Starting phenix.real_space_refine on Tue Sep 24 01:00:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/09_2024/7jna_22403.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/09_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_22403/09_2024/7jna_22403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/09_2024/7jna_22403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/09_2024/7jna_22403.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jna_22403/09_2024/7jna_22403.cif" } 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. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6432 Number of models: 1 Model: "" Number of chains: 3 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: "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: "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 Restraints were copied for chains: J, O, C, B Time building chain proxies: 3.84, per 1000 atoms: 0.60 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.76 Conformation dependent library (CDL) restraints added in 973.7 milliseconds 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: 0.73 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: 1.83 Time building geometry restraints manager: 2.06 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: 0.00 - 1.01: 7951 1.01 - 2.02: 805 2.02 - 3.03: 164 3.03 - 4.04: 50 4.04 - 5.05: 24 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: 3579 15.44 - 30.87: 430 30.87 - 46.31: 53 46.31 - 61.74: 12 61.74 - 77.18: 6 Dihedral angle restraints: 4080 sinusoidal: 1611 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 4077 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: 2.03 - 2.60: 71 2.60 - 3.18: 5627 3.18 - 3.75: 9913 3.75 - 4.33: 12885 4.33 - 4.90: 21232 Nonbonded interactions: 49728 Sorted by model distance: nonbonded pdb=" SG CYS C 128 " pdb=" SG CYS C 149 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 128 " pdb=" SG CYS B 149 " model vdw 2.028 3.760 nonbonded pdb=" OH TYR B 156 " pdb=" OE1 GLU B 224 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OE1 GLU A 224 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR C 156 " pdb=" OE1 GLU C 224 " model vdw 2.215 3.040 ... (remaining 49723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.490 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- 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= 0.317 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 : 2.028 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 : 0.733 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: 0.2222 time to fit residues: 58.5460 Evaluate side-chains 130 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6594 Z= 0.390 Angle : 0.818 7.774 8994 Z= 0.392 Chirality : 0.052 0.278 1062 Planarity : 0.006 0.043 1131 Dihedral : 8.368 52.457 1209 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.11 % Allowed : 22.93 % Favored : 71.96 % 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: -2.54 (0.27), residues: 828 helix: 0.78 (0.30), residues: 267 sheet: -3.36 (0.25), residues: 249 loop : -2.26 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.003 0.001 HIS A 130 PHE 0.030 0.003 PHE A 236 TYR 0.020 0.002 TYR A 201 ARG 0.003 0.001 ARG B 259 *********************** 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 186 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7795 (pm20) cc_final: 0.7131 (pp30) REVERT: A 259 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7506 (mtm110) REVERT: A 309 LEU cc_start: 0.8180 (tp) cc_final: 0.7621 (tp) REVERT: A 330 TRP cc_start: 0.8507 (t-100) cc_final: 0.8179 (t-100) REVERT: B 259 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7556 (mtm110) REVERT: B 260 GLN cc_start: 0.8444 (pp30) cc_final: 0.7718 (pp30) REVERT: B 309 LEU cc_start: 0.8086 (tp) cc_final: 0.7667 (tp) outliers start: 29 outliers final: 16 residues processed: 176 average time/residue: 0.1883 time to fit residues: 42.9575 Evaluate side-chains 133 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 225 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 238 THR 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 225 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6594 