Starting phenix.real_space_refine on Wed Jan 17 20:55:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/01_2024/7jna_22403.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/01_2024/7jna_22403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/01_2024/7jna_22403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/01_2024/7jna_22403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/01_2024/7jna_22403.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/01_2024/7jna_22403.pdb" } resolution = 3.6 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= 0.004 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 24 5.16 5 C 4176 2.51 5 N 1071 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C GLU 286": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6432 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2074 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 13, 'TRANS': 264} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2074 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 13, 'TRANS': 264} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2074 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 13, 'TRANS': 264} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.08, per 1000 atoms: 0.63 Number of scatterers: 6432 At special positions: 0 Unit cell: (83.106, 82.08, 127.224, 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 24 16.00 O 1161 8.00 N 1071 7.00 C 4176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG E 1 " - " ASN A 155 " " NAG J 1 " - " ASN B 155 " " NAG O 1 " - " ASN C 155 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 32.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 62 through 98 removed outlier: 3.535A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.523A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.984A pdb=" N GLN A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 338 Processing helix chain 'B' and resid 62 through 98 removed outlier: 3.535A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.523A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.984A pdb=" N GLN B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 338 Processing helix chain 'C' and resid 62 through 98 removed outlier: 3.535A pdb=" N PHE C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.524A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.984A pdb=" N GLN C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 130 removed outlier: 6.450A pdb=" N GLN A 186 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS A 128 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 184 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS A 130 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 182 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 283 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE A 236 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A 284 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR A 238 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 286 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 240 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 172 Processing sheet with id=AA8, first strand: chain 'B' and resid 125 through 130 removed outlier: 6.450A pdb=" N GLN B 186 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 128 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 184 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS B 130 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 182 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 283 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE B 236 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL B 284 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR B 238 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU B 286 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 240 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AB1, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AB2, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 130 removed outlier: 6.450A pdb=" N GLN C 186 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS C 128 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE C 184 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS C 130 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 182 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 283 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE C 236 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL C 284 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR C 238 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU C 286 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 240 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AB6, first strand: chain 'C' and resid 244 through 247 270 hydrogen bonds defined for protein. 