Starting phenix.real_space_refine on Tue Feb 11 09:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cxr_30495/02_2025/7cxr_30495.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cxr_30495/02_2025/7cxr_30495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cxr_30495/02_2025/7cxr_30495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cxr_30495/02_2025/7cxr_30495.map" model { file = "/net/cci-nas-00/data/ceres_data/7cxr_30495/02_2025/7cxr_30495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cxr_30495/02_2025/7cxr_30495.cif" } resolution = 3.4 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= 0.003 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3406 2.51 5 N 858 2.21 5 O 876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2584 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 7, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2584 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 7, 'TRANS': 299} Chain breaks: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.73 Number of scatterers: 5168 At special positions: 0 Unit cell: (90.221, 114.135, 93.482, 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 28 16.00 O 876 8.00 N 858 7.00 C 3406 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 597.6 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 9 through 69 removed outlier: 3.811A pdb=" N GLN A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 99 removed outlier: 3.594A pdb=" N LYS A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 157 through 186 Processing helix chain 'A' and resid 191 through 208 removed outlier: 4.360A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 236 removed outlier: 5.740A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 4.386A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 removed outlier: 4.138A pdb=" N THR A 273 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 305 through 338 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 69 removed outlier: 3.811A pdb=" N GLN B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 58 " --> pdb=" O GLN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 99 removed outlier: 3.594A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 157 through 186 Processing helix chain 'B' and resid 191 through 208 removed outlier: 4.360A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 202 " --> pdb=" O TYR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 236 removed outlier: 5.740A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 4.386A pdb=" N TYR B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 297 removed outlier: 4.137A pdb=" N THR B 273 " --> pdb=" O TRP B 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 305 through 338 Proline residue: B 313 - end of helix 422 hydrogen bonds defined for protein. 1266 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: 1.45 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 788 1.32 - 1.44: 1614 1.44 - 1.57: 2870 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5314 Sorted by residual: bond pdb=" C ILE A 181 " pdb=" O ILE A 181 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" C ILE B 181 " pdb=" O ILE B 181 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N ILE A 181 " pdb=" CA ILE A 181 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N ILE B 181 " pdb=" CA ILE B 181 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" C PRO B 313 " pdb=" O PRO B 313 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.30e-02 5.92e+03 9.36e+00 ... (remaining 5309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 6582 1.43 - 2.85: 448 2.85 - 4.27: 115 4.27 - 5.70: 27 5.70 - 7.12: 4 Bond angle restraints: 7176 Sorted by residual: angle pdb=" N ILE B 181 " pdb=" CA ILE B 181 " pdb=" C ILE B 181 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.93e+01 angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 110.62 104.93 5.69 1.02e+00 9.61e-01 3.12e+01 angle pdb=" CA LEU B 121 " pdb=" C LEU B 121 " pdb=" O LEU B 121 " ideal model delta sigma weight residual 122.03 115.76 6.27 1.17e+00 7.31e-01 2.87e+01 angle pdb=" CA LEU A 121 " pdb=" C LEU A 121 " pdb=" O LEU A 121 " ideal model delta sigma weight residual 122.03 115.97 6.06 1.17e+00 7.31e-01 2.68e+01 angle pdb=" C THR B 48 " pdb=" CA THR B 48 " pdb=" CB THR B 48 " ideal model delta sigma weight residual 110.68 117.80 -7.12 1.70e+00 3.46e-01 1.76e+01 ... (remaining 7171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 2617 16.42 - 32.84: 368 32.84 - 49.26: 72 49.26 - 65.68: 25 65.68 - 82.10: 10 Dihedral angle restraints: 3092 sinusoidal: 1282 harmonic: 1810 Sorted by residual: dihedral pdb=" C LEU A 58 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " pdb=" CB LEU A 58 " ideal model delta harmonic sigma weight residual -122.60 -112.58 -10.02 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" C LEU B 58 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " pdb=" CB LEU B 58 " ideal model delta harmonic sigma weight residual -122.60 -112.87 -9.73 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CA LEU A 58 " pdb=" CB LEU A 58 " ideal model delta harmonic sigma weight residual 122.80 113.45 9.35 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 3089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 668 0.070 - 0.139: 77 0.139 - 0.209: 10 0.209 - 0.279: 7 0.279 - 0.349: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA LEU B 58 " pdb=" N LEU B 58 " pdb=" C LEU B 58 " pdb=" CB LEU