Starting phenix.real_space_refine (version: dev) on Fri Feb 17 13:49:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/02_2023/7qbc_13886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/02_2023/7qbc_13886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/02_2023/7qbc_13886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/02_2023/7qbc_13886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/02_2023/7qbc_13886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/02_2023/7qbc_13886.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.088 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 Process input model Symmetric amino acids flipped Residue "A ASP 39": "OD1" <-> "OD2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5054 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2169 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "B" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2169 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.73, per 1000 atoms: 0.74 Number of scatterers: 5054 At special positions: 0 Unit cell: (75.9, 78.1, 96.8, 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 22 16.00 O 904 8.00 N 728 7.00 C 3400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 25 " " NAG B 502 " - " ASN B 32 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 724.5 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 73.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 37 through 73 removed outlier: 3.520A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.583A pdb=" N ILE A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 123 through 154 removed outlier: 3.865A pdb=" N VAL A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.514A pdb=" N GLY A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 237 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.471A pdb=" N LEU A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.731A pdb=" N ILE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 297 removed outlier: 3.642A pdb=" N THR A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 37 through 73 removed outlier: 3.519A pdb=" N THR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.583A pdb=" N ILE B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 123 through 154 removed outlier: 3.864A pdb=" N VAL B 136 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.513A pdb=" N GLY B 163 " --> pdb=" O PHE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 237 Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.471A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 244 through 249' Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.732A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 297 removed outlier: 3.641A pdb=" N THR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.823A pdb=" N TYR A 26 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 33 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.823A pdb=" N TYR B 26 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 33 " --> pdb=" O TYR B 26 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 966 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: 1.26 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 738 1.31 - 1.44: 1336 1.44 - 1.56: 3062 1.56 - 1.69: 14 1.69 - 1.81: 40 Bond restraints: 5190 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.12e+02 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.10e+02 bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C2 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.00e-02 1.00e+04 1.83e+01 ... (remaining 5185 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.43: 165 106.43 - 113.47: 3078 113.47 - 120.52: 2150 120.52 - 127.56: 1729 127.56 - 134.61: 44 Bond angle restraints: 7166 Sorted by residual: angle pdb=" N TYR A 181 " pdb=" CA TYR A 181 " pdb=" C TYR A 181 " ideal model delta sigma weight residual 111.28 105.83 5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" N TYR B 181 " pdb=" CA TYR B 181 " pdb=" C TYR B 181 " ideal model delta sigma weight residual 111.28 105.94 5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" C2 NAG B 502 " pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 109.64 112.21 -2.57 5.38e-01 3.45e+00 2.28e+01 angle pdb=" C2 NAG A 502 " pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 109.64 112.16 -2.52 5.38e-01 3.45e+00 2.20e+01 angle pdb=" N MET B 294 " pdb=" CA MET B 294 " pdb=" C MET B 294 " ideal model delta sigma weight residual 113.28 107.62 5.66 1.22e+00 6.72e-01 2.15e+01 ... (remaining 7161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 2572 15.42 - 30.84: 239 30.84 - 46.25: 59 46.25 - 61.67: 20 61.67 - 77.09: 8 Dihedral angle restraints: 2898 sinusoidal: 1072 harmonic: 1826 Sorted by residual: dihedral pdb=" CA PHE B 55 " pdb=" C PHE B 55 " pdb=" N GLY B 56 " pdb=" CA GLY B 56 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE A 55 " pdb=" C PHE A 55 " pdb=" N GLY A 56 " pdb=" CA GLY A 56 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR B 144 " pdb=" C THR B 144 " pdb=" N SER B 145 " pdb=" CA SER B 145 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 652 0.046 - 0.092: 204 0.092 - 0.138: 48 0.138 - 