Starting phenix.real_space_refine on Wed Mar 5 18:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4e_29718/03_2025/8g4e_29718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4e_29718/03_2025/8g4e_29718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g4e_29718/03_2025/8g4e_29718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4e_29718/03_2025/8g4e_29718.map" model { file = "/net/cci-nas-00/data/ceres_data/8g4e_29718/03_2025/8g4e_29718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4e_29718/03_2025/8g4e_29718.cif" } resolution = 2.98 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= 0.013 sd= 0.081 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 7 5.16 5 C 1957 2.51 5 N 543 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3097 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 163} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 478 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "B" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1348 Unusual residues: {'CRO': 1} Classifications: {'peptide': 164, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157, None: 1} Not linked: pdbres="CRO B 66 " pdbres="VAL B 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.83 Number of scatterers: 3097 At special positions: 0 Unit cell: (66.825, 77.9625, 66.825, 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 7 16.00 O 590 8.00 N 543 7.00 C 1957 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 346.6 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 37.1% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.665A pdb=" N ARG A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.651A pdb=" N PHE B 71 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 72 " --> pdb=" O GLN B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.535A pdb=" N SER B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 22 removed outlier: 3.729A pdb=" N VAL B 219 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR B 151 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 164 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 21 " --> pdb=" O LEU B 125 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 489 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: 0.77 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1048 1.34 - 1.46: 444 1.46 - 1.57: 1654 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3158 Sorted by residual: bond pdb=" C MET B 88 " pdb=" N PRO B 89 " ideal model delta sigma weight residual 1.333 1.367 -0.033 1.44e-02 4.82e+03 5.39e+00 bond pdb=" C1 CRO B 66 " pdb=" N2 CRO B 66 " ideal model delta sigma weight residual 1.289 1.328 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" CZ CRO B 66 " pdb=" OH CRO B 66 " ideal model delta sigma weight residual 1.341 1.373 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CA1 CRO B 66 " pdb=" N1 CRO B 66 " ideal model delta sigma weight residual 1.448 1.475 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C3 CRO B 66 " pdb=" CA3 CRO B 66 " ideal model delta sigma weight residual 1.547 1.526 0.021 2.00e-02 2.50e+03 1.11e+00 ... (remaining 3153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 4044 1.00 - 1.99: 181 1.99 - 2.99: 38 2.99 - 3.99: 12 3.99 - 4.99: 3 Bond angle restraints: 4278 Sorted by residual: angle pdb=" N GLY B 33 " pdb=" CA GLY B 33 " pdb=" C GLY B 33 " ideal model delta sigma weight residual 111.08 115.61 -4.53 1.62e+00 3.81e-01 7.83e+00 angle pdb=" N MET B 88 " pdb=" CA MET B 88 " pdb=" C MET B 88 " ideal model delta sigma weight residual 109.81 114.80 -4.99 2.21e+00 2.05e-01 5.09e+00 angle pdb=" C ASP B 129 " pdb=" CA ASP B 129 " pdb=" CB ASP B 129 " ideal model delta sigma weight residual 111.26 108.23 3.03 1.67e+00 3.59e-01 3.29e+00 angle pdb=" C ILE B 128 " pdb=" N ASP B 129 " pdb=" CA ASP B 129 " ideal model delta sigma weight residual 123.47 126.22 -2.75 1.53e+00 4.27e-01 3.24e+00 angle pdb=" CA GLY A 178 " pdb=" C GLY A 178 " pdb=" N TYR A 179 " ideal model delta sigma weight residual 118.50 116.80 1.70 9.90e-01 1.02e+00 2.95e+00 ... (remaining 4273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 1649 17.53 - 35.06: 162 35.06 - 52.60: 47 52.60 - 70.13: 13 70.13 - 87.66: 3 Dihedral angle restraints: 1874 sinusoidal: 746 harmonic: 1128 Sorted by residual: dihedral pdb=" CB GLU B 111 " pdb=" CG GLU B 111 " pdb=" CD GLU B 111 " pdb=" OE1 GLU B 111 " ideal model delta sinusoidal sigma weight residual 0.00 87.66 -87.66 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASN B 23 " pdb=" CB ASN B 23 " pdb=" CG ASN B 23 " pdb=" OD1 ASN B 23 " ideal model delta sinusoidal sigma weight residual -90.00 -156.78 66.78 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CG