Z= 0.246 Angle : 0.609 8.190 8994 Z= 0.308 Chirality : 0.045 0.336 1062 Planarity : 0.004 0.037 1131 Dihedral : 6.832 40.042 1209 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.17 % Allowed : 28.40 % Favored : 68.43 % 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: -1.82 (0.29), residues: 828 helix: 1.50 (0.31), residues: 267 sheet: -2.89 (0.27), residues: 261 loop : -1.97 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 287 HIS 0.003 0.001 HIS A 131 PHE 0.018 0.002 PHE C 232 TYR 0.013 0.002 TYR A 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 140 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7934 (pm20) cc_final: 0.7195 (pp30) REVERT: A 156 TYR cc_start: 0.7618 (p90) cc_final: 0.7394 (p90) REVERT: A 318 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: A 330 TRP cc_start: 0.8470 (t-100) cc_final: 0.7701 (t-100) REVERT: B 172 GLN cc_start: 0.8788 (tt0) cc_final: 0.8432 (tp-100) REVERT: B 260 GLN cc_start: 0.8400 (pp30) cc_final: 0.7636 (pp30) REVERT: C 319 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6696 (mptt) REVERT: C 330 TRP cc_start: 0.8401 (t-100) cc_final: 0.7686 (t-100) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.1867 time to fit residues: 32.0129 Evaluate side-chains 124 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 PHE 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 295 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 125 LEU 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: 9.9990 chunk 38 optimal weight: 0.4980 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6594 Z= 0.209 Angle : 0.584 6.651 8994 Z= 0.294 Chirality : 0.043 0.275 1062 Planarity : 0.004 0.032 1131 Dihedral : 6.348 43.847 1209 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.41 % Allowed : 28.04 % Favored : 67.55 % 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: -1.33 (0.30), residues: 828 helix: 1.86 (0.32), residues: 267 sheet: -2.52 (0.29), residues: 261 loop : -1.76 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 287 HIS 0.002 0.001 HIS C 130 PHE 0.018 0.002 PHE C 232 TYR 0.018 0.001 TYR C 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 156 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7928 (pm20) cc_final: 0.7240 (pp30) REVERT: A 172 GLN cc_start: 0.8840 (tp40) cc_final: 0.8604 (tp40) REVERT: A 318 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: A 330 TRP cc_start: 0.8447 (t-100) cc_final: 0.7754 (t-100) REVERT: B 172 GLN cc_start: 0.8814 (tt0) cc_final: 0.8500 (tp40) REVERT: B 238 THR cc_start: 0.9487 (t) cc_final: 0.9244 (p) REVERT: B 260 GLN cc_start: 0.8385 (pp30) cc_final: 0.7558 (pp30) REVERT: C 172 GLN cc_start: 0.8824 (tt0) cc_final: 0.8419 (tt0) REVERT: C 287 TRP cc_start: 0.9252 (m100) cc_final: 0.8881 (m100) REVERT: C 296 GLN cc_start: 0.7666 (pt0) cc_final: 0.7408 (pt0) REVERT: C 319 LYS cc_start: 0.7184 (ttpt) cc_final: 0.6705 (tptt) REVERT: C 330 TRP cc_start: 0.8389 (t-100) cc_final: 0.7771 (t-100) outliers start: 25 outliers final: 16 residues processed: 147 average time/residue: 0.1520 time to fit residues: 30.5864 Evaluate side-chains 135 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 268 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 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: 0.7425 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6594 Z= 0.242 Angle : 0.585 7.054 8994 Z= 0.301 Chirality : 0.043 0.230 1062 Planarity : 0.004 0.035 1131 Dihedral : 5.978 47.567 1209 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.11 % Allowed : 29.45 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.30), residues: 828 helix: 1.97 (0.31), residues: 267 sheet: -2.54 (0.29), residues: 255 loop : -1.58 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 287 HIS 0.002 0.001 HIS C 130 PHE 0.017 0.002 PHE A 236 TYR 0.011 0.001 TYR C 156 ARG 0.005 0.001 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 166 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8915 (tp40) cc_final: 0.8638 (tp40) REVERT: A 305 ASN cc_start: 0.7613 (t0) cc_final: 0.7341 (t0) REVERT: A 318 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: A 330 TRP cc_start: 0.8485 (t-100) cc_final: 0.7843 (t-100) REVERT: B 172 GLN cc_start: 0.8862 (tt0) cc_final: 0.8543 (tp40) REVERT: B 238 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9287 (p) REVERT: B 260 GLN cc_start: 0.8477 (pp30) cc_final: 0.7649 (pp30) REVERT: C 172 GLN cc_start: 0.8930 (tt0) cc_final: 0.8453 (tt0) REVERT: C 253 ARG cc_start: 0.7226 (tpt170) cc_final: 0.6667 (tpt-90) REVERT: C 319 LYS cc_start: 0.7359 (ttpt) cc_final: 0.6879 (tptt) REVERT: C 330 TRP cc_start: 0.8351 (t-100) cc_final: 0.7795 (t-100) outliers start: 29 outliers final: 21 residues processed: 152 average time/residue: 0.1500 time to fit residues: 31.3537 Evaluate side-chains 151 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 225 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 238 THR 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 104 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 8 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6594 Z= 0.195 Angle : 0.601 6.713 8994 Z= 0.307 Chirality : 0.045 0.225 1062 Planarity : 0.004 0.030 1131 Dihedral : 5.813 48.600 1209 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.82 % Allowed : 29.45 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.16 (0.30), residues: 828 helix: 2.11 (0.32), residues: 267 sheet: -2.57 (0.27), residues: 282 loop : -1.47 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 287 HIS 0.003 0.001 HIS C 130 PHE 0.015 0.001 PHE A 232 TYR 0.020 0.001 TYR A 156 ARG 0.005 0.001 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 6 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 174 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7439 (p90) REVERT: A 172 GLN cc_start: 0.8901 (tp40) cc_final: 0.8656 (tp40) REVERT: A 318 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: A 330 TRP cc_start: 0.8465 (t-100) cc_final: 0.7864 (t-100) REVERT: B 172 GLN cc_start: 0.8845 (tt0) cc_final: 0.8540 (tp40) REVERT: B 260 GLN cc_start: 0.8494 (pp30) cc_final: 0.7648 (pp30) REVERT: B 287 TRP cc_start: 0.9291 (m100) cc_final: 0.8541 (m100) REVERT: B 296 GLN cc_start: 0.7569 (pt0) cc_final: 0.7332 (pt0) REVERT: B 319 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6986 (tppt) REVERT: B 330 TRP cc_start: 0.8022 (t-100) cc_final: 0.7692 (t-100) REVERT: C 253 ARG cc_start: 0.7231 (tpt170) cc_final: 0.6721 (tpt-90) REVERT: C 330 TRP cc_start: 0.8315 (t-100) cc_final: 0.7780 (t-100) outliers start: 33 outliers final: 21 residues processed: 157 average time/residue: 0.1681 time to fit residues: 35.2947 Evaluate side-chains 155 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS 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 165 VAL 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 A residue 318 PHE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL 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 319 LYS Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.0270 chunk 48 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6594 Z= 0.193 Angle : 0.618 8.456 8994 Z= 0.317 Chirality : 0.049 0.507 1062 Planarity : 0.004 0.032 1131 Dihedral : 5.809 48.399 1209 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.64 % Allowed : 28.92 % Favored : 65.43 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.30), residues: 828 helix: 2.23 (0.32), residues: 267 sheet: -2.53 (0.27), residues: 276 loop : -1.24 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 287 HIS 0.002 0.001 HIS C 130 PHE 0.015 0.001 PHE C 232 TYR 0.020 0.001 TYR A 156 ARG 0.008 0.001 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 7 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 174 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8427 (ttt) REVERT: A 105 TYR cc_start: 0.8698 (m-10) cc_final: 0.8443 (m-80) REVERT: A 172 GLN cc_start: 0.8901 (tt0) cc_final: 0.8653 (tp40) REVERT: A 318 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: A 330 TRP cc_start: 0.8436 (t-100) cc_final: 0.7890 (t-100) REVERT: B 172 GLN cc_start: 0.8813 (tt0) cc_final: 0.8508 (tp40) REVERT: B 260 GLN cc_start: 0.8439 (pp30) cc_final: 0.7641 (pp30) REVERT: B 287 TRP cc_start: 0.9303 (m100) cc_final: 0.8530 (m100) REVERT: B 319 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7222 (tppt) REVERT: B 330 TRP cc_start: 0.7989 (t-100) cc_final: 0.7699 (t-100) REVERT: C 98 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7449 (p90) REVERT: C 253 ARG cc_start: 0.7256 (tpt170) cc_final: 0.6731 (tpt-90) REVERT: C 318 PHE cc_start: 0.7222 (m-10) cc_final: 0.6629 (m-10) REVERT: C 330 TRP cc_start: 0.8365 (t-100) cc_final: 0.7843 (t-100) outliers start: 32 outliers final: 22 residues processed: 153 average time/residue: 0.1607 time to fit residues: 33.3665 Evaluate side-chains 159 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 VAL 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 A residue 318 PHE Chi-restraints excluded: chain B residue 125 LEU 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 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 318 PHE Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6594 Z= 0.214 Angle : 0.608 8.361 8994 Z= 0.310 Chirality : 0.045 0.301 1062 Planarity : 0.004 0.030 1131 Dihedral : 5.484 47.331 1209 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.76 % Allowed : 29.10 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.30), residues: 828 helix: 2.40 (0.32), residues: 261 sheet: -2.55 (0.26), residues: 276 loop : -1.21 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 287 HIS 0.002 0.001 HIS B 130 PHE 0.016 0.001 PHE C 232 TYR 0.021 0.001 TYR A 156 ARG 0.008 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 8 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 176 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8490 (ttt) REVERT: A 105 TYR cc_start: 0.8699 (m-10) cc_final: 0.8489 (m-80) REVERT: A 147 MET cc_start: 0.6890 (tmm) cc_final: 0.6524 (mtt) REVERT: A 172 GLN cc_start: 0.8915 (tt0) cc_final: 0.8635 (tp40) REVERT: A 260 GLN cc_start: 0.8571 (pp30) cc_final: 0.7863 (pp30) REVERT: A 261 GLU cc_start: 0.8176 (mp0) cc_final: 0.7974 (mp0) REVERT: A 318 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: A 330 TRP cc_start: 0.8356 (t-100) cc_final: 0.7936 (t-100) REVERT: B 98 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7809 (p90) REVERT: B 172 GLN cc_start: 0.8849 (tt0) cc_final: 0.8526 (tp40) REVERT: B 260 GLN cc_start: 0.8521 (pp30) cc_final: 0.7620 (pp30) REVERT: B 319 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7119 (tptt) REVERT: B 330 TRP cc_start: 0.8031 (t-100) cc_final: 0.7769 (t-100) REVERT: C 124 GLN cc_start: 0.8233 (pm20) cc_final: 0.7363 (pp30) REVERT: C 253 ARG cc_start: 0.7249 (tpt170) cc_final: 0.6733 (tpt-90) REVERT: C 296 GLN cc_start: 0.7715 (pt0) cc_final: 0.7438 (pt0) REVERT: C 318 PHE cc_start: 0.7100 (m-10) cc_final: 0.6571 (m-10) REVERT: C 330 TRP cc_start: 0.8389 (t-100) cc_final: 0.7905 (t-100) outliers start: 27 outliers final: 23 residues processed: 161 average time/residue: 0.1609 time to fit residues: 34.8639 Evaluate side-chains 160 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 VAL 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 A residue 318 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL 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 319 LYS Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6594 Z= 0.243 Angle : 0.664 7.789 8994 Z= 0.340 Chirality : 0.055 0.632 1062 Planarity : 0.004 0.038 1131 Dihedral : 5.865 46.443 1209 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.47 % Allowed : 28.57 % Favored : 65.96 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.30), residues: 828 helix: 2.42 (0.32), residues: 261 sheet: -2.51 (0.28), residues: 249 loop : -1.10 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP A 287 HIS 0.002 0.001 HIS C 98 PHE 0.016 0.002 PHE C 232 TYR 0.020 0.002 TYR A 156 ARG 0.010 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 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 162 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8715 (m-10) cc_final: 0.8508 (m-80) REVERT: A 172 GLN cc_start: 0.8940 (tt0) cc_final: 0.8679 (tp40) REVERT: A 260 GLN cc_start: 0.8595 (pp30) cc_final: 0.7845 (pp30) REVERT: A 318 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: A 330 TRP cc_start: 0.8338 (t-100) cc_final: 0.7957 (t-100) REVERT: B 172 GLN cc_start: 0.8881 (tt0) cc_final: 