0.184: 10 0.184 - 0.230: 2 Chirality restraints: 916 Sorted by residual: chirality pdb=" CB VAL B 191 " pdb=" CA VAL B 191 " pdb=" CG1 VAL B 191 " pdb=" CG2 VAL B 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL A 191 " pdb=" CA VAL A 191 " pdb=" CG1 VAL A 191 " pdb=" CG2 VAL A 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 913 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 293 " 0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C SER A 293 " -0.075 2.00e-02 2.50e+03 pdb=" O SER A 293 " 0.029 2.00e-02 2.50e+03 pdb=" N MET A 294 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 293 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C SER B 293 " 0.074 2.00e-02 2.50e+03 pdb=" O SER B 293 " -0.028 2.00e-02 2.50e+03 pdb=" N MET B 294 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 179 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR A 179 " 0.071 2.00e-02 2.50e+03 pdb=" O THR A 179 " -0.027 2.00e-02 2.50e+03 pdb=" N MET A 180 " -0.024 2.00e-02 2.50e+03 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 40 2.62 - 3.19: 4851 3.19 - 3.76: 7546 3.76 - 4.33: 10065 4.33 - 4.90: 16455 Nonbonded interactions: 38957 Sorted by model distance: nonbonded pdb=" O LYS B 100 " pdb=" OG SER B 104 " model vdw 2.055 2.440 nonbonded pdb=" O LYS A 100 " pdb=" OG SER A 104 " model vdw 2.056 2.440 nonbonded pdb=" O LEU B 102 " pdb=" OG SER B 107 " model vdw 2.194 2.440 nonbonded pdb=" O LEU A 102 " pdb=" OG SER A 107 " model vdw 2.195 2.440 nonbonded pdb=" O ILE A 142 " pdb=" OG SER A 145 " model vdw 2.210 2.440 ... (remaining 38952 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' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3400 2.51 5 N 728 2.21 5 O 904 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.560 Check model and map are aligned: 0.080 Process input model: 17.780 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.008 0.117 5190 Z= 0.484 Angle : 0.962 8.181 7166 Z= 0.565 Chirality : 0.048 0.230 916 Planarity : 0.007 0.047 812 Dihedral : 14.254 77.087 1718 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 0.43 % 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: -2.40 (0.31), residues: 614 helix: -1.04 (0.24), residues: 414 sheet: -3.35 (1.02), residues: 24 loop : -2.33 (0.40), residues: 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.556 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.1367 time to fit residues: 20.1462 Evaluate side-chains 87 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5190 Z= 0.234 Angle : 0.640 7.192 7166 Z= 0.315 Chirality : 0.041 0.132 916 Planarity : 0.005 0.055 812 Dihedral : 9.367 59.954 836 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.06 % 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: -0.35 (0.34), residues: 614 helix: 0.64 (0.26), residues: 422 sheet: -3.05 (1.21), residues: 20 loop : -1.98 (0.43), residues: 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.546 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 109 average time/residue: 0.1522 time to fit residues: 21.9373 Evaluate side-chains 109 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0681 time to fit residues: 1.2194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 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 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 5190 Z= 0.281 Angle : 0.634 6.202 7166 Z= 0.314 Chirality : 0.041 0.123 916 Planarity : 0.005 0.073 812 Dihedral : 9.683 58.200 836 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 1.91 % 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: 0.60 (0.34), residues: 614 helix: 1.41 (0.26), residues: 412 sheet: -2.59 (1.30), residues: 20 loop : -1.59 (0.42), residues: 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.557 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.1563 time to fit residues: 23.7567 Evaluate side-chains 106 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0506 time to fit residues: 1.1946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN B 21 GLN B 205 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 5190 Z= 0.315 Angle : 0.649 7.846 7166 Z= 0.314 Chirality : 0.042 0.152 916 Planarity : 0.005 0.065 812 Dihedral : 10.439 59.543 836 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 2.77 % 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: 0.91 (0.35), residues: 614 helix: 1.62 (0.25), residues: 416 sheet: -2.85 (1.14), residues: 20 loop : -1.41 (0.47), residues: 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.542 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 108 average time/residue: 0.1521 time to fit residues: 21.7534 Evaluate side-chains 99 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0532 time to fit residues: 1.2969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.0050 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5190 Z= 0.218 Angle : 0.570 7.621 7166 Z= 0.284 Chirality : 0.039 0.122 916 Planarity : 0.005 0.065 812 Dihedral : 10.192 58.690 836 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 1.70 % 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: 1.36 (0.35), residues: 614 helix: 2.02 (0.25), residues: 412 sheet: -2.87 (1.11), residues: 20 loop : -1.30 (0.48), residues: 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.533 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.1596 time to fit residues: 21.1153 Evaluate side-chains 99 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0577 time to fit residues: 1.