Starting phenix.real_space_refine on Tue Mar 3 13:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cxr_30495/03_2026/7cxr_30495.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cxr_30495/03_2026/7cxr_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_30495/03_2026/7cxr_30495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cxr_30495/03_2026/7cxr_30495.map" model { file = "/net/cci-nas-00/data/ceres_data/7cxr_30495/03_2026/7cxr_30495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cxr_30495/03_2026/7cxr_30495.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.32, per 1000 atoms: 0.26 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: 0.43 Conformation dependent library (CDL) restraints added in 235.4 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: 0.09 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: 0.58 Time building geometry restraints manager: 0.59 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: 0.00 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: 0.940 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.350 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.570 ------------------------------------------------------------------------------- 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= 0.384 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 14 TYR 0.019 0.002 TYR A 171 PHE 0.016 0.002 PHE A 23 TRP 0.013 0.002 TRP A 285 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00707 ( 5314) covalent geometry : angle 0.87385 ( 7176) hydrogen bonds : bond 0.12276 ( 422) hydrogen bonds : angle 5.74524 ( 1266) *********************** 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 : 0.201 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: 0.0951 time to fit residues: 16.8802 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 : 0.213 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4893 r_free = 0.4893 target = 0.271734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.249643 restraints weight = 7891.832| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 1.82 r_work: 0.4631 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5314 Z= 0.188 Angle : 0.693 6.646 7176 Z= 0.361 Chirality : 0.041 0.162 764 Planarity : 0.005 0.037 892 Dihedral : 5.140 43.131 676 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.68 % Allowed : 20.54 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.34), residues: 606 helix: 1.09 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.89 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 158 TYR 0.019 0.002 TYR A 239 PHE 0.017 0.001 PHE B 23 TRP 0.019 0.002 TRP A 285 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 5314) covalent geometry : angle 0.69322 ( 7176) hydrogen bonds : bond 0.05510 ( 422) hydrogen bonds : angle 4.40025 ( 1266) *********************** 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 108 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8274 (tt0) cc_final: 0.7866 (tp30) REVERT: A 182 LEU cc_start: 0.8497 (tp) cc_final: 0.8260 (mt) REVERT: A 232 PHE cc_start: 0.7482 (t80) cc_final: 0.7119 (t80) REVERT: A 241 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6459 (mp10) REVERT: B 9 LEU cc_start: -0.1106 (OUTLIER) cc_final: -0.1689 (tp) REVERT: B 127 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7540 (t80) REVERT: B 236 LEU cc_start: 0.7827 (mt) cc_final: 0.7612 (tt) outliers start: 15 outliers final: 7 residues processed: 103 average time/residue: 0.0749 time to fit residues: 10.0036 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 : 0.192 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 41 optimal weight: 0.0020 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.271608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.250837 restraints weight = 7840.989| |-----------------------------------------------------------------------------| r_work (start): 0.4728 rms_B_bonded: 2.02 r_work: 0.4629 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5314 Z= 0.142 Angle : 0.602 7.043 7176 Z= 0.308 Chirality : 0.038 0.143 764 Planarity : 0.004 0.038 892 Dihedral : 4.434 21.064 672 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.96 % Allowed : 22.86 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.35), residues: 606 helix: 1.83 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.85 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.013 0.001 TYR B 33 PHE 0.012 0.001 PHE B 23 TRP 0.022 0.002 TRP B 210 HIS 0.002 0.000 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5314) covalent geometry : angle 0.60246 ( 7176) hydrogen bonds : bond 0.04816 ( 422) hydrogen bonds : angle 4.17782 ( 1266) *********************** 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 113 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7696 (pttp) cc_final: 0.7425 (pttm) REVERT: A 98 GLU cc_start: 0.8347 (tt0) cc_final: 0.8104 (tp30) REVERT: A 210 TRP cc_start: 0.7099 (t-100) cc_final: 0.6058 (m-90) REVERT: A 232 PHE cc_start: 0.7298 (t80) cc_final: 0.7015 (t80) REVERT: A 241 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: A 312 PHE cc_start: 0.7944 (m-10) cc_final: 0.7665 (m-10) REVERT: B 39 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7916 (pt0) REVERT: B 127 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7588 (t80) outliers start: 11 outliers final: 4 residues processed: 108 average time/residue: 0.0735 time to fit residues: 10.3357 Evaluate side-chains 100 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL 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 39 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 44 GLN B 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.266826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.244659 restraints weight = 7734.796| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 1.87 r_work: 0.4588 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5314 Z= 0.158 Angle : 0.632 7.012 7176 Z= 0.325 Chirality : 0.039 0.144 764 Planarity : 0.004 0.039 892 Dihedral : 4.151 17.184 666 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.21 % Allowed : 23.21 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.35), residues: 606 helix: 2.02 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.65 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 90 TYR 0.011 0.001 TYR A 171 PHE 0.013 0.001 PHE A 23 TRP 