Starting phenix.real_space_refine on Mon Mar 11 00:29:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/03_2024/7voj_32050_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/03_2024/7voj_32050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/03_2024/7voj_32050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/03_2024/7voj_32050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/03_2024/7voj_32050_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/03_2024/7voj_32050_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Al 2 5.89 5 S 32 5.16 5 C 4074 2.51 5 N 1052 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6318 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3150 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3150 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' AL': 1, 'ACY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' AL': 1, 'ACY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.13, per 1000 atoms: 0.65 Number of scatterers: 6318 At special positions: 0 Unit cell: (84.162, 84.162, 113.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 Al 2 13.00 O 1158 8.00 N 1052 7.00 C 4074 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 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.845A pdb=" N VAL A 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 36 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR A 41 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 71 through 101 Processing helix chain 'A' and resid 106 through 126 removed outlier: 4.314A pdb=" N PHE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 157 through 182 Processing helix chain 'A' and resid 188 through 215 removed outlier: 5.818A pdb=" N PHE A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 240 removed outlier: 4.754A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 4.397A pdb=" N TRP A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 293 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 307 through 330 Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.658A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 398 Processing helix chain 'B' and resid 2 through 17 Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.845A pdb=" N VAL B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 36 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 37 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR B 41 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 71 through 101 Processing helix chain 'B' and resid 106 through 126 removed outlier: 4.314A pdb=" N PHE B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 135 through 149 Processing helix chain 'B' and resid 157 through 182 Processing helix chain 'B' and resid 188 through 215 removed outlier: 5.818A pdb=" N PHE B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 240 removed outlier: 4.754A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 4.397A pdb=" N TRP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 293 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 307 through 330 Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.658A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 398 482 hydrogen bonds defined for protein. 1356 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: 1.77 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1610 1.33 - 1.45: 1186 1.45 - 1.57: 3588 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6440 Sorted by residual: bond pdb=" C CYS A 184 " pdb=" O CYS A 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C CYS B 184 " pdb=" O CYS B 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C GLY A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" C GLY B 102 " pdb=" N ALA B 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" CA TYR B 50 " pdb=" C TYR B 50 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.37e-02 5.33e+03 3.59e+00 ... (remaining 6435 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.48: 150 106.48 - 113.37: 3558 113.37 - 120.26: 2666 120.26 - 127.15: 2272 127.15 - 134.04: 52 Bond angle restraints: 8698 Sorted by residual: angle pdb=" N PHE B 51 " pdb=" CA PHE B 51 " pdb=" C PHE B 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE A 51 " pdb=" CA PHE A 51 " pdb=" C PHE A 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE B 182 " pdb=" CA PHE B 182 " pdb=" C PHE B 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N