Starting phenix.real_space_refine on Thu Nov 14 12:28:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/11_2024/8sks_40566.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/11_2024/8sks_40566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/11_2024/8sks_40566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/11_2024/8sks_40566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/11_2024/8sks_40566.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/11_2024/8sks_40566.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians Mn 4 7.51 5 S 16 5.16 5 C 3992 2.51 5 N 1092 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6232 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1557 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 3.32, per 1000 atoms: 0.53 Number of scatterers: 6232 At special positions: 0 Unit cell: (71.69, 86.67, 86.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 4 24.99 S 16 16.00 O 1128 8.00 N 1092 7.00 C 3992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 918.1 milliseconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 69.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 removed outlier: 4.275A pdb=" N LEU A 38 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 105 Proline residue: A 86 - end of helix removed outlier: 3.627A pdb=" N THR A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'B' and resid 34 through 39 removed outlier: 4.276A pdb=" N LEU B 38 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 76 removed outlier: 3.914A pdb=" N HIS B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 105 Proline residue: B 86 - end of helix removed outlier: 3.628A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.516A pdb=" N TYR B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'C' and resid 34 through 39 removed outlier: 4.276A pdb=" N LEU C 38 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 105 Proline residue: C 86 - end of helix removed outlier: 3.627A pdb=" N THR C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'D' and resid 34 through 39 removed outlier: 4.275A pdb=" N LEU D 38 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 105 Proline residue: D 86 - end of helix removed outlier: 3.628A pdb=" N THR D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 185 through 188 Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 165 removed outlier: 7.322A pdb=" N GLY A 146 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 183 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 148 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 181 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 150 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 165 removed outlier: 7.323A pdb=" N GLY B 146 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP B 183 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 148 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 181 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 150 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 165 removed outlier: 7.323A pdb=" N GLY C 146 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP C 183 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY C 148 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 181 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 150 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 165 removed outlier: 7.322A pdb=" N GLY D 146 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP D 183 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY D 148 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 181 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 150 " --> pdb=" O LEU D 179 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.83 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: 2041 1.34 - 1.46: 1253 1.46 - 1.57: 3094 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 6412 Sorted by residual: bond pdb=" CA LYS D 221 " pdb=" C LYS D 221 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.28e-02 6.10e+03 1.61e+00 bond pdb=" CA VAL A 196 " pdb=" CB VAL A 196 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.45e+00 bond pdb=" CA LYS C 221 " pdb=" C LYS C 221 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA LYS B 221 " pdb=" C LYS B 221 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA VAL B 196 " pdb=" CB VAL B 196 " ideal model delta sigma weight residual 1.527 1.542 -0.016 1.31e-02 5.83e+03 1.41e+00 ... (remaining 6407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 