0.011 0.001 TRP A 285 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5314) covalent geometry : angle 0.63227 ( 7176) hydrogen bonds : bond 0.05168 ( 422) hydrogen bonds : angle 4.23849 ( 1266) *********************** 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 125 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7378 (t-100) cc_final: 0.6519 (m-90) REVERT: A 312 PHE cc_start: 0.8002 (m-10) cc_final: 0.7710 (m-10) REVERT: B 127 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7517 (t80) REVERT: B 316 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7655 (mp) REVERT: B 326 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7222 (mm) outliers start: 18 outliers final: 8 residues processed: 117 average time/residue: 0.0827 time to fit residues: 12.0842 Evaluate side-chains 105 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS 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 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 Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.266146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.244114 restraints weight = 7910.432| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 1.90 r_work: 0.4564 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5314 Z= 0.150 Angle : 0.629 7.032 7176 Z= 0.323 Chirality : 0.039 0.142 764 Planarity : 0.004 0.041 892 Dihedral : 4.124 17.442 666 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.75 % Allowed : 25.71 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.35), residues: 606 helix: 1.99 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.56 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.011 0.001 TYR A 239 PHE 0.021 0.001 PHE A 232 TRP 0.016 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5314) covalent geometry : angle 0.62937 ( 7176) hydrogen bonds : bond 0.04921 ( 422) hydrogen bonds : angle 4.17837 ( 1266) *********************** 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 117 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7267 (t-100) cc_final: 0.6616 (m-90) REVERT: A 268 MET cc_start: 0.5598 (tpt) cc_final: 0.5250 (mpp) REVERT: A 312 PHE cc_start: 0.8238 (m-10) cc_final: 0.7923 (m-10) REVERT: B 34 ARG cc_start: 0.7107 (mtp180) cc_final: 0.6876 (mpp80) REVERT: B 127 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7515 (t80) REVERT: B 210 TRP cc_start: 0.7625 (t-100) cc_final: 0.6955 (m-90) REVERT: B 316 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7700 (mp) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 0.0978 time to fit residues: 13.1926 Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 292 THR 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 233 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 316 LEU 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 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4809 r_free = 0.4809 target = 0.262925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.241925 restraints weight = 7877.840| |-----------------------------------------------------------------------------| r_work (start): 0.4613 rms_B_bonded: 1.88 r_work: 0.4539 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5314 Z= 0.165 Angle : 0.663 6.826 7176 Z= 0.343 Chirality : 0.040 0.159 764 Planarity : 0.004 0.041 892 Dihedral : 4.186 17.682 666 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.93 % Allowed : 26.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.35), residues: 606 helix: 1.94 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.52 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 34 TYR 0.012 0.001 TYR B 33 PHE 0.019 0.001 PHE B 23 TRP 0.015 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5314) covalent geometry : angle 0.66289 ( 7176) hydrogen bonds : bond 0.05130 ( 422) hydrogen bonds : angle 4.22480 ( 1266) *********************** 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 114 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.5624 (tpt) cc_final: 0.5209 (mpp) REVERT: A 312 PHE cc_start: 0.8260 (m-10) cc_final: 0.7836 (m-10) REVERT: B 127 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7418 (t80) REVERT: B 210 TRP cc_start: 0.7652 (t-100) cc_final: 0.7088 (m-90) outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 0.0807 time to fit residues: 10.9722 Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 315 LEU 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 28 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.259536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.238844 restraints weight = 7565.946| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 1.99 r_work: 0.4512 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.6513 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= 0.172 Angle : 0.679 8.084 7176 Z= 0.347 Chirality : 0.040 0.155 764 Planarity : 0.004 0.044 892 Dihedral : 4.264 17.188 666 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.29 % Allowed : 26.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.35), residues: 606 helix: 1.78 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.44 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 34 TYR 0.012 0.001 TYR A 100 PHE 0.024 0.001 PHE B 23 TRP 0.015 0.001 TRP A 16 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5314) covalent geometry : angle 0.67949 ( 7176) hydrogen bonds : bond 0.05244 ( 422) hydrogen bonds : angle 4.29757 ( 1266) *********************** 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 113 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7457 (t80) REVERT: B 203 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7846 (tp) REVERT: B 210 TRP cc_start: 0.7809 (t-100) cc_final: 0.7199 (m-90) outliers start: 24 outliers final: 15 residues processed: 106 average time/residue: 0.0757 time to fit residues: 10.4013 Evaluate side-chains 101 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 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 A residue 292 THR Chi-restraints excluded: chain A residue 326 LEU 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 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 329 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS B 44 GLN B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.259512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.238591 restraints weight = 7836.224| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 