PHE A 182 " pdb=" CA PHE A 182 " pdb=" C PHE A 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 110.62 117.44 -6.82 1.02e+00 9.61e-01 4.48e+01 ... (remaining 8693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 3354 14.31 - 28.62: 372 28.62 - 42.93: 88 42.93 - 57.24: 30 57.24 - 71.55: 6 Dihedral angle restraints: 3850 sinusoidal: 1526 harmonic: 2324 Sorted by residual: dihedral pdb=" CA ARG B 154 " pdb=" C ARG B 154 " pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG A 154 " pdb=" C ARG A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 866 0.081 - 0.162: 110 0.162 - 0.243: 14 0.243 - 0.324: 2 0.324 - 0.404: 4 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PHE B 182 " pdb=" N PHE B 182 " pdb=" C PHE B 182 " pdb=" CB PHE B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 182 " pdb=" N PHE A 182 " pdb=" C PHE A 182 " pdb=" CB PHE A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 51 " pdb=" N PHE A 51 " pdb=" C PHE A 51 " pdb=" CB PHE A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 993 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 180 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER B 180 " -0.068 2.00e-02 2.50e+03 pdb=" O SER B 180 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE B 181 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 180 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 180 " 0.068 2.00e-02 2.50e+03 pdb=" O SER A 180 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 181 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 184 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO B 185 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.042 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 96 2.63 - 3.20: 5512 3.20 - 3.76: 9632 3.76 - 4.33: 12838 4.33 - 4.90: 21621 Nonbonded interactions: 49699 Sorted by model distance: nonbonded pdb=" OD1 ASP A 160 " pdb="AL AL A 603 " model vdw 2.061 2.020 nonbonded pdb=" OD1 ASP B 160 " pdb="AL AL B 603 " model vdw 2.061 2.020 nonbonded pdb=" OD2 ASP B 160 " pdb="AL AL B 603 " model vdw 2.113 2.020 nonbonded pdb=" OD2 ASP A 160 " pdb="AL AL A 603 " model vdw 2.113 2.020 nonbonded pdb=" O ACY B 601 " pdb="AL AL B 603 " model vdw 2.116 2.020 ... (remaining 49694 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.220 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 21.790 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 40.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 0.057 6440 Z= 0.528 Angle : 1.008 10.902 8698 Z= 0.626 Chirality : 0.062 0.404 996 Planarity : 0.007 0.071 1094 Dihedral : 13.588 71.548 2346 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 1.73 % Allowed : 12.39 % Favored : 85.88 % 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: -2.46 (0.26), residues: 792 helix: -1.27 (0.17), residues: 664 sheet: None (None), residues: 0 loop : -2.54 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 129 HIS 0.003 0.001 HIS A 340 PHE 0.016 0.002 PHE B 134 TYR 0.015 0.002 TYR A 236 ARG 0.003 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.773 Fit side-chains REVERT: A 5 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.5751 (mmp-170) REVERT: A 96 GLN cc_start: 0.7767 (mm110) cc_final: 0.7501 (mm-40) REVERT: A 201 ASP cc_start: 0.7736 (t0) cc_final: 0.7447 (t70) REVERT: A 209 ASP cc_start: 0.7532 (m-30) cc_final: 0.7159 (m-30) REVERT: A 226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p) REVERT: A 370 SER cc_start: 0.9002 (m) cc_final: 0.8750 (p) REVERT: B 5 ARG cc_start: 0.6463 (mtt-85) cc_final: 0.5741 (mmp-170) REVERT: B 96 GLN cc_start: 0.7758 (mm110) cc_final: 0.7491 (mm-40) REVERT: B 201 ASP cc_start: 0.7733 (t0) cc_final: 0.7444 (t70) REVERT: B 209 ASP cc_start: 0.7539 (m-30) cc_final: 0.7165 (m-30) REVERT: B 226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p) outliers start: 12 outliers final: 10 residues processed: 149 average time/residue: 1.0498 time to fit residues: 165.0165 Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 289 ASN A 293 ASN A 330 GLN A 403 ASN B 96 GLN B 289 ASN B 293 ASN B 330 GLN B 403 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6440 Z= 0.155 Angle : 0.497 5.685 8698 Z= 0.273 Chirality : 0.035 0.141 996 Planarity : 0.004 0.041 1094 Dihedral : 5.478 56.898 874 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.88 % Allowed : 19.74 % Favored : 77.38 % 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 (0.30), residues: 792 helix: 1.27 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.66 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.004 0.001 HIS A 193 PHE 0.019 0.001 PHE B 206 TYR 0.010 0.001 TYR B 50 ARG 0.001 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.766 Fit side-chains REVERT: A 5 ARG cc_start: 0.6564 (mtt-85) cc_final: 0.6156 (mmp-170) REVERT: A 201 ASP cc_start: 0.7693 (t0) cc_final: 0.7432 (t70) REVERT: A 209 ASP cc_start: 0.7111 (m-30) cc_final: 0.6678 (m-30) REVERT: B 5 ARG cc_start: 0.6558 (mtt-85) cc_final: 0.6147 (mmp-170) REVERT: B 201 ASP cc_start: 0.7691 (t0) cc_final: 0.7431 (t70) REVERT: B 209 ASP cc_start: 0.7121 (m-30) cc_final: 0.6688 (m-30) outliers start: 20 outliers final: 8 residues processed: 120 average time/residue: 0.9703 time to fit residues: 123.6468 Evaluate side-chains 94 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6440 Z= 0.153 Angle : 0.457 5.547 8698 Z= 0.244 Chirality : 0.034 0.147 996 Planarity : 0.004 0.043 1094 Dihedral : 4.579 48.587 862 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.87 % Allowed : 23.49 % Favored : 74.64 % 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: 2.03 (0.31), residues: 792 helix: 2.17 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -2.55 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.003 0.000 HIS A 193 PHE 0.016 0.001 PHE B 206 TYR 0.011 0.001 TYR B 50 ARG 0.008 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.713 Fit side-chains REVERT: A 5 ARG cc_start: 0.6947 (mtt-85) cc_final: 0.6235 (mmp-170) REVERT: A 201 ASP cc_start: 0.7733 (t0) cc_final: 0.7435 (t70) REVERT: A 209 ASP cc_start: 0.7180 (m-30) cc_final: 0.6697 (m-30) REVERT: A 291 TYR cc_start: 0.7979 (t80) cc_final: 0.7677 (t80) REVERT: B 5 ARG cc_start: 0.6942 (mtt-85) cc_final: 0.6232 (mmp-170) REVERT: B 41 TYR cc_start: 0.7685 (m-80) cc_final: 0.7424 (m-80) REVERT: B 201 ASP cc_start: 0.7737 (t0) cc_final: 0.7446 (t70) REVERT: B 209 ASP cc_start: 0.7187 (m-30) cc_final: 0.6707 (m-30) REVERT: B 291 TYR cc_start: 0.7981 (t80) cc_final: 0.7683 (t80) outliers start: 13 outliers final: 6 residues processed: 109 average time/residue: 0.9264 time to fit residues: 107.6325 Evaluate side-chains 94 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6440 Z= 0.154 Angle : 0.462 6.973 8698 Z= 0.242 Chirality : 0.035 0.139 996 Planarity : 0.003 0.038 1094 Dihedral : 4.074 28.394 862 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.31 % Allowed : 24.50 % Favored : 73.20 % 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: 2.37 (0.31), residues: 792 helix: 2.43 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -2.63 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.003 0.001 HIS A 193 PHE 0.016 0.001 PHE B 206 TYR 0.012 0.001 TYR A 50 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.757 Fit side-chains REVERT: A 5 ARG cc_start: 0.7022 (mtt-85) cc_final: 0.6437 (mmp-170) REVERT: A 201 ASP cc_start: 0.7749 (t0) cc_final: 0.7464 (t70) REVERT: A 209 ASP cc_start: 0.7175 (m-30) cc_final: 0.6678 (m-30) REVERT: A 291 TYR cc_start: 0.7966 (t80) cc_final: 0.7652 (t80) REVERT: A 334 SER cc_start: 0.8679 (m) cc_final: 0.8382 (p) REVERT: B 5 ARG cc_start: 0.7009 (mtt-85) cc_final: 0.6423 (mmp-170) REVERT: B 201 ASP cc_start: 0.7752 (t0) cc_final: 0.7464 (t70) REVERT: B 209 ASP cc_start: 0.7179 (m-30) cc_final: 0.6678 (m-30) REVERT: B 291 TYR cc_start: 0.7967 (t80) cc_final: 0.7655 (t80) REVERT: B 334 SER cc_start: 0.8678 (m) cc_final: 0.8381 (p) outliers start: 16 outliers final: 4 residues processed: 104 average time/residue: 0.9230 time to fit residues: 102.1684 Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6440 Z= 0.179 Angle : 0.470 6.028 8698 Z= 0.246 Chirality : 0.035 0.139 996 Planarity : 0.003 0.038 1094 Dihedral : 3.841 17.593 858 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.31 % Allowed : 25.50 % Favored : 72.19 % 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: 2.52 (0.31), residues: 792 helix: 2.54 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -2.62 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.004 0.001 HIS A 193 PHE 0.009 0.001 PHE A 206 TYR 0.014 0.001 TYR B 50 ARG 0.007 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.668 Fit side-chains REVERT: A 5 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6490 (mmp-170) REVERT: A 147 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8582 (tt) REVERT: A 201 ASP cc_start: 0.7686 (t0) cc_final: 0.7395 (t70) REVERT: A 209 ASP cc_start: 0.7228 (m-30) cc_final: 0.6716 (m-30) REVERT: A 291 TYR cc_start: 0.7977 (t80) cc_final: 0.7723 (t80) REVERT: B 5 ARG cc_start: 0.7031 (mtt-85) cc_final: 0.6504 (mmp-170) REVERT: B 147 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 201 ASP cc_start: 0.7690 (t0) cc_final: 0.7401 (t70) REVERT: B 209 ASP cc_start: 0.7231 (m-30) cc_final: 0.6717 (m-30) REVERT: B 291 TYR cc_start: 0.7980 (t80) cc_final: 0.7722 (t80) REVERT: B 376 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8445 (m) outliers start: 16 outliers final: 9 residues processed: 105 average time/residue: 0.8393 time to fit residues: 94.5463 Evaluate side-chains 96 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 0.0270 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 293 ASN B 266 HIS B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6440 Z= 0.233 Angle : 0.504 6.615 8698 Z= 0.264 Chirality : 0.036 0.136 996 Planarity : 0.003 0.036 1094 Dihedral : 3.941 18.498 858 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.60 % Allowed : 25.36 % Favored : 71.04 % 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: 2.48 (0.31), residues: 792 helix: 2.51 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -2.70 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.005 0.001 HIS B 193 PHE 0.016 0.001 PHE A 206 TYR 0.014 0.002 TYR A 50 ARG 0.008 0.001 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.761 Fit side-chains REVERT: A 5 ARG cc_start: 0.7102 (mtt-85) cc_final: 0.6625 (mmp-170) REVERT: A 147 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 201 ASP cc_start: 0.7703 (t0) cc_final: 0.7432 (t70) REVERT: A 209 ASP cc_start: 0.7249 (m-30) cc_final: 0.6757 (m-30) REVERT: A 291 TYR cc_start: 0.8008 (t80) cc_final: 0.7754 (t80) REVERT: B 5 ARG cc_start: 0.7076 (mtt-85) cc_final: 0.6596 (mmp-170) REVERT: B 147 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8620 (tt) REVERT: B 201 ASP cc_start: 0.7708 (t0) cc_final: 0.7436 (t70) REVERT: B 209 ASP cc_start: 0.7185 (m-30) cc_final: 0.6687 (m-30) REVERT: B 291 TYR cc_start: 0.8005 (t80) cc_final: 0.7755 (t80) outliers start: 25 outliers final: 11 residues processed: 108 average time/residue: 0.8965 time to fit residues: 103.9556 Evaluate side-chains 101 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 293 ASN B 266 HIS B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6440 Z= 0.153 Angle : 0.460 6.179 8698 Z= 0.241 Chirality : 0.034 0.130 996 Planarity : 0.003 0.034 1094 Dihedral : 3.809 18.644 858 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 26.80 % Favored : 70.61 % 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: 2.71 (0.31), residues: 792 helix: 2.68 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.66 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS A 193 PHE 0.011 0.001 PHE B 206 TYR 0.014 0.001 TYR B 50 ARG 0.007 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.787 Fit side-chains REVERT: A 5 ARG cc_start: 0.7111 (mtt-85) cc_final: 0.6618 (mmp-170) REVERT: A 7 ILE cc_start: 0.8397 (tt) cc_final: 0.8142 (mt) REVERT: A 147 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8603 (tt) REVERT: A 201 ASP cc_start: 0.7666 (t0) cc_final: 0.7386 (t70) REVERT: A 209 ASP cc_start: 0.7182 (m-30) cc_final: 0.6644 (m-30) REVERT: B 5 ARG cc_start: 0.7107 (mtt-85) cc_final: 0.6608 (mmp-170) REVERT: B 7 ILE cc_start: 0.8391 (tt) cc_final: 0.8136 (mt) REVERT: B 147 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8597 (tt) REVERT: B 201 ASP cc_start: 0.7673 (t0) cc_final: 0.7393 (t70) REVERT: B 209 ASP cc_start: 0.7190 (m-30) cc_final: 0.6653 (m-30) outliers start: 18 outliers final: 9 residues processed: 105 average time/residue: 0.9530 time to fit residues: 107.0652 Evaluate side-chains 89 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6440 Z= 0.139 Angle : 0.461 7.575 8698 Z= 0.238 Chirality : 0.034 0.128 996 Planarity : 0.003 0.033 1094 Dihedral : 3.699 18.170 858 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.59 % Allowed : 26.95 % Favored : 71.47 % 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: 2.90 (0.31), residues: 792 helix: 2.76 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.60 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.002 0.001 HIS B 193 PHE 0.011 0.001 PHE B 206 TYR 0.013 0.001 TYR A 50 