0.8559 (tp40) REVERT: B 260 GLN cc_start: 0.8549 (pp30) cc_final: 0.7661 (pp30) REVERT: B 319 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7129 (tptt) REVERT: B 330 TRP cc_start: 0.8069 (t-100) cc_final: 0.7843 (t-100) REVERT: C 124 GLN cc_start: 0.8237 (pm20) cc_final: 0.7392 (pp30) REVERT: C 253 ARG cc_start: 0.7256 (tpt170) cc_final: 0.6744 (tpt-90) REVERT: C 296 GLN cc_start: 0.7720 (pt0) cc_final: 0.7505 (pt0) REVERT: C 318 PHE cc_start: 0.6947 (m-10) cc_final: 0.6459 (m-10) REVERT: C 330 TRP cc_start: 0.8358 (t-100) cc_final: 0.7935 (t-100) outliers start: 31 outliers final: 24 residues processed: 144 average time/residue: 0.1416 time to fit residues: 28.5273 Evaluate side-chains 157 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 128 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 VAL 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 A residue 318 PHE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 230 TRP 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 319 LYS Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6594 Z= 0.211 Angle : 0.616 8.234 8994 Z= 0.315 Chirality : 0.050 0.486 1062 Planarity : 0.004 0.035 1131 Dihedral : 5.520 44.369 1209 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.94 % Allowed : 28.57 % Favored : 66.49 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.30), residues: 828 helix: 2.45 (0.32), residues: 261 sheet: -2.46 (0.26), residues: 273 loop : -1.10 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 287 HIS 0.003 0.001 HIS C 130 PHE 0.015 0.001 PHE C 232 TYR 0.021 0.002 TYR A 156 ARG 0.008 0.001 ARG C 259 ********************** REFINEMENT MACRO_CYCLE 10 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: 28 poor density : 135 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8943 (tt0) cc_final: 0.8650 (tp40) REVERT: A 260 GLN cc_start: 0.8625 (pp30) cc_final: 0.7804 (pp30) REVERT: A 318 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: A 330 TRP cc_start: 0.8338 (t-100) cc_final: 0.8009 (t-100) REVERT: B 98 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7818 (p90) REVERT: B 172 GLN cc_start: 0.8851 (tt0) cc_final: 0.8555 (tp40) REVERT: B 260 GLN cc_start: 0.8566 (pp30) cc_final: 0.7691 (pp30) REVERT: B 319 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7145 (tptt) REVERT: C 124 GLN cc_start: 0.8229 (pm20) cc_final: 0.7347 (pp30) REVERT: C 172 GLN cc_start: 0.9014 (tt0) cc_final: 0.8362 (tp40) REVERT: C 253 ARG cc_start: 0.7231 (tpt170) cc_final: 0.6743 (tpt-90) REVERT: C 296 GLN cc_start: 0.7825 (pt0) cc_final: 0.7583 (pt0) REVERT: C 318 PHE cc_start: 0.6979 (m-10) cc_final: 0.6553 (m-10) REVERT: C 330 TRP cc_start: 0.8315 (t-100) cc_final: 0.7946 (t-100) outliers start: 28 outliers final: 23 residues processed: 146 average time/residue: 0.1587 time to fit residues: 31.6880 Evaluate side-chains 155 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 128 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 VAL 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 A residue 317 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 230 TRP 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 319 LYS Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.168569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136023 restraints weight = 8780.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139624 restraints weight = 6791.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140744 restraints weight = 4658.275| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6594 Z= 0.231 Angle : 0.599 7.755 8994 Z= 0.309 Chirality : 0.049 0.415 1062 Planarity : 0.004 0.036 1131 Dihedral : 5.110 40.981 1209 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.41 % Allowed : 29.10 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 828 helix: 2.46 (0.32), residues: 261 sheet: -2.49 (0.26), residues: 273 loop : -1.15 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 287 HIS 0.002 0.001 HIS C 130 PHE 0.016 0.002 PHE C 232 TYR 0.021 0.002 TYR A 156 ARG 0.008 0.001 ARG C 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.94 seconds wall clock time: 29 minutes 39.11 seconds (1779.11 seconds total)