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.0070 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 205 ASN B 85 GLN B 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5190 Z= 0.234 Angle : 0.577 7.008 7166 Z= 0.288 Chirality : 0.039 0.132 916 Planarity : 0.005 0.060 812 Dihedral : 10.009 59.210 836 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 2.98 % 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: 1.42 (0.35), residues: 614 helix: 2.03 (0.25), residues: 414 sheet: -2.72 (1.09), residues: 20 loop : -1.25 (0.49), residues: 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.513 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 108 average time/residue: 0.1572 time to fit residues: 22.1000 Evaluate side-chains 99 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0588 time to fit residues: 1.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.0070 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5190 Z= 0.189 Angle : 0.556 6.940 7166 Z= 0.280 Chirality : 0.038 0.122 916 Planarity : 0.005 0.062 812 Dihedral : 9.608 59.779 836 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.85 % 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 (0.36), residues: 614 helix: 2.06 (0.25), residues: 416 sheet: -2.71 (1.05), residues: 20 loop : -1.27 (0.50), residues: 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.634 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 104 average time/residue: 0.1602 time to fit residues: 21.9433 Evaluate side-chains 103 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 85 GLN B 149 GLN B 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5190 Z= 0.216 Angle : 0.572 6.702 7166 Z= 0.293 Chirality : 0.039 0.126 916 Planarity : 0.005 0.059 812 Dihedral : 9.418 59.118 836 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 2.13 % 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: 1.44 (0.36), residues: 614 helix: 2.03 (0.25), residues: 416 sheet: -2.77 (1.06), residues: 20 loop : -1.24 (0.51), residues: 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.556 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 114 average time/residue: 0.1562 time to fit residues: 23.5349 Evaluate side-chains 103 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0525 time to fit residues: 0.8469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 149 GLN B 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 5190 Z= 0.268 Angle : 0.627 7.590 7166 Z= 0.316 Chirality : 0.041 0.139 916 Planarity : 0.005 0.060 812 Dihedral : 9.475 59.818 836 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 1.28 % 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: 1.44 (0.36), residues: 614 helix: 2.03 (0.25), residues: 416 sheet: -2.56 (1.14), residues: 20 loop : -1.27 (0.50), residues: 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.602 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 111 average time/residue: 0.1702 time to fit residues: 24.4224 Evaluate side-chains 102 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0532 time to fit residues: 0.9473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 85 GLN B 149 GLN B 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 5190 Z= 0.238 Angle : 0.661 9.728 7166 Z= 0.342 Chirality : 0.040 0.137 916 Planarity : 0.005 0.060 812 Dihedral : 9.316 58.981 836 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 1.06 % 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: 1.38 (0.35), residues: 614 helix: 2.01 (0.25), residues: 416 sheet: -2.70 (1.08), residues: 20 loop : -1.32 (0.50), residues: 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.524 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 0.1665 time to fit residues: 23.0582 Evaluate side-chains 103 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0481 time to fit residues: 0.8643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 85 GLN B 205 ASN B 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.177740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145689 restraints weight = 6564.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149432 restraints weight = 3884.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151824 restraints weight = 2891.605| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 5190 Z= 0.252 Angle : 0.680 9.122 7166 Z= 0.345 Chirality : 0.040 0.136 916 Planarity : 0.005 0.059 812 Dihedral : 9.308 58.407 836 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.85 % 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: 1.45 (0.36), residues: 614 helix: 2.04 (0.25), residues: 416 sheet: -2.62 (1.10), residues: 20 loop : -1.25 (0.51), residues: 178 =============================================================================== Job complete usr+sys time: 1214.06 seconds wall clock time: 22 minutes 48.29 seconds (1368.29 seconds total)