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.866 Fit side-chains REVERT: A 5 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6501 (mmp-170) REVERT: A 7 ILE cc_start: 0.8400 (tt) cc_final: 0.8155 (mt) REVERT: A 41 TYR cc_start: 0.7113 (m-10) cc_final: 0.6802 (m-80) REVERT: A 201 ASP cc_start: 0.7652 (t0) cc_final: 0.7430 (t0) REVERT: A 209 ASP cc_start: 0.7120 (m-30) cc_final: 0.6540 (m-30) REVERT: B 5 ARG cc_start: 0.7106 (mtt-85) cc_final: 0.6498 (mmp-170) REVERT: B 7 ILE cc_start: 0.8394 (tt) cc_final: 0.8149 (mt) REVERT: B 201 ASP cc_start: 0.7659 (t0) cc_final: 0.7370 (t70) REVERT: B 209 ASP cc_start: 0.7129 (m-30) cc_final: 0.6548 (m-30) outliers start: 11 outliers final: 10 residues processed: 101 average time/residue: 0.9946 time to fit residues: 106.7723 Evaluate side-chains 100 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6440 Z= 0.161 Angle : 0.481 8.721 8698 Z= 0.252 Chirality : 0.034 0.132 996 Planarity : 0.004 0.062 1094 Dihedral : 3.725 17.845 858 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.73 % Allowed : 27.81 % Favored : 70.46 % 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: 2.95 (0.31), residues: 792 helix: 2.79 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.57 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 193 PHE 0.010 0.001 PHE B 264 TYR 0.015 0.001 TYR B 50 ARG 0.015 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.757 Fit side-chains REVERT: A 5 ARG cc_start: 0.7035 (mtt-85) cc_final: 0.6598 (mmp-170) REVERT: A 7 ILE cc_start: 0.8416 (tt) cc_final: 0.8173 (mt) REVERT: A 41 TYR cc_start: 0.7130 (m-10) cc_final: 0.6831 (m-80) REVERT: A 201 ASP cc_start: 0.7666 (t0) cc_final: 0.7448 (t0) REVERT: A 209 ASP cc_start: 0.7119 (m-30) cc_final: 0.6551 (m-30) REVERT: B 5 ARG cc_start: 0.7096 (mtt-85) cc_final: 0.6612 (mmp-170) REVERT: B 7 ILE cc_start: 0.8410 (tt) cc_final: 0.8167 (mt) REVERT: B 201 ASP cc_start: 0.7672 (t0) cc_final: 0.7380 (t70) REVERT: B 209 ASP cc_start: 0.7123 (m-30) cc_final: 0.6557 (m-30) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.9523 time to fit residues: 98.3765 Evaluate side-chains 94 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.0370 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6440 Z= 0.177 Angle : 0.503 9.392 8698 Z= 0.259 Chirality : 0.035 0.133 996 Planarity : 0.003 0.033 1094 Dihedral : 3.714 18.054 858 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.59 % Allowed : 28.24 % Favored : 70.17 % 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: 2.87 (0.31), residues: 792 helix: 2.78 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -2.66 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.004 0.001 HIS B 193 PHE 0.012 0.001 PHE B 206 TYR 0.016 0.001 TYR A 50 ARG 0.008 0.000 ARG B 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.794 Fit side-chains REVERT: A 5 ARG cc_start: 0.6963 (mtt-85) cc_final: 0.6604 (mmp-170) REVERT: A 7 ILE cc_start: 0.8413 (tt) cc_final: 0.8166 (mt) REVERT: A 41 TYR cc_start: 0.7200 (m-10) cc_final: 0.6945 (m-80) REVERT: A 201 ASP cc_start: 0.7682 (t0) cc_final: 0.7462 (t0) REVERT: A 209 ASP cc_start: 0.7196 (m-30) cc_final: 0.6625 (m-30) REVERT: B 5 ARG cc_start: 0.7087 (mtt-85) cc_final: 0.6612 (mmp-170) REVERT: B 7 ILE cc_start: 0.8406 (tt) cc_final: 0.8159 (mt) REVERT: B 201 ASP cc_start: 0.7685 (t0) cc_final: 0.7396 (t70) REVERT: B 209 ASP cc_start: 0.7207 (m-30) cc_final: 0.6644 (m-30) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 1.0258 time to fit residues: 104.6400 Evaluate side-chains 98 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106921 restraints weight = 7355.572| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.15 r_work: 0.3103 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6440 Z= 0.153 Angle : 0.485 9.354 8698 Z= 0.252 Chirality : 0.034 0.129 996 Planarity : 0.003 0.034 1094 Dihedral : 3.665 17.735 858 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.30 % Allowed : 28.82 % Favored : 69.88 % 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: 3.00 (0.31), residues: 792 helix: 2.83 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.57 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.002 0.001 HIS A 193 PHE 0.009 0.001 PHE B 206 TYR 0.016 0.001 TYR B 50 ARG 0.008 0.000 ARG B 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.61 seconds wall clock time: 46 minutes 11.11 seconds (2771.11 seconds total)