B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA GLN A 44 " pdb=" N GLN A 44 " pdb=" C GLN A 44 " pdb=" CB GLN A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 761 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 46 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ASN A 46 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN A 46 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS A 47 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 120 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C LEU B 120 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU B 120 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 121 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 120 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C LEU A 120 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 120 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 121 " -0.012 2.00e-02 2.50e+03 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 582 2.74 - 3.28: 5643 3.28 - 3.82: 8714 3.82 - 4.36: 9209 4.36 - 4.90: 15363 Nonbonded interactions: 39511 Sorted by model distance: nonbonded pdb=" NE2 GLN A 222 " pdb=" OD1 ASN A 289 " model vdw 2.199 3.120 nonbonded pdb=" NE2 GLN B 222 " pdb=" OD1 ASN B 289 " model vdw 2.200 3.120 nonbonded pdb=" ND2 ASN A 105 " pdb=" O VAL A 116 " model vdw 2.208 3.120 nonbonded pdb=" ND2 ASN B 105 " pdb=" O VAL B 116 " model vdw 2.209 3.120 nonbonded pdb=" O ILE A 183 " pdb=" NH1 ARG A 188 " model vdw 2.257 3.120 ... (remaining 39506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 1.880 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: 0.000 Check model and map are aligned: 1.400 Set scattering table: 0.000 Process input model: 15.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 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 : 0.007 0.043 5314 Z= 0.443 Angle : 0.874 7.125 7176 Z= 0.568 Chirality : 0.057 0.349 764 Planarity : 0.005 0.037 892 Dihedral : 16.560 82.104 1920 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.60 % Favored : 93.07 % Rotamer: Outliers : 3.39 % Allowed : 11.96 % Favored : 84.64 % Cbeta Deviations : 0.17 % 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: -2.27 (0.30), residues: 606 helix: -1.00 (0.20), residues: 502 sheet: None (None), residues: 0 loop : -3.24 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 285 HIS 0.003 0.001 HIS A 30 PHE 0.016 0.002 PHE A 23 TYR 0.019 0.002 TYR A 171 ARG 0.002 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: -0.0530 (OUTLIER) cc_final: -0.1005 (tp) REVERT: A 98 GLU cc_start: 0.8125 (tt0) cc_final: 0.7550 (tp30) REVERT: A 137 LYS cc_start: 0.7918 (tttt) cc_final: 0.7714 (ttpp) REVERT: A 232 PHE cc_start: 0.7338 (t80) cc_final: 0.6904 (t80) REVERT: B 9 LEU cc_start: -0.1407 (OUTLIER) cc_final: -0.1685 (tp) REVERT: B 104 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8139 (tptp) REVERT: B 204 SER cc_start: 0.8748 (t) cc_final: 0.8494 (t) REVERT: B 232 PHE cc_start: 0.7580 (t80) cc_final: 0.7107 (t80) REVERT: B 236 LEU cc_start: 0.8187 (mt) cc_final: 0.7612 (tt) outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 0.2209 time to fit residues: 38.8959 Evaluate side-chains 105 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 242 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 44 GLN A 230 GLN A 334 HIS B 44 GLN B 185 ASN B 222 GLN B 241 GLN B 334 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.272311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.250431 restraints weight = 7789.601| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 1.78 r_work: 0.4642 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5314 Z= 0.239 Angle : 0.687 6.352 7176 Z= 0.355 Chirality : 0.041 0.168 764 Planarity : 0.005 0.036 892 Dihedral : 5.142 44.976 676 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.68 % Allowed : 20.36 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.34), residues: 606 helix: 1.15 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.86 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 285 HIS 0.003 0.001 HIS B 283 PHE 0.016 0.001 PHE B 312 TYR 0.021 0.002 TYR A 239 ARG 0.005 0.001 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8255 (tt0) cc_final: 0.7850 (tp30) REVERT: A 182 LEU cc_start: 0.8489 (tp) cc_final: 0.8246 (mt) REVERT: A 232 PHE cc_start: 0.7460 (t80) cc_final: 0.7095 (t80) REVERT: A 241 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6450 (mp10) REVERT: A 312 PHE cc_start: 0.7937 (m-10) cc_final: 0.7683 (m-10) REVERT: B 9 LEU cc_start: -0.0960 (OUTLIER) cc_final: -0.1546 (tp) REVERT: B 127 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7517 (t80) REVERT: B 236 LEU cc_start: 0.7802 (mt) cc_final: 0.7597 (tt) outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 0.1797 time to fit residues: 24.5767 Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 294 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 222 GLN B 196 HIS B 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.268589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.246669 restraints weight = 7719.337| |-----------------------------------------------------------------------------| r_work (start): 0.4654 rms_B_bonded: 1.84 r_work: 0.4581 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5314 Z= 0.242 Angle : 0.653 6.898 7176 Z= 0.336 Chirality : 0.040 0.144 764 Planarity : 0.004 0.041 892 Dihedral : 4.558 20.932 672 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.86 % Allowed : 22.68 % Favored : 74.46 % 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: 1.51 (0.35), residues: 606 helix: 1.68 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.97 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 210 HIS 0.003 0.001 HIS A 283 PHE 0.018 0.001 PHE B 23 TYR 0.013 0.001 TYR B 33 ARG 0.003 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7201 (t-100) cc_final: 0.6334 (m-90) REVERT: B 39 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: B 127 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 215 MET cc_start: 0.5673 (mmm) cc_final: 0.5425 (mmp) REVERT: B 316 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7646 (mp) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 0.1771 time to fit residues: 25.9150 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.268203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.245783 restraints weight = 7986.768| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 1.91 r_work: 0.4606 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5314 Z= 0.186 Angle : 0.608 7.179 7176 Z= 0.312 Chirality : 0.038 0.140 764 Planarity : 0.004 0.040 892 Dihedral : 4.099 17.862 666 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.14 % Allowed : 24.46 % Favored : 73.39 % 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: 2.00 (0.35), residues: 606 helix: 1.99 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.63 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.010 0.001 PHE B 23 TYR 0.011 0.001 TYR B 33 ARG 0.003 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7300 (t-100) cc_final: 0.6557 (m-90) REVERT: A 241 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: A 312 PHE cc_start: 0.7988 (m-10) cc_final: 0.7705 (m-10) REVERT: B 127 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7481 (t80) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 0.2125 time to fit residues: 28.2903 Evaluate side-chains 93 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 0.0070 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.267520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.245678 restraints weight = 7884.949| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 1.87 r_work: 0.4573 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5314 Z= 0.187 Angle : 0.605 7.088 7176 Z= 0.309 Chirality : 0.038 0.150 764 Planarity : 0.004 0.041 892 Dihedral : 4.049 17.531 666 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.39 % Allowed : 25.71 % Favored : 70.89 % 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: 2.16 (0.35), residues: 606 helix: 2.08 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.50 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.014 0.001 PHE B 23 TYR 0.009 0.001 TYR B 171 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7291 (t-100) cc_final: 0.6513 (m-90) REVERT: A 312 PHE cc_start: 0.8227 (m-10) cc_final: 0.7906 (m-10) REVERT: B 127 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7447 (t80) REVERT: B 210 TRP cc_start: 0.7599 (t-100) cc_final: 0.6820 (m-90) outliers start: 19 outliers final: 9 residues processed: 103 average time/residue: 0.2072 time to fit residues: 26.5298 Evaluate side-chains 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.267550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.245973 restraints weight = 7856.826| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 1.88 r_work: 0.4574 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5314 Z= 0.178 Angle : 0.611 6.748 7176 Z= 0.309 Chirality : 0.038 0.163 764 Planarity : 0.004 0.041 892 Dihedral : 3.994 18.228 666 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.11 % Allowed : 26.43 % Favored : 69.46 % 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: 2.31 (0.35), residues: 606 helix: 2.16 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.38 (0.63), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 16 HIS 0.001 0.000 HIS A 283 PHE 0.010 0.001 PHE A 226 TYR 0.009 0.001 TYR A 239 ARG 0.004 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7288 (t-100) cc_final: 0.6597 (m-90) REVERT: A 312 PHE cc_start: 0.8229 (m-10) cc_final: 0.7903 (m-10) REVERT: B 127 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7363 (t80) REVERT: B 210 TRP cc_start: 0.7633 (t-100) cc_final: 0.6880 (m-90) outliers start: 23 outliers final: 10 residues processed: 115 average time/residue: 0.1944 time to fit residues: 28.0083 Evaluate side-chains 102 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 115 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.262062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.241141 restraints weight = 7746.904| |-----------------------------------------------------------------------------| r_work (start): 0.4607 rms_B_bonded: 1.84 r_work: 0.4532 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5314 Z= 0.244 Angle : 0.684 9.922 7176 Z= 0.348 Chirality : 0.040 0.157 764 Planarity : 0.004 0.042 892 Dihedral : 4.167 17.046 666 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.46 % Allowed : 26.61 % Favored : 68.93 % 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: 1.98 (0.34), residues: 606 helix: 1.94 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.44 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 16 HIS 0.002 0.001 HIS A 283 PHE 0.010 0.001 PHE B 226 TYR 0.011 0.001 TYR A 171 ARG 0.006 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7409 (t-100) cc_final: 0.6672 (m-90) REVERT: A 312 PHE cc_start: 0.8251 (m-10) cc_final: 0.7841 (m-10) REVERT: B 115 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7380 (t160) REVERT: B 127 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7441 (t80) REVERT: B 203 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 210 TRP cc_start: 0.7691 (t-100) cc_final: 0.7108 (m-90) outliers start: 25 outliers final: 14 residues processed: 111 average time/residue: 0.1977 time to fit residues: 27.4265 Evaluate side-chains 100 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 30 HIS B 115 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.263093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.241812 restraints weight = 7760.370| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 1.85 r_work: 0.4539 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5314 Z= 0.210 Angle : 0.690 10.847 7176 Z= 0.344 Chirality : 0.040 0.161 764 Planarity : 0.004 0.051 892 Dihedral : 4.170 16.573 666 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.11 % Allowed : 26.25 % Favored : 69.64 % 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: 2.07 (0.35), residues: 606 helix: 1.96 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.18 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 16 HIS 0.002 0.001 HIS B 30 PHE 0.010 0.001 PHE A 23 TYR 0.016 0.001 TYR A 100 ARG 0.007 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.538 Fit side-chains REVERT: A 127 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: A 312 PHE cc_start: 0.8197 (m-10) cc_final: 0.7996 (m-10) REVERT: B 127 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7418 (t80) REVERT: B 203 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7693 (tp) REVERT: B 210 TRP cc_start: 0.7617 (t-100) cc_final: 0.6949 (m-90) outliers start: 23 outliers final: 17 residues processed: 95 average time/residue: 0.1596 time to fit residues: 19.8994 Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.263795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.242678 restraints weight = 7704.871| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 1.84 r_work: 0.4550 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5314 Z= 0.197 Angle : 0.691 9.625 7176 Z= 0.347 Chirality : 0.040 0.188 764 Planarity : 0.004 0.059 892 Dihedral : 4.132 16.704 666 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 27.32 % Favored : 69.82 % 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: 2.17 (0.35), residues: 606 helix: 2.03 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.17 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 16 HIS 0.002 0.000 HIS A 30 PHE 0.012 0.001 PHE A 23 TYR 0.018 0.001 TYR B 100 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8223 (m-10) cc_final: 0.7978 (m-10) REVERT: B 127 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7374 (t80) REVERT: B 203 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7636 (tp) REVERT: B 207 MET cc_start: 0.7090 (tmm) cc_final: 0.6434 (tmm) REVERT: B 210 TRP cc_start: 0.7619 (t-100) cc_final: 0.7088 (m-90) outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 0.1670 time to fit residues: 20.5356 Evaluate side-chains 93 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 30 HIS B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.262882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.242701 restraints weight = 7801.782| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 1.82 r_work: 0.4551 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5314 Z= 0.201 Angle : 0.698 9.134 7176 Z= 0.350 Chirality : 0.039 0.173 764 Planarity : 0.004 0.060 892 Dihedral : 4.144 16.726 666 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.93 % Allowed : 26.79 % Favored : 69.29 % 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: 2.12 (0.35), residues: 606 helix: 1.99 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.12 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 16 HIS 0.002 0.000 HIS A 283 PHE 0.014 0.001 PHE A 23 TYR 0.014 0.001 TYR B 100 ARG 0.006 0.001 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: A 291 LEU cc_start: 0.7613 (tp) cc_final: 0.7019 (mp) REVERT: B 98 GLU cc_start: 0.8575 (tp30) cc_final: 0.8345 (tp30) REVERT: B 127 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 203 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7654 (tp) REVERT: B 207 MET cc_start: 0.7183 (tmm) cc_final: 0.6469 (tmm) REVERT: B 210 TRP cc_start: 0.7632 (t-100) cc_final: 0.7119 (m-90) outliers start: 22 outliers final: 16 residues processed: 102 average time/residue: 0.1638 time to fit residues: 21.9432 Evaluate side-chains 103 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.262079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.242050 restraints weight = 7810.441| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 1.86 r_work: 0.4550 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5314 Z= 0.212 Angle : 0.702 9.398 7176 Z= 0.353 Chirality : 0.040 0.189 764 Planarity : 0.004 0.061 892 Dihedral : 4.165 16.788 666 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.93 % Allowed : 26.61 % Favored : 69.46 % 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: 2.04 (0.35), residues: 606 helix: 1.92 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.06 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.015 0.001 PHE A 23 TYR 0.014 0.001 TYR B 239 ARG 0.006 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.20 seconds wall clock time: 46 minutes 49.81 seconds (2809.81 seconds total)