ARG A 176 " pdb=" CD ARG A 176 " pdb=" NE ARG A 176 " pdb=" CZ ARG A 176 " ideal model delta sinusoidal sigma weight residual 180.00 -136.68 -43.32 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 1871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 239 0.023 - 0.046: 139 0.046 - 0.069: 56 0.069 - 0.092: 23 0.092 - 0.115: 22 Chirality restraints: 479 Sorted by residual: chirality pdb=" CB1 CRO B 66 " pdb=" CG1 CRO B 66 " pdb=" OG1 CRO B 66 " pdb=" CA1 CRO B 66 " both_signs ideal model delta sigma weight residual False -2.35 -2.47 0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA ILE B 47 " pdb=" N ILE B 47 " pdb=" C ILE B 47 " pdb=" CB ILE B 47 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 476 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 CRO B 66 " -0.008 2.00e-02 2.50e+03 3.30e-02 2.72e+01 pdb=" CG2 CRO B 66 " -0.046 2.00e-02 2.50e+03 pdb=" C1 CRO B 66 " 0.017 2.00e-02 2.50e+03 pdb=" C2 CRO B 66 " 0.026 2.00e-02 2.50e+03 pdb=" CA1 CRO B 66 " 0.012 2.00e-02 2.50e+03 pdb=" CA2 CRO B 66 " 0.014 2.00e-02 2.50e+03 pdb=" CA3 CRO B 66 " -0.069 2.00e-02 2.50e+03 pdb=" N2 CRO B 66 " 0.026 2.00e-02 2.50e+03 pdb=" N3 CRO B 66 " -0.014 2.00e-02 2.50e+03 pdb=" O2 CRO B 66 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 268 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 269 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 235 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 236 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 706 2.79 - 3.32: 2581 3.32 - 3.85: 4854 3.85 - 4.37: 5790 4.37 - 4.90: 10416 Nonbonded interactions: 24347 Sorted by model distance: nonbonded pdb=" NE2 GLN B 183 " pdb=" OD1 ASN B 185 " model vdw 2.266 3.120 nonbonded pdb=" N ASP A 230 " pdb=" OD1 ASP A 230 " model vdw 2.330 3.120 nonbonded pdb=" OG1 THR A 202 " pdb=" ND1 HIS A 205 " model vdw 2.333 3.120 nonbonded pdb=" O PRO B 56 " pdb=" OG1 THR B 59 " model vdw 2.339 3.040 nonbonded pdb=" NZ LYS A 162 " pdb=" OE2 GLU A 166 " model vdw 2.378 3.120 ... (remaining 24342 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.710 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.030 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.003 0.039 3158 Z= 0.187 Angle : 0.528 4.986 4278 Z= 0.293 Chirality : 0.040 0.115 479 Planarity : 0.004 0.041 559 Dihedral : 15.966 87.661 1148 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.16 % Allowed : 16.67 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.43), residues: 390 helix: 1.08 (0.45), residues: 137 sheet: 0.68 (0.51), residues: 117 loop : -0.82 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.320 Fit side-chains REVERT: A 293 ASN cc_start: 0.7980 (m-40) cc_final: 0.7628 (m110) REVERT: B 34 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7799 (mt-10) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 1.3149 time to fit residues: 80.9056 Evaluate side-chains 44 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120567 restraints weight = 3616.026| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.04 r_work: 0.3223 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3158 Z= 0.238 Angle : 0.558 6.490 4278 Z= 0.292 Chirality : 0.044 0.141 479 Planarity : 0.004 0.046 559 Dihedral : 7.087 69.853 433 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.79 % Allowed : 16.67 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.43), residues: 390 helix: 1.29 (0.43), residues: 142 sheet: 0.94 (0.51), residues: 116 loop : -0.69 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.005 0.001 HIS A 205 PHE 0.011 0.002 PHE A 298 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7041 (mpt-90) REVERT: A 301 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7869 (m) REVERT: B 34 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 177 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6376 (tt0) outliers start: 22 outliers final: 13 residues processed: 51 average time/residue: 1.2065 time to fit residues: 63.3945 Evaluate side-chains 48 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123345 restraints weight = 3622.733| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.04 r_work: 0.3249 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3158 Z= 0.165 Angle : 0.508 6.386 4278 Z= 0.266 Chirality : 0.042 0.123 479 Planarity : 0.004 0.043 559 Dihedral : 6.495 71.092 429 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.56 % Allowed : 19.75 % Favored : 74.69 % 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: 1.17 (0.43), residues: 390 helix: 1.73 (0.44), residues: 142 sheet: 1.22 (0.51), residues: 113 loop : -0.63 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.007 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.001 