8176 0.98 - 1.97: 419 1.97 - 2.95: 89 2.95 - 3.93: 28 3.93 - 4.92: 12 Bond angle restraints: 8724 Sorted by residual: angle pdb=" C VAL A 196 " pdb=" N ARG A 197 " pdb=" CA ARG A 197 " ideal model delta sigma weight residual 120.09 124.62 -4.53 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL B 196 " pdb=" N ARG B 197 " pdb=" CA ARG B 197 " ideal model delta sigma weight residual 120.09 124.61 -4.52 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL D 196 " pdb=" N ARG D 197 " pdb=" CA ARG D 197 " ideal model delta sigma weight residual 120.09 124.61 -4.52 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL C 196 " pdb=" N ARG C 197 " pdb=" CA ARG C 197 " ideal model delta sigma weight residual 120.09 124.58 -4.49 1.25e+00 6.40e-01 1.29e+01 angle pdb=" N VAL C 184 " pdb=" CA VAL C 184 " pdb=" C VAL C 184 " ideal model delta sigma weight residual 112.29 109.52 2.77 9.40e-01 1.13e+00 8.66e+00 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3408 16.49 - 32.99: 256 32.99 - 49.48: 28 49.48 - 65.98: 8 65.98 - 82.47: 4 Dihedral angle restraints: 3704 sinusoidal: 1448 harmonic: 2256 Sorted by residual: dihedral pdb=" CA TRP B 149 " pdb=" C TRP B 149 " pdb=" N LEU B 150 " pdb=" CA LEU B 150 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP C 149 " pdb=" C TRP C 149 " pdb=" N LEU C 150 " pdb=" CA LEU C 150 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP D 149 " pdb=" C TRP D 149 " pdb=" N LEU D 150 " pdb=" CA LEU D 150 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 467 0.026 - 0.052: 286 0.052 - 0.078: 111 0.078 - 0.104: 24 0.104 - 0.131: 16 Chirality restraints: 904 Sorted by residual: chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 901 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 197 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 198 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 197 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 198 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 198 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 198 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 197 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 198 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 198 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 198 " -0.022 5.00e-02 4.00e+02 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 36 2.48 - 3.09: 4537 3.09 - 3.69: 9955 3.69 - 4.30: 15215 4.30 - 4.90: 25365 Nonbonded interactions: 55108 Sorted by model distance: nonbonded pdb=" OD2 ASP C 183 " pdb="MN MN C 301 " model vdw 1.880 2.320 nonbonded pdb=" OD2 ASP B 183 " pdb="MN MN B 301 " model vdw 1.881 2.320 nonbonded pdb=" OD2 ASP D 183 " pdb="MN MN D 301 " model vdw 1.881 2.320 nonbonded pdb=" OD2 ASP A 183 " pdb="MN MN A 301 " model vdw 1.881 2.320 nonbonded pdb=" NE2 HIS D 50 " pdb="MN MN D 301 " model vdw 2.017 2.400 ... (remaining 55103 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' selection = chain 'C' selection = chain 'D' } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.950 Find NCS groups from input model: 0.230 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.004 0.028 6412 Z= 0.246 Angle : 0.551 4.917 8724 Z= 0.324 Chirality : 0.039 0.131 904 Planarity : 0.004 0.039 1140 Dihedral : 11.977 82.471 2272 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.81 (0.29), residues: 784 helix: 0.78 (0.23), residues: 504 sheet: 1.20 (0.52), residues: 72 loop : -0.02 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.004 0.001 HIS D 187 PHE 0.005 0.001 PHE B 90 TYR 0.023 0.002 TYR C 69 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.616 Fit side-chains REVERT: A 70 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 124 ASP cc_start: 0.8531 (m-30) cc_final: 0.8160 (m-30) REVERT: A 200 TYR cc_start: 0.9364 (t80) cc_final: 0.9120 (t80) REVERT: B 70 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 124 ASP cc_start: 0.8508 (m-30) cc_final: 0.8105 (m-30) REVERT: B 200 TYR cc_start: 0.9356 (t80) cc_final: 0.9143 (t80) REVERT: C 70 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 124 ASP cc_start: 0.8491 (m-30) cc_final: 0.8071 (m-30) REVERT: C 200 TYR cc_start: 0.9358 (t80) cc_final: 0.9097 (t80) REVERT: D 70 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 124 ASP cc_start: 0.8481 (m-30) cc_final: 0.8072 (m-30) REVERT: D 200 TYR cc_start: 0.9355 (t80) cc_final: 0.9142 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 1.2310 time to fit residues: 167.7414 Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6412 Z= 0.326 Angle : 0.571 5.103 8724 Z= 0.309 Chirality : 0.042 0.119 904 Planarity : 0.004 0.038 1140 Dihedral : 7.239 84.175 844 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.74 % Allowed : 8.07 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.07 (0.30), residues: 784 helix: 0.83 (0.23), residues: 508 sheet: 1.75 (0.60), residues: 72 loop : 0.30 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 147 HIS 0.004 0.001 HIS D 187 PHE 0.007 0.002 PHE D 101 TYR 0.010 0.002 TYR A 33 ARG 0.002 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.729 Fit side-chains REVERT: A 48 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 70 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 200 TYR cc_start: 0.9395 (t80) cc_final: 0.9127 (t80) REVERT: B 70 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 200 TYR cc_start: 0.9396 (t80) cc_final: 0.9175 (t80) REVERT: C 48 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8148 (tm-30) REVERT: C 70 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7799 (tm-30) REVERT: C 200 TYR cc_start: 0.9397 (t80) cc_final: 0.9176 (t80) REVERT: D 48 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 70 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 200 TYR cc_start: 0.9395 (t80) cc_final: 0.9168 (t80) outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 1.3466 time to fit residues: 195.4911 Evaluate side-chains 107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 206 ASN C 206 ASN D 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6412 Z= 0.215 Angle : 0.509 5.017 8724 Z= 0.273 Chirality : 0.040 0.123 904 Planarity : 0.004 0.037 1140 Dihedral : 7.124 83.852 844 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.48 % Allowed : 10.76 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.06 (0.30), residues: 784 helix: 0.85 (0.22), residues: 508 sheet: 1.71 (0.63), residues: 72 loop : 0.26 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 147 HIS 0.002 0.001 HIS B 54 PHE 0.005 0.001 PHE B 101 TYR 0.008 0.001 TYR D 33 ARG 0.001 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.742 Fit side-chains REVERT: A 48 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 70 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 200 TYR cc_start: 0.9384 (t80) cc_final: 0.9135 (t80) REVERT: A 211 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7780 (tp30) REVERT: B 48 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 70 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 200 TYR cc_start: 0.9381 (t80) cc_final: 0.9132 (t80) REVERT: B 211 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7758 (tp30) REVERT: C 48 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 70 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 200 TYR cc_start: 0.9381 (t80) cc_final: 0.9131 (t80) REVERT: C 211 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7770 (tp30) REVERT: C 218 MET cc_start: 0.8042 (tpp) cc_final: 0.7841 (mpp) REVERT: D 48 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8064 (tm-30) REVERT: D 70 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 200 TYR cc_start: 0.9379 (t80) cc_final: 0.9116 (t80) REVERT: D 211 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7762 (tp30) REVERT: D 218 MET cc_start: 0.8060 (tpp) cc_final: 0.7860 (mpp) outliers start: 22 outliers final: 13 residues processed: 124 average time/residue: 1.2816 time to fit residues: 166.5826 Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6412 Z= 0.279 Angle : 0.535 5.100 8724 Z= 0.285 Chirality : 0.040 0.121 904 Planarity : 0.004 0.037 1140 Dihedral : 7.089 82.550 844 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.48 % Allowed : 12.82 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.96 (0.29), residues: 784 helix: 0.78 (0.22), residues: 508 sheet: 1.64 (0.64), residues: 72 loop : 0.19 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 147 HIS 0.003 0.001 HIS B 54 PHE 0.006 0.001 PHE D 101 TYR 0.010 0.001 TYR B 33 ARG 0.001 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.720 Fit side-chains REVERT: A 70 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 200 TYR cc_start: 0.9395 (t80) cc_final: 0.9150 (t80) REVERT: A 211 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7858 (tp30) REVERT: A 218 MET cc_start: 0.8087 (tpp) cc_final: 0.7752 (mpp) REVERT: B 48 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 70 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 200 TYR cc_start: 0.9394 (t80) cc_final: 