 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 375 through 377 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 removed outlier: 5.211A pdb=" N GLU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 133 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 5.212A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL D 133 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AB3, first strand: chain 'D' and resid 375 through 377 553 hydrogen bonds defined for protein. 1548 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: 3.50 Time building geometry restraints manager: 5.06 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: 2684 2.78 - 3.31: 10867 3.31 - 3.84: 19963 3.84 - 4.37: 24569 4.37 - 4.90: 42092 Nonbonded interactions: 100175 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 100170 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.830 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.640 ------------------------------------------------------------------------------- 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= 0.391 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 : 1.404 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: 1.6952 time to fit residues: 405.0902 Evaluate side-chains 121 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 289 GLN D 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12796 Z= 0.201 Angle : 0.549 7.769 17296 Z= 0.298 Chirality : 0.043 0.134 1900 Planarity : 0.004 0.038 2200 Dihedral : 4.288 28.541 1732 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.10 % Allowed : 10.03 % Favored : 87.87 % 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: 1.64 (0.21), residues: 1560 helix: 2.79 (0.22), residues: 552 sheet: 1.23 (0.49), residues: 116 loop : -0.00 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 464 HIS 0.005 0.001 HIS B 216 PHE 0.011 0.001 PHE A 374 TYR 0.017 0.001 TYR C 328 ARG 0.003 0.000 ARG D 477 *********************** 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: 28 poor density : 129 time to evaluate : 1.517 Fit side-chains REVERT: A 121 GLU cc_start: 0.7491 (tp30) cc_final: 0.7188 (tp30) REVERT: A 440 MET cc_start: 0.8757 (mmm) cc_final: 0.8501 (mmm) REVERT: A 443 MET cc_start: 0.8147 (mtp) cc_final: 0.7870 (ttm) REVERT: C 355 ASP cc_start: 0.7493 (t0) cc_final: 0.7234 (t0) REVERT: C 451 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: C 525 MET cc_start: 0.8954 (tpt) cc_final: 0.8692 (tpp) REVERT: C 540 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: B 406 ASP cc_start: 0.8062 (m-30) cc_final: 0.7840 (m-30) outliers start: 28 outliers final: 11 residues processed: 150 average time/residue: 1.4870 time to fit residues: 239.8238 Evaluate side-chains 130 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 540 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 187 ILE 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: 4.9990 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 479 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12796 Z= 0.368 Angle : 0.648 7.151 17296 Z= 0.350 Chirality : 0.047 0.191 1900 Planarity : 0.005 0.040 2200 Dihedral : 4.644 38.850 1732 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.07 % Allowed : 10.40 % Favored : 86.53 % 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: 1.32 (0.21), residues: 1560 helix: 2.56 (0.22), residues: 552 sheet: 0.84 (0.46), residues: 116 loop : -0.19 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 464 HIS 0.008 0.002 HIS B 216 PHE 0.013 0.002 PHE A 374 TYR 0.016 0.002 TYR C 418 ARG 0.004 0.001 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 169 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 1.520 Fit side-chains REVERT: A 365 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: A 443 MET cc_start: 0.8191 (mtp) cc_final: 0.7885 (ttm) REVERT: C 355 ASP cc_start: 0.7592 (t0) cc_final: 0.7264 (t0) REVERT: C 451 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: B 468 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: D 121 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: D 336 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7619 (tt0) outliers start: 41 outliers final: 17 residues processed: 158 average time/residue: 1.5059 time to fit residues: 255.4800 Evaluate side-chains 135 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 136 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 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 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 222 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12796 Z= 0.308 Angle : 0.597 6.755 17296 Z= 0.322 Chirality : 0.045 0.193 1900 Planarity : 0.004 0.041 2200 Dihedral : 4.564 42.324 1732 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: 1.26 (0.21), residues: 1560 helix: 2.50 (0.22), residues: 552 sheet: 0.78 (0.44), residues: 116 loop : -0.22 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 464 HIS 0.007 0.001 HIS B 216 PHE 0.013 0.002 PHE B 374 TYR 0.015 0.002 TYR C 328 ARG 0.004 0.000 ARG C 480 *********************** 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: 33 poor density : 124 time to evaluate : 1.515 Fit side-chains REVERT: A 443 MET cc_start: 0.8141 (mtp) cc_final: 0.7879 (ttm) REVERT: C 355 ASP cc_start: 0.7623 (t0) cc_final: 0.7276 (t0) REVERT: C 451 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: D 336 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7636 (tm-30) REVERT: D 362 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7257 (mm-30) outliers start: 33 outliers final: 18 residues processed: 151 average time/residue: 1.4716 time to fit residues: 238.9587 Evaluate side-chains 137 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 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 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 459 LYS Chi-restraints excluded: chain D residue 222 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12796 Z= 0.212 Angle : 0.537 5.800 17296 Z= 0.290 Chirality : 0.043 0.206 1900 Planarity : 0.004 0.039 2200 Dihedral : 4.376 42.513 1732 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.69 % Allowed : 12.87 % Favored : 84.43 % 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: 1.35 (0.21), residues: 1560 helix: 2.57 (0.22), residues: 552 sheet: 0.75 (0.44), residues: 116 loop : -0.15 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 454 HIS 0.004 0.001 HIS B 216 PHE 0.012 0.001 PHE A 374 TYR 0.012 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 160 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.6980 (t70) cc_final: 0.6582 (m-30) REVERT: C 355 ASP cc_start: 0.7571 (t0) cc_final: 0.7248 (t0) REVERT: C 451 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: B 361 GLN cc_start: 0.8886 (pm20) cc_final: 0.8614 (pm20) REVERT: D 121 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: D 362 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: D 543 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8035 (mtmm) outliers start: 36 outliers final: 16 residues processed: 154 average time/residue: 1.5324 time to fit residues: 253.4082 Evaluate side-chains 137 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 424 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 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 222 HIS 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: 0.1980 chunk 88 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS C 479 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12796 Z= 0.192 Angle : 0.526 6.573 17296 Z= 0.283 Chirality : 0.042 0.221 1900 Planarity : 0.003 0.038 2200 Dihedral : 4.279 42.369 1732 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.40 % Allowed : 14.15 % Favored : 83.46 % 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: 1.42 (0.21), residues: 1560 helix: 2.64 (0.22), residues: 552 sheet: 0.76 (0.45), residues: 116 loop : -0.11 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 454 HIS 0.004 0.001 HIS B 216 PHE 0.012 0.001 PHE D 374 TYR 0.011 0.001 TYR C 328 ARG 0.002 0.000 ARG B 112 *********************** 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 158 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7492 (tp30) cc_final: 0.7140 (tp30) REVERT: A 226 ASP cc_start: 0.6928 (t70) cc_final: 0.6584 (m-30) REVERT: C 355 ASP cc_start: 0.7578 (t0) cc_final: 0.7290 (t0) REVERT: C 451 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: B 229 LYS cc_start: 0.7623 (tptm) cc_final: 0.7388 (tptp) REVERT: B 361 GLN cc_start: 0.8882 (pm20) cc_final: 0.8593 (pm20) REVERT: D 121 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: D 336 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7369 (tm-30) REVERT: D 362 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: D 543 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7986 (mtmm) outliers start: 32 outliers final: 17 residues processed: 151 average time/residue: 1.5540 time to fit residues: 251.7065 Evaluate side-chains 143 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 206 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 222 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 0.0070 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 0.0370 chunk 93 optimal weight: 6.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS C 479 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.002 0.032 12796 Z= 0.134 Angle : 0.480 6.337 17296 Z= 0.258 Chirality : 0.041 0.215 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.034 41.110 1732 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.10 % Allowed : 14.52 % Favored : 83.38 % 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: 1.65 (0.22), residues: 1560 helix: 2.75 (0.22), residues: 552 sheet: 0.57 (0.44), residues: 148 loop : 0.13 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 395 HIS 0.004 0.001 HIS D 191 PHE 0.012 0.001 PHE D 374 TYR 0.010 0.001 TYR A 328 ARG 0.001 0.000 ARG A 106 *********************** 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 155 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7469 (tp30) cc_final: 0.7149 (tp30) REVERT: A 226 ASP cc_start: 0.6893 (t70) cc_final: 0.6547 (m-30) REVERT: C 355 ASP cc_start: 0.7548 (t0) cc_final: 0.7263 (t0) REVERT: B 229 LYS cc_start: 0.7617 (tptm) cc_final: 0.7414 (tptp) REVERT: D 121 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6251 (tt0) REVERT: D 336 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7330 (tm-30) REVERT: D 362 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: D 543 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7809 (mtmm) outliers start: 28 outliers final: 13 residues processed: 149 average time/residue: 1.5492 time to fit residues: 247.6974 Evaluate side-chains 136 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE 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: 0.5980 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 0.0670 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS C 479 GLN C 510 