1.83 r_work: 0.4511 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.6799 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= 0.167 Angle : 0.697 10.558 7176 Z= 0.352 Chirality : 0.040 0.165 764 Planarity : 0.004 0.051 892 Dihedral : 4.312 18.437 666 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.82 % Allowed : 26.07 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.35), residues: 606 helix: 1.79 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.43 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 90 TYR 0.010 0.001 TYR A 239 PHE 0.022 0.001 PHE B 23 TRP 0.016 0.001 TRP A 16 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5314) covalent geometry : angle 0.69700 ( 7176) hydrogen bonds : bond 0.05157 ( 422) hydrogen bonds : angle 4.29261 ( 1266) *********************** 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 115 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 127 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7364 (t80) REVERT: B 203 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 210 TRP cc_start: 0.7729 (t-100) cc_final: 0.7172 (m-90) outliers start: 27 outliers final: 18 residues processed: 105 average time/residue: 0.0619 time to fit residues: 8.7256 Evaluate side-chains 105 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 194 VAL 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 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 203 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 329 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.0040 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.259542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.240654 restraints weight = 7780.243| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 1.74 r_work: 0.4553 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5314 Z= 0.152 Angle : 0.697 9.452 7176 Z= 0.350 Chirality : 0.039 0.176 764 Planarity : 0.004 0.058 892 Dihedral : 4.299 17.400 666 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.11 % Allowed : 26.79 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.35), residues: 606 helix: 1.83 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.39 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 90 TYR 0.010 0.001 TYR A 239 PHE 0.021 0.001 PHE B 23 TRP 0.020 0.001 TRP B 16 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5314) covalent geometry : angle 0.69665 ( 7176) hydrogen bonds : bond 0.04889 ( 422) hydrogen bonds : angle 4.24149 ( 1266) *********************** 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 110 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: A 132 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 127 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7401 (t80) REVERT: B 203 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7750 (tp) REVERT: B 210 TRP cc_start: 0.7673 (t-100) cc_final: 0.7124 (m-90) outliers start: 23 outliers final: 16 residues processed: 101 average time/residue: 0.0765 time to fit residues: 9.9137 Evaluate side-chains 104 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 194 VAL 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 A residue 309 MET Chi-restraints excluded: chain A residue 326 LEU 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 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 310 CYS 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: 2.9990 chunk 38 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 115 ASN 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 = 0.261248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.242675 restraints weight = 7940.964| |-----------------------------------------------------------------------------| r_work (start): 0.4664 rms_B_bonded: 1.84 r_work: 0.4575 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.7060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5314 Z= 0.143 Angle : 0.680 9.213 7176 Z= 0.341 Chirality : 0.040 0.181 764 Planarity : 0.005 0.058 892 Dihedral : 4.183 16.955 666 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.68 % Allowed : 28.21 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.35), residues: 606 helix: 1.93 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.39 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 90 TYR 0.010 0.001 TYR B 33 PHE 0.020 0.001 PHE B 23 TRP 0.018 0.001 TRP B 16 HIS 0.002 0.000 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5314) covalent geometry : angle 0.68006 ( 7176) hydrogen bonds : bond 0.04622 ( 422) hydrogen bonds : angle 4.17274 ( 1266) ********************** 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 105 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: B 34 ARG cc_start: 0.6914 (mtp85) cc_final: 0.6713 (mtp85) REVERT: B 203 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7677 (tp) REVERT: B 210 TRP cc_start: 0.7616 (t-100) cc_final: 0.7088 (m-90) outliers start: 15 outliers final: 11 residues processed: 98 average time/residue: 0.0728 time to fit residues: 9.3071 Evaluate side-chains 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 115 ASN 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 310 CYS 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 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4827 r_free = 0.4827 target = 0.264432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.245558 restraints weight = 7747.392| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 1.89 r_work: 0.4563 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.7131 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= 0.142 Angle : 0.682 9.053 7176 Z= 0.341 Chirality : 0.039 0.188 764 Planarity : 0.005 0.060 892 Dihedral : 4.129 16.936 666 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 29.46 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.35), residues: 606 helix: 2.00 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.31 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.010 0.001 TYR B 33 PHE 0.020 0.001 PHE B 23 TRP 0.017 0.001 TRP B 16 HIS 0.002 0.000 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5314) covalent geometry : angle 0.68160 ( 7176) hydrogen bonds : bond 0.04480 ( 422) hydrogen bonds : angle 4.12219 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1239.77 seconds wall clock time: 21 minutes 54.65 seconds (1314.65 seconds total)