0.9146 (t80) REVERT: B 211 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7823 (tp30) REVERT: B 218 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7842 (mpp) REVERT: C 70 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 200 TYR cc_start: 0.9394 (t80) cc_final: 0.9148 (t80) REVERT: C 211 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7810 (tp30) REVERT: C 218 MET cc_start: 0.8164 (tpp) cc_final: 0.7928 (mpp) REVERT: D 70 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 200 TYR cc_start: 0.9389 (t80) cc_final: 0.9135 (t80) REVERT: D 211 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7804 (tp30) REVERT: D 218 MET cc_start: 0.8150 (tpp) cc_final: 0.7917 (mpp) outliers start: 22 outliers final: 16 residues processed: 120 average time/residue: 1.1913 time to fit residues: 150.1420 Evaluate side-chains 117 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 65 optimal weight: 0.0050 chunk 18 optimal weight: 0.6980 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6412 Z= 0.157 Angle : 0.485 4.939 8724 Z= 0.260 Chirality : 0.038 0.121 904 Planarity : 0.004 0.038 1140 Dihedral : 7.046 83.703 844 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.01 % Allowed : 13.77 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.05 (0.29), residues: 784 helix: 0.88 (0.22), residues: 508 sheet: 1.38 (0.58), residues: 80 loop : 0.22 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 147 HIS 0.002 0.001 HIS B 54 PHE 0.004 0.001 PHE D 101 TYR 0.007 0.001 TYR D 33 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.733 Fit side-chains REVERT: A 70 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 200 TYR cc_start: 0.9374 (t80) cc_final: 0.9155 (t80) REVERT: A 211 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7812 (tp30) REVERT: A 218 MET cc_start: 0.8046 (tpp) cc_final: 0.7797 (mpp) REVERT: B 70 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 200 TYR cc_start: 0.9372 (t80) cc_final: 0.9151 (t80) REVERT: B 211 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7744 (tp30) REVERT: C 70 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 200 TYR cc_start: 0.9371 (t80) cc_final: 0.9156 (t80) REVERT: C 211 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7745 (tp30) REVERT: D 70 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 119 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8248 (mp0) REVERT: D 200 TYR cc_start: 0.9369 (t80) cc_final: 0.9146 (t80) REVERT: D 211 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7734 (tp30) outliers start: 19 outliers final: 13 residues processed: 135 average time/residue: 1.0843 time to fit residues: 154.3883 Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6412 Z= 0.210 Angle : 0.519 5.024 8724 Z= 0.276 Chirality : 0.039 0.120 904 Planarity : 0.004 0.037 1140 Dihedral : 7.044 83.372 844 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.16 % Allowed : 14.72 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.05 (0.29), residues: 784 helix: 0.87 (0.22), residues: 508 sheet: 1.68 (0.62), residues: 72 loop : 0.17 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.002 0.001 HIS D 187 PHE 0.005 0.001 PHE D 101 TYR 0.008 0.001 TYR C 33 ARG 0.001 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.750 Fit side-chains REVERT: A 70 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 200 TYR cc_start: 0.9395 (t80) cc_final: 0.9183 (t80) REVERT: A 211 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7778 (tp30) REVERT: B 70 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 200 TYR cc_start: 0.9393 (t80) cc_final: 0.9180 (t80) REVERT: B 211 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7733 (tp30) REVERT: B 218 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7852 (mpp) REVERT: C 70 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 200 TYR cc_start: 0.9384 (t80) cc_final: 0.9169 (t80) REVERT: C 211 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7776 (tp30) REVERT: C 218 MET cc_start: 0.8122 (tpp) cc_final: 0.7826 (mpp) REVERT: D 70 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7670 (tm-30) REVERT: D 200 TYR cc_start: 0.9384 (t80) cc_final: 0.9160 (t80) REVERT: D 211 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7771 (tp30) REVERT: D 218 MET cc_start: 0.8109 (tpp) cc_final: 0.7818 (mpp) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.9985 time to fit residues: 134.3179 Evaluate side-chains 119 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6412 Z= 0.240 Angle : 0.524 