783 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: 1.59 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1990 1.34 - 1.45: 1037 1.45 - 1.57: 3531 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6594 Sorted by residual: bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.16e+00 bond pdb=" N ILE A 89 " pdb=" CA ILE A 89 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.78e+00 bond pdb=" N ILE C 89 " pdb=" CA ILE C 89 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.64e+00 bond pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.19e+00 bond pdb=" N LYS B 319 " pdb=" CA LYS B 319 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.10e+00 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.88: 204 106.88 - 113.66: 3664 113.66 - 120.45: 2438 120.45 - 127.24: 2622 127.24 - 134.03: 66 Bond angle restraints: 8994 Sorted by residual: angle pdb=" C SER B 206 " pdb=" N PHE B 207 " pdb=" CA PHE B 207 " ideal model delta sigma weight residual 120.29 124.94 -4.65 1.42e+00 4.96e-01 1.07e+01 angle pdb=" C SER C 206 " pdb=" N PHE C 207 " pdb=" CA PHE C 207 " ideal model delta sigma weight residual 120.29 124.89 -4.60 1.42e+00 4.96e-01 1.05e+01 angle pdb=" C SER A 206 " pdb=" N PHE A 207 " pdb=" CA PHE A 207 " ideal model delta sigma weight residual 120.29 124.88 -4.59 1.42e+00 4.96e-01 1.05e+01 angle pdb=" CA ILE B 89 " pdb=" C ILE B 89 " pdb=" O ILE B 89 " ideal model delta sigma weight residual 121.17 117.90 3.27 1.06e+00 8.90e-01 9.53e+00 angle pdb=" CA ILE A 89 " pdb=" C ILE A 89 " pdb=" O ILE A 89 " ideal model delta sigma weight residual 121.17 117.91 3.26 1.06e+00 8.90e-01 9.48e+00 ... (remaining 8989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.44: 3581 15.44 - 30.87: 430 30.87 - 46.31: 57 46.31 - 61.74: 12 61.74 - 77.18: 6 Dihedral angle restraints: 4086 sinusoidal: 1617 harmonic: 2469 Sorted by residual: dihedral pdb=" CA ASN B 190 " pdb=" C ASN B 190 " pdb=" N LYS B 191 " pdb=" CA LYS B 191 " ideal model delta harmonic sigma weight residual -180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN A 190 " pdb=" C ASN A 190 " pdb=" N LYS A 191 " pdb=" CA LYS A 191 " ideal model delta harmonic sigma weight residual 180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASN C 190 " pdb=" C ASN C 190 " pdb=" N LYS C 191 " pdb=" CA LYS C 191 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 4083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 722 0.039 - 0.079: 228 0.079 - 0.118: 97 0.118 - 0.158: 9 0.158 - 0.197: 6 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 162 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 1059 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG E 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG J 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG O 2 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.151 2.00e-02 2.50e+03 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 841 2.75 - 3.29: 6563 3.29 - 3.83: 10337 3.83 - 4.36: 11863 4.36 - 4.90: 20118 Nonbonded interactions: 49722 Sorted by model distance: nonbonded pdb=" OH TYR B 156 " pdb=" OE1 GLU B 224 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR A 156 " pdb=" OE1 GLU A 224 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR C 156 " pdb=" OE1 GLU C 224 " model vdw 2.215 2.440 nonbonded pdb=" ND1 HIS C 130 " pdb=" OE2 GLU C 181 " model vdw 2.262 2.520 nonbonded pdb=" ND1 HIS A 130 " pdb=" OE2 GLU A 181 " model vdw 2.262 2.520 ... (remaining 49717 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' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.000 Extract box with map and model: 2.100 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.860 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6594 Z= 0.319 Angle : 0.719 5.049 8994 Z= 0.407 Chirality : 0.045 0.197 1062 Planarity : 0.025 0.295 1131 Dihedral : 12.954 77.175 2469 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.83 (0.24), residues: 828 helix: -0.91 (0.27), residues: 267 sheet: -3.40 (0.25), residues: 255 loop : -3.02 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 330 HIS 0.003 0.001 