ASN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12796 Z= 0.191 Angle : 0.521 7.425 17296 Z= 0.279 Chirality : 0.042 0.212 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.128 39.216 1732 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 15.42 % Favored : 82.93 % 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: 1.63 (0.21), residues: 1560 helix: 2.74 (0.22), residues: 552 sheet: 0.59 (0.44), residues: 148 loop : 0.11 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 454 HIS 0.004 0.001 HIS B 216 PHE 0.012 0.001 PHE D 374 TYR 0.013 0.001 TYR C 328 ARG 0.002 0.000 ARG B 112 *********************** 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 148 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7517 (tp30) cc_final: 0.7152 (tp30) REVERT: A 226 ASP cc_start: 0.6921 (t70) cc_final: 0.6561 (m-30) REVERT: C 355 ASP cc_start: 0.7563 (t0) cc_final: 0.7289 (t0) REVERT: D 121 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: D 336 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7353 (tm-30) REVERT: D 362 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: D 543 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7856 (mtmm) outliers start: 22 outliers final: 15 residues processed: 142 average time/residue: 1.6004 time to fit residues: 244.8313 Evaluate side-chains 138 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 206 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 303 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 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: 3.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 0.0000 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN C 509 ASN C 510 ASN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12796 Z= 0.156 Angle : 0.500 6.629 17296 Z= 0.269 Chirality : 0.041 0.226 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.057 38.020 1732 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.42 % Allowed : 16.17 % Favored : 82.41 % 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: 1.67 (0.22), residues: 1560 helix: 2.74 (0.22), residues: 552 sheet: 0.58 (0.44), residues: 148 loop : 0.16 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 395 HIS 0.004 0.001 HIS D 191 PHE 0.011 0.001 PHE D 374 TYR 0.011 0.001 TYR B 328 ARG 0.001 0.000 ARG A 480 *********************** 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 141 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7506 (tp30) cc_final: 0.7150 (tp30) REVERT: A 226 ASP cc_start: 0.6890 (t70) cc_final: 0.6536 (m-30) REVERT: C 355 ASP cc_start: 0.7566 (t0) cc_final: 0.7272 (t0) REVERT: B 361 GLN cc_start: 0.8795 (pm20) cc_final: 0.8512 (pm20) REVERT: D 121 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6332 (tt0) REVERT: D 336 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7336 (tm-30) REVERT: D 362 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: D 543 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7813 (mtmm) outliers start: 19 outliers final: 14 residues processed: 135 average time/residue: 1.5673 time to fit residues: 227.3967 Evaluate side-chains 133 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 206 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12796 Z= 0.249 Angle : 0.566 7.623 17296 Z= 0.303 Chirality : 0.043 0.241 1900 Planarity : 0.004 0.038 2200 Dihedral : 4.251 37.746 1732 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.80 % Allowed : 15.79 % Favored : 82.41 % 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: 2.69 (0.22), residues: 552 sheet: 0.86 (0.45), residues: 116 loop : -0.03 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 464 HIS 0.005 0.001 HIS B 216 PHE 0.013 0.001 PHE C 374 TYR 0.013 0.001 TYR C 328 ARG 0.002 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 : 1.602 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7548 (tp30) cc_final: 0.7136 (tp30) REVERT: A 226 ASP cc_start: 0.6937 (t70) cc_final: 0.6574 (m-30) REVERT: C 355 ASP cc_start: 0.7596 (t0) cc_final: 0.7300 (t0) REVERT: D 121 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6497 (tt0) REVERT: D 336 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7364 (tm-30) REVERT: D 362 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: D 543 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7850 (mtmm) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 1.5230 time to fit residues: 232.4837 Evaluate side-chains 139 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 206 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 303 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.0050 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN C 509 ASN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.092626 restraints weight = 15465.316| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.69 r_work: 0.2852 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12796 Z= 0.203 Angle : 0.534 6.700 17296 Z= 0.286 Chirality : 0.042 0.224 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.213 37.666 1732 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.27 % Allowed : 16.47 % Favored : 82.26 % 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: 1.56 (0.21), residues: 1560 helix: 2.72 (0.22), residues: 552 sheet: 0.87 (0.45), residues: 116 loop : -0.00 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.005 0.001 HIS D 191 PHE 0.012 0.001 PHE D 374 TYR 0.013 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: 4678.23 seconds wall clock time: 82 minutes 30.88 seconds (4950.88 seconds total)