5.064 8724 Z= 0.278 Chirality : 0.040 0.119 904 Planarity : 0.004 0.036 1140 Dihedral : 7.048 83.138 844 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.32 % Allowed : 15.51 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.04 (0.30), residues: 784 helix: 0.89 (0.23), residues: 508 sheet: 1.46 (0.62), residues: 72 loop : 0.15 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.003 0.001 HIS C 187 PHE 0.005 0.001 PHE B 101 TYR 0.009 0.001 TYR C 33 ARG 0.001 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.667 Fit side-chains REVERT: A 70 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 200 TYR cc_start: 0.9401 (t80) cc_final: 0.9187 (t80) REVERT: A 211 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7900 (tp30) REVERT: A 218 MET cc_start: 0.8081 (tpp) cc_final: 0.7796 (mpp) REVERT: B 70 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 200 TYR cc_start: 0.9397 (t80) cc_final: 0.9186 (t80) REVERT: B 211 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7775 (tp30) REVERT: C 70 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 200 TYR cc_start: 0.9397 (t80) cc_final: 0.9188 (t80) REVERT: C 211 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7760 (tp30) REVERT: C 218 MET cc_start: 0.8121 (tpp) cc_final: 0.7762 (mpp) REVERT: D 70 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7665 (tm-30) REVERT: D 119 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8203 (mp0) REVERT: D 200 TYR cc_start: 0.9397 (t80) cc_final: 0.9180 (t80) REVERT: D 211 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7758 (tp30) REVERT: D 218 MET cc_start: 0.8117 (tpp) cc_final: 0.7760 (mpp) outliers start: 21 outliers final: 20 residues processed: 113 average time/residue: 1.0452 time to fit residues: 123.7212 Evaluate side-chains 120 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.0270 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6412 Z= 0.209 Angle : 0.531 6.975 8724 Z= 0.282 Chirality : 0.039 0.119 904 Planarity : 0.004 0.036 1140 Dihedral : 7.056 83.340 844 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.64 % Allowed : 14.87 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.05 (0.29), residues: 784 helix: 0.91 (0.22), residues: 508 sheet: 1.46 (0.62), residues: 72 loop : 0.15 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 147 HIS 0.002 0.001 HIS C 187 PHE 0.005 0.001 PHE D 101 TYR 0.007 0.001 TYR C 33 ARG 0.001 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.777 Fit side-chains REVERT: A 70 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 119 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8153 (mp0) REVERT: A 200 TYR cc_start: 0.9388 (t80) cc_final: 0.9175 (t80) REVERT: A 211 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7839 (tp30) REVERT: A 218 MET cc_start: 0.8053 (tpp) cc_final: 0.7765 (mpp) REVERT: B 70 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 119 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8195 (mp0) REVERT: B 200 TYR cc_start: 0.9385 (t80) cc_final: 0.9174 (t80) REVERT: B 211 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7743 (tp30) REVERT: C 70 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 119 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8194 (mp0) REVERT: C 200 TYR cc_start: 0.9385 (t80) cc_final: 0.9178 (t80) REVERT: C 211 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7734 (tp30) REVERT: C 218 MET cc_start: 0.8092 (tpp) cc_final: 0.7743 (mpp) REVERT: D 70 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7658 (tm-30) REVERT: D 119 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8197 (mp0) REVERT: D 200 TYR cc_start: 0.9385 (t80) cc_final: 0.9169 (t80) REVERT: D 211 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7753 (tp30) REVERT: D 218 MET cc_start: 0.8090 (tpp) cc_final: 0.7742 (mpp) outliers start: 23 outliers final: 22 residues processed: 128 average time/residue: 1.1681 time to fit residues: 157.2660 Evaluate side-chains 126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6412 Z= 0.222 Angle : 0.530 7.906 8724 Z= 0.280 Chirality : 0.040 0.118 904 Planarity : 0.004 0.036 1140 Dihedral : 7.015 82.907 844 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.11 % Allowed : 14.87 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.09 (0.30), residues: 784 helix: 0.97 (0.22), residues: 508 sheet: 1.35 (0.62), residues: 72 loop : 0.12 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 147 HIS 0.002 0.001 HIS C 187 PHE 0.005 0.001 PHE D 101 TYR 0.008 0.001 TYR C 