HIS A 131 PHE 0.015 0.002 PHE C 204 TYR 0.007 0.001 TYR C 156 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 TYR cc_start: 0.7187 (p90) cc_final: 0.6979 (p90) REVERT: B 309 LEU cc_start: 0.7550 (tp) cc_final: 0.7307 (tp) REVERT: C 242 MET cc_start: 0.7600 (mtm) cc_final: 0.7003 (ptp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2266 time to fit residues: 59.3121 Evaluate side-chains 130 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 279 GLN B 172 GLN C 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6594 Z= 0.324 Angle : 0.753 7.917 8994 Z= 0.362 Chirality : 0.052 0.277 1062 Planarity : 0.005 0.042 1131 Dihedral : 8.450 59.034 1209 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.29 % Allowed : 23.81 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.44 (0.28), residues: 828 helix: 0.87 (0.30), residues: 267 sheet: -3.21 (0.26), residues: 249 loop : -2.31 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS B 98 PHE 0.025 0.002 PHE A 236 TYR 0.018 0.002 TYR A 201 ARG 0.003 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 TYR cc_start: 0.8027 (m-80) cc_final: 0.7669 (m-80) REVERT: A 124 GLN cc_start: 0.7802 (pm20) cc_final: 0.7119 (pp30) REVERT: A 238 THR cc_start: 0.9551 (t) cc_final: 0.9297 (p) REVERT: A 259 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7514 (mtm110) REVERT: A 319 LYS cc_start: 0.7114 (ttpt) cc_final: 0.6483 (mptt) REVERT: A 330 TRP cc_start: 0.8492 (t-100) cc_final: 0.8176 (t-100) REVERT: B 260 GLN cc_start: 0.8368 (pp30) cc_final: 0.7530 (pp30) REVERT: B 309 LEU cc_start: 0.7965 (tp) cc_final: 0.7563 (tp) REVERT: B 319 LYS cc_start: 0.7278 (ttpt) cc_final: 0.6817 (tppt) outliers start: 30 outliers final: 15 residues processed: 169 average time/residue: 0.2235 time to fit residues: 49.1120 Evaluate side-chains 134 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 297 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6594 Z= 0.259 Angle : 0.631 9.097 8994 Z= 0.316 Chirality : 0.045 0.254 1062 Planarity : 0.004 0.036 1131 Dihedral : 7.360 50.374 1209 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.29 % Allowed : 27.69 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.75 (0.29), residues: 828 helix: 1.57 (0.31), residues: 267 sheet: -2.83 (0.27), residues: 255 loop : -2.01 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 330 HIS 0.002 0.001 HIS A 131 PHE 0.022 0.002 PHE B 236 TYR 0.014 0.001 TYR C 111 ARG 0.004 0.001 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7957 (pm20) cc_final: 0.7337 (pp30) REVERT: A 172 GLN cc_start: 0.9016 (tt0) cc_final: 0.8592 (tp40) REVERT: A 305 ASN cc_start: 0.7333 (t0) cc_final: 0.7090 (t0) REVERT: A 318 PHE cc_start: 0.7659 (t80) cc_final: 0.7201 (m-80) REVERT: A 330 TRP cc_start: 0.8451 (t-100) cc_final: 0.7712 (t-100) REVERT: B 260 GLN cc_start: 0.8402 (pp30) cc_final: 0.7627 (pp30) REVERT: B 309 LEU cc_start: 0.8276 (tp) cc_final: 0.7978 (tp) REVERT: B 319 LYS cc_start: 0.7590 (ttpt) cc_final: 0.6818 (tptt) REVERT: C 101 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8407 (ttp) REVERT: C 318 PHE cc_start: 0.7407 (m-80) cc_final: 0.6777 (m-10) REVERT: C 319 LYS cc_start: 0.7175 (ttpt) cc_final: 0.6914 (tppt) REVERT: C 330 TRP cc_start: 0.8395 (t-100) cc_final: 0.7692 (t-100) outliers start: 30 outliers final: 24 residues processed: 142 average time/residue: 0.1731 time to fit residues: 32.9236 Evaluate side-chains 142 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6594 Z= 0.209 Angle : 0.596 9.391 8994 Z= 0.297 Chirality : 0.043 0.262 1062 Planarity : 0.004 0.030 1131 Dihedral : 6.897 47.058 1209 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.17 % Allowed : 29.28 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.30), residues: 828 helix: 1.88 (0.31), residues: 267 sheet: -2.61 (0.27), residues: 282 loop : -1.84 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 287 HIS 0.002 0.001 HIS A 131 PHE 0.017 0.002 PHE C 232 TYR 0.014 0.002 TYR B 156 ARG 0.005 0.001 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.9033 (tt0) cc_final: 0.8760 (tp40) REVERT: A 260 GLN cc_start: 0.8470 (pp30) cc_final: 0.7886 (pp30) REVERT: A 305 ASN cc_start: 0.7561 (t0) cc_final: 0.7299 (t0) REVERT: A 318 PHE cc_start: 0.7651 (t80) cc_final: 0.7241 (m-80) REVERT: A 330 TRP cc_start: 0.8451 (t-100) cc_final: 0.7769 (t-100) REVERT: B 260 GLN cc_start: 0.8393 (pp30) cc_final: 0.7637 (pp30) REVERT: B 309 LEU cc_start: 0.8271 (tp) cc_final: 0.7949 (tp) REVERT: B 319 LYS cc_start: 0.7439 (ttpt) cc_final: 0.6990 (tppt) REVERT: C 101 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8337 (ttp) REVERT: C 287 TRP cc_start: 0.9242 (m100) cc_final: 0.8813 (m100) REVERT: C 318 PHE cc_start: 0.7357 (m-80) cc_final: 0.6777 (m-10) REVERT: C 319 LYS cc_start: 0.7158 (ttpt) cc_final: 0.6881 (tppt) REVERT: C 330 TRP cc_start: 0.8443 (t-100) cc_final: 0.7791 (t-100) outliers start: 35 outliers final: 23 residues processed: 151 average time/residue: 0.1571 time to fit residues: 32.6956 Evaluate side-chains 140 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6594 Z= 0.198 Angle : 0.578 6.719 8994 Z= 0.293 Chirality : 0.042 0.227 1062 Planarity : 0.004 0.035 1131 Dihedral : 6.448 48.861 1209 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 7.94 % Allowed : 27.69 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 828 helix: 2.03 (0.31), residues: 267 sheet: -2.47 (0.27), residues: 282 loop : -1.60 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 287 HIS 0.002 0.001 HIS B 98 PHE 0.015 0.001 PHE B 236 TYR 0.019 0.002 TYR B 156 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 133 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8502 (pp30) cc_final: 0.7805 (pp30) REVERT: A 305 ASN cc_start: 0.7580 (t0) cc_final: 0.7212 (t0) REVERT: A 318 PHE cc_start: 0.7617 (t80) cc_final: 0.7217 (m-80) REVERT: A 330 TRP cc_start: 0.8472 (t-100) cc_final: 0.7840 (t-100) REVERT: B 154 ILE cc_start: 0.7638 (mp) cc_final: 0.7430 (mp) REVERT: B 260 GLN cc_start: 0.8467 (pp30) cc_final: 0.7726 (pp30) REVERT: B 318 PHE cc_start: 0.7135 (m-10) cc_final: 0.6732 (m-10) REVERT: B 319 LYS cc_start: 0.7382 (ttpt) cc_final: 0.6979 (tppt) REVERT: C 101 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8399 (ttp) REVERT: C 154 ILE cc_start: 0.7683 (mp) cc_final: 0.7407 (mp) REVERT: C 287 TRP cc_start: 0.9239 (m100) cc_final: 0.8840 (m100) REVERT: C 318 PHE cc_start: 0.7359 (m-80) cc_final: 0.6787 (m-10) REVERT: C 330 TRP cc_start: 0.8347 (t-100) cc_final: 0.7786 (t-100) outliers start: 45 outliers final: 34 residues processed: 159 average time/residue: 0.1666 time to fit residues: 36.1709 Evaluate side-chains 157 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5711 > 50: distance: 74 - 79: 12.336 distance: 79 - 80: 20.222 distance: 80 - 81: 6.889 distance: 80 - 83: 18.660 distance: 81 - 82: 9.706 distance: 81 - 86: 16.569 distance: 83 - 84: 5.048 distance: 83 - 85: 22.258 distance: 86 - 87: 10.943 distance: 87 - 88: 27.510 distance: 87 - 90: 12.051 distance: 88 - 89: 27.039 distance: 88 - 91: 17.516 distance: 91 - 92: 21.147 distance: 92 - 93: 18.094 distance: 92 - 95: 6.208 distance: 93 - 94: 9.785 distance: 93 - 99: 26.864 distance: 95 - 96: 7.965 distance: 96 - 97: 6.288 distance: 96 - 98: 4.977 distance: 99 - 100: 21.427 distance: 99 - 105: 21.035 distance: 100 - 101: 19.441 distance: 100 - 103: 18.071 distance: 101 - 102: 14.008 distance: 101 - 106: 24.833 distance: 103 - 104: 18.254 distance: 104 - 105: 29.426 distance: 106 - 107: 10.547 distance: 107 - 108: 6.564 distance: 107 - 110: 5.547 distance: 108 - 109: 12.623 distance: 108 - 120: 9.812 distance: 110 - 111: 9.016 distance: 111 - 112: 8.170 distance: 111 - 113: 5.426 distance: 112 - 114: 6.004 distance: 113 - 116: 7.450 distance: 114 - 115: 6.418 distance: 115 - 117: 7.286 distance: 116 - 118: 7.033 distance: 117 - 119: 6.350 distance: 118 - 119: 5.508 distance: 120 - 121: 7.767 distance: 121 - 122: 9.245 distance: 121 - 124: 9.572 distance: 122 - 123: 19.359 distance: 122 - 128: 9.166 distance: 124 - 125: 3.734 distance: 125 - 126: 10.336 distance: 125 - 127: 4.379 distance: 128 - 129: 11.436 distance: 129 - 130: 7.162 distance: 129 - 132: 12.681 distance: 130 - 131: 8.674 distance: 130 - 135: 18.089 distance: 131 - 156: 11.754 distance: 132 - 133: 7.848 distance: 132 - 134: 21.617 distance: 135 - 136: 10.790 distance: 136 - 137: 9.229 distance: 136 - 139: 8.779 distance: 137 - 138: 9.843 distance: 137 - 143: 12.446 distance: 138 - 163: 5.960 distance: 139 - 140: 13.874 distance: 139 - 141: 4.856 distance: 140 - 142: 11.217 distance: 143 - 144: 8.839 distance: 144 - 145: 6.440 distance: 144 - 147: 7.756 distance: 145 - 146: 12.332 distance: 145 - 148: 4.720 distance: 146 - 169: 7.785 distance: 148 - 149: 7.323 distance: 149 - 152: 8.068 distance: 150 - 151: 4.384 distance: 151 - 173: 7.771 distance: 152 - 153: 5.095 distance: 153 - 154: 8.185 distance: 153 - 155: 8.266