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: A 210 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6546 (mpt-90) REVERT: A 301 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7825 (m) REVERT: B 34 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8040 (mt-10) REVERT: B 177 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6370 (tt0) outliers start: 18 outliers final: 7 residues processed: 45 average time/residue: 1.2627 time to fit residues: 58.5225 Evaluate side-chains 43 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 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 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120769 restraints weight = 3681.613| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.06 r_work: 0.3219 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3158 Z= 0.215 Angle : 0.535 7.036 4278 Z= 0.278 Chirality : 0.043 0.130 479 Planarity : 0.004 0.045 559 Dihedral : 6.063 69.530 424 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.48 % Allowed : 19.75 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.43), residues: 390 helix: 1.72 (0.44), residues: 142 sheet: 1.24 (0.51), residues: 113 loop : -0.68 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.009 0.001 PHE B 165 TYR 0.011 0.001 TYR B 200 ARG 0.003 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: A 210 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6579 (mpt-90) REVERT: A 301 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7840 (m) REVERT: A 313 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6497 (t0) REVERT: B 34 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8122 (mt-10) outliers start: 21 outliers final: 10 residues processed: 48 average time/residue: 1.2925 time to fit residues: 63.8138 Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120734 restraints weight = 3617.098| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.02 r_work: 0.3242 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3158 Z= 0.217 Angle : 0.540 7.390 4278 Z= 0.280 Chirality : 0.043 0.126 479 Planarity : 0.004 0.046 559 Dihedral : 6.041 68.842 424 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 7.10 % Allowed : 18.52 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.43), residues: 390 helix: 1.73 (0.44), residues: 142 sheet: 1.26 (0.50), residues: 113 loop : -0.68 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.009 0.002 PHE A 298 TYR 0.011 0.001 TYR B 200 ARG 0.001 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: A 210 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6630 (mpt-90) REVERT: A 291 ASP cc_start: 0.7912 (t0) cc_final: 0.7691 (t0) REVERT: A 301 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7826 (m) REVERT: B 34 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8102 (mt-10) outliers start: 23 outliers final: 16 residues processed: 50 average time/residue: 1.1205 time to fit residues: 57.7740 Evaluate side-chains 51 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 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 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121878 restraints weight = 3702.934| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.06 r_work: 0.3246 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3158 Z= 0.196 Angle : 0.540 8.618 4278 Z= 0.282 Chirality : 0.043 0.125 479 Planarity : 0.004 0.046 559 Dihedral : 6.007 69.251 424 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 7.10 % Allowed : 18.83 % Favored : 74.07 % 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: 1.26 (0.43), residues: 390 helix: 1.77 (0.44), residues: 142 sheet: 1.35 (0.51), residues: 113 loop : -0.63 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.001 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 165 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: A 166 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: A 210 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6973 (mpt-90) REVERT: A 291 ASP cc_start: 0.7926 (t0) cc_final: 0.7711 (t0) REVERT: A 301 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7813 (m) REVERT: B 34 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8054 (mt-10) outliers start: 23 outliers final: 15 residues processed: 51 average time/residue: 1.2344 time to fit residues: 64.8229 Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123504 restraints weight = 3585.564| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.02 r_work: 0.3266 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3158 Z= 0.175 Angle : 0.529 8.921 4278 Z= 0.275 Chirality : 0.043 0.124 479 Planarity : 0.004 0.045 559 Dihedral : 5.941 69.347 424 