33 ARG 0.001 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.758 Fit side-chains REVERT: A 70 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 119 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8158 (mp0) REVERT: A 200 TYR cc_start: 0.9395 (t80) cc_final: 0.9186 (t80) REVERT: A 211 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7865 (tp30) REVERT: A 218 MET cc_start: 0.8055 (tpp) cc_final: 0.7813 (OUTLIER) REVERT: B 70 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 119 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8206 (mp0) REVERT: B 200 TYR cc_start: 0.9393 (t80) cc_final: 0.9185 (t80) REVERT: B 211 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7765 (tp30) REVERT: C 70 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 119 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8234 (mp0) REVERT: C 200 TYR cc_start: 0.9392 (t80) cc_final: 0.9187 (t80) REVERT: C 211 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7769 (tp30) REVERT: D 70 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7683 (tm-30) REVERT: D 119 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8213 (mp0) REVERT: D 200 TYR cc_start: 0.9392 (t80) cc_final: 0.9179 (t80) REVERT: D 211 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7767 (tp30) outliers start: 26 outliers final: 29 residues processed: 125 average time/residue: 1.2296 time to fit residues: 161.1312 Evaluate side-chains 132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6412 Z= 0.191 Angle : 0.546 9.317 8724 Z= 0.289 Chirality : 0.039 0.120 904 Planarity : 0.004 0.036 1140 Dihedral : 7.056 83.263 844 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.64 % Allowed : 15.51 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.08 (0.29), residues: 784 helix: 0.95 (0.22), residues: 508 sheet: 1.37 (0.63), residues: 72 loop : 0.15 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.002 0.001 HIS C 187 PHE 0.004 0.001 PHE D 101 TYR 0.007 0.001 TYR B 190 ARG 0.001 0.000 ARG B 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.657 Fit side-chains REVERT: A 70 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 119 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8152 (mp0) REVERT: A 200 TYR cc_start: 0.9383 (t80) cc_final: 0.9172 (t80) REVERT: A 211 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7828 (tp30) REVERT: A 218 MET cc_start: 0.8079 (tpp) cc_final: 0.7833 (OUTLIER) REVERT: B 70 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 119 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8233 (mp0) REVERT: B 200 TYR cc_start: 0.9381 (t80) cc_final: 0.9170 (t80) REVERT: B 211 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7742 (tp30) REVERT: C 70 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 119 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8220 (mp0) REVERT: C 200 TYR cc_start: 0.9380 (t80) cc_final: 0.9173 (t80) REVERT: C 211 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7737 (tp30) REVERT: C 218 MET cc_start: 0.8074 (mpp) cc_final: 0.7712 (mpp) REVERT: D 70 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 119 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8214 (mp0) REVERT: D 200 TYR cc_start: 0.9379 (t80) cc_final: 0.9172 (t80) REVERT: D 211 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7734 (tp30) REVERT: D 218 MET cc_start: 0.8078 (mpp) cc_final: 0.7717 (mpp) outliers start: 23 outliers final: 19 residues processed: 128 average time/residue: 1.1381 time to fit residues: 153.1924 Evaluate side-chains 124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 160 GLN B 158 HIS B 160 GLN C 158 HIS C 160 GLN D 158 HIS D 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.073502 restraints weight = 12764.152| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.32 r_work: 0.2877 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6412 Z= 0.265 Angle : 0.554 10.454 8724 Z= 0.290 Chirality : 0.041 0.117 904 Planarity : 0.004 0.036 1140 Dihedral : 7.020 82.517 844 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.32 % Allowed : 15.03 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.06 (0.30), residues: 784 helix: 0.99 (0.23), residues: 508 sheet: 1.21 (0.62), residues: 72 loop : 0.07 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.003 0.001 HIS C 187 PHE 0.005 0.001 PHE B 101 TYR 0.010 0.001 TYR D 190 ARG 0.001 0.000 ARG B 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.33 seconds wall clock time: 59 minutes 56.98 seconds (3596.98 seconds total)