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.79 % Allowed : 18.83 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.43), residues: 390 helix: 1.87 (0.44), residues: 142 sheet: 1.39 (0.51), residues: 113 loop : -0.57 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 PHE 0.007 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7322 (mpt-90) REVERT: A 301 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7823 (m) REVERT: B 34 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8086 (mt-10) outliers start: 22 outliers final: 12 residues processed: 49 average time/residue: 1.3040 time to fit residues: 65.7723 Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120370 restraints weight = 3700.914| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.04 r_work: 0.3238 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3158 Z= 0.243 Angle : 0.569 10.063 4278 Z= 0.295 Chirality : 0.044 0.132 479 Planarity : 0.004 0.048 559 Dihedral : 5.867 68.019 423 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.86 % Allowed : 20.06 % Favored : 74.07 % 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: 1.17 (0.43), residues: 390 helix: 1.59 (0.43), residues: 142 sheet: 1.38 (0.51), residues: 113 loop : -0.62 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.009 0.002 PHE A 298 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6795 (mpt-90) REVERT: A 301 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7833 (m) REVERT: B 34 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 73 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8416 (ttt-90) outliers start: 19 outliers final: 13 residues processed: 48 average time/residue: 1.3034 time to fit residues: 64.3236 Evaluate side-chains 48 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.153267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122203 restraints weight = 3666.759| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.05 r_work: 0.3229 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3158 Z= 0.209 Angle : 0.563 10.706 4278 Z= 0.294 Chirality : 0.043 0.151 479 Planarity : 0.004 0.047 559 Dihedral : 5.868 69.026 423 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.86 % Allowed : 20.06 % Favored : 74.07 % 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: 1.18 (0.43), residues: 390 helix: 1.58 (0.44), residues: 142 sheet: 1.21 (0.50), residues: 116 loop : -0.45 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7158 (mpt-90) REVERT: A 301 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7836 (m) REVERT: B 34 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8069 (mt-10) outliers start: 19 outliers final: 15 residues processed: 46 average time/residue: 1.2975 time to fit residues: 61.3646 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.0170 chunk 34 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125725 restraints weight = 3579.769| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.03 r_work: 0.3240 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3158 Z= 0.181 Angle : 0.555 11.168 4278 Z= 0.290 Chirality : 0.043 0.164 479 Planarity : 0.004 0.046 559 Dihedral : 5.918 70.368 423 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.56 % Allowed : 19.75 % Favored : 74.69 % 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: 1.26 (0.43), residues: 390 helix: 1.62 (0.44), residues: 142 sheet: 1.44 (0.50), residues: 113 loop : -0.52 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 PHE 0.007 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7358 (mpt-90) REVERT: A 301 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7813 (m) REVERT: B 34 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 73 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8404 (ttt-90) outliers start: 18 outliers final: 12 residues processed: 46 average time/residue: 1.3025 time to fit residues: 61.6279 Evaluate side-chains 48 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.154257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123081 restraints weight = 3604.855| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.04 r_work: 0.3229 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3158 Z= 0.225 Angle : 0.579 11.209 4278 Z= 0.301 Chirality : 0.044 0.177 479 Planarity : 0.004 0.047 559 Dihedral : 5.881 69.450 423 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.56 % Allowed : 20.99 % Favored : 73.46 % 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: 1.16 (0.43), residues: 390 helix: 1.49 (0.44), residues: 142 sheet: 1.45 (0.50), residues: 113 loop : -0.59 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2707.51 seconds wall clock time: 47 minutes 12.52 seconds (2832.52 seconds total)