Starting phenix.real_space_refine on Tue Sep 24 15:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/09_2024/8grx_34216.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/09_2024/8grx_34216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/09_2024/8grx_34216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/09_2024/8grx_34216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/09_2024/8grx_34216.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/09_2024/8grx_34216.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.116 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 42 5.16 5 C 5256 2.51 5 N 1474 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8328 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1140 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3024 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 352} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: D, C Time building chain proxies: 6.44, per 1000 atoms: 0.77 Number of scatterers: 8328 At special positions: 0 Unit cell: (124.063, 150.412, 77.9509, 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 42 16.00 O 1556 8.00 N 1474 7.00 C 5256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 245 " - pdb=" SG CYS B 296 " distance=2.02 Simple disulfide: pdb=" SG CYS B 345 " - pdb=" SG CYS B 396 " distance=2.04 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: 2.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 22 sheets defined 27.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 removed outlier: 3.953A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 54 through 82 Processing helix chain 'A' and resid 87 through 125 Processing helix chain 'A' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.953A pdb=" N LEU C 43 " --> pdb=" O TRP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 54 through 82 Processing helix chain 'C' and resid 87 through 125 Processing helix chain 'C' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET B 117 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP B 192 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG B 193 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU B 241 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU B 235 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN B 320 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 317 " --> pdb=" O LEU B 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 268 Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL B 341 " --> pdb=" O MET B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336 Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET D 117 " --> pdb=" O TRP D 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 129 Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP D 192 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG D 193 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU D 241 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU D 235 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN D 320 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET D 317 " --> pdb=" O LEU D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 268 Processing sheet with id=AC3, first strand: chain 'D' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL D 341 " --> pdb=" O MET D 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 334 through 336 439 hydrogen bonds defined for protein. 1167 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: 2.51 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1926 1.33 - 1.45: 1864 1.45 - 1.57: 4692 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8550 Sorted by residual: bond pdb=" C HIS D 363 " pdb=" N PRO D 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C HIS B 363 " pdb=" N PRO B 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C GLY D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C GLY B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C PHE B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 8.46e+00 ... (remaining 8545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 10724 2.13 - 4.25: 712 4.25 - 6.38: 112 6.38 - 8.50: 32 8.50 - 10.63: 18 Bond angle restraints: 11598 Sorted by residual: angle pdb=" C GLU B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C GLU D 67 " pdb=" N PRO D 68 " pdb=" CA PRO D 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C ARG D 267 " pdb=" N PRO D 268 " pdb=" CA PRO D 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C ARG B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C GLY D 184 " pdb=" N PRO D 185 " pdb=" CA PRO D 185 " ideal model delta sigma weight residual 119.84 126.74 -6.90 1.25e+00 6.40e-01 3.05e+01 ... (remaining 11593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.18: 4960 25.18 - 50.36: 147 50.36 - 75.54: 17 75.54 - 100.72: 2 100.72 - 125.90: 4 Dihedral angle restraints: 5130 sinusoidal: 2086 harmonic: 3044 Sorted by residual: dihedral pdb=" CA GLN B 330 " pdb=" C GLN B 330 " pdb=" N PRO B 331 " pdb=" CA PRO B 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLN D 330 " pdb=" C GLN D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLY B 184 " pdb=" C GLY B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -67.33 -112.67 0 5.00e+00 4.00e-02 5.08e+02 ... (remaining 5127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 758 0.040 - 0.080: 302 0.080 - 0.120: 116 0.120 - 0.159: 38 0.159 - 0.199: 2 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA SER A 54 " pdb=" N SER A 54 " pdb=" C SER A 54 " pdb=" CB SER A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA SER C 54 " pdb=" N SER C 54 " pdb=" C SER C 54 " pdb=" CB SER C 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CG LEU D 235 " pdb=" CB LEU D 235 " pdb=" CD1 LEU D 235 " pdb=" CD2 LEU D 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1213 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 131 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 132 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 131 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 132 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ALA A 86 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 87 " -0.009 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 10 2.60 - 3.17: 6655 3.17 - 3.75: 12911 3.75 - 4.32: 18472 4.32 - 4.90: 29810 Nonbonded interactions: 67858 Sorted by model distance: nonbonded pdb=" SG CYS D 144 " pdb=" SG CYS D 196 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS D 245 " pdb=" SG CYS D 296 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS D 49 " pdb=" SG CYS D 98 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 345 " pdb=" SG CYS D 396 " model vdw 2.035 3.760 nonbonded pdb=" OG SER D 102 " pdb=" O GLY D 105 " model vdw 2.373 3.040 ... (remaining 67853 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 'C' } ncs_group { reference = chain 'B' 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: 1.500 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.020 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 8550 Z= 0.429 Angle : 1.264 10.628 11598 Z= 0.795 Chirality : 0.051 0.199 1216 Planarity : 0.005 0.057 1514 Dihedral : 12.300 125.903 3170 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.46 % Favored : 96.15 % Rotamer: Outliers : 0.22 % Allowed : 5.83 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 8.11 % 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 (0.25), residues: 1040 helix: 1.26 (0.28), residues: 256 sheet: -0.08 (0.28), residues: 310 loop : -1.28 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 26 HIS 0.003 0.001 HIS D 209 PHE 0.010 0.002 PHE B 177 TYR 0.020 0.002 TYR B 197 ARG 0.005 0.001 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 1.3096 time to fit residues: 213.4659 Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 94 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 46 GLN A 58 GLN A 81 GLN A 117 GLN A 128 GLN A 140 HIS A 156 GLN B 92 HIS B 190 HIS B 205 GLN B 266 GLN B 280 ASN B 290 HIS B 301 ASN B 346 GLN C 46 GLN C 58 GLN C 81 GLN C 117 GLN C 128 GLN C 140 HIS C 156 GLN D 92 HIS D 190 HIS D 205 GLN D 280 ASN D 290 HIS D 301 ASN D 346 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8550 Z= 0.237 Angle : 0.576 6.565 11598 Z= 0.305 Chirality : 0.038 0.128 1216 Planarity : 0.006 0.094 1514 Dihedral : 5.788 93.493 1164 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.15 % Favored : 98.65 % Rotamer: Outliers : 1.79 % Allowed : 10.20 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 5.41 % 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: 1.23 (0.26), residues: 1040 helix: 3.51 (0.28), residues: 254 sheet: 0.30 (0.28), residues: 316 loop : -0.30 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 32 HIS 0.003 0.001 HIS B 92 PHE 0.009 0.001 PHE B 351 TYR 0.015 0.001 TYR D 372 ARG 0.002 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7555 (ptm) REVERT: A 125 MET cc_start: 0.7618 (mmm) cc_final: 0.7354 (mmt) REVERT: A 151 ASP cc_start: 0.8142 (m-30) cc_final: 0.7870 (m-30) REVERT: B 32 TRP cc_start: 0.7257 (p90) cc_final: 0.6707 (p90) REVERT: B 223 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8007 (ttp80) REVERT: C 64 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7555 (ptm) REVERT: C 125 MET cc_start: 0.7616 (mmm) cc_final: 0.7352 (mmt) REVERT: C 151 ASP cc_start: 0.8135 (m-30) cc_final: 0.7867 (m-30) REVERT: D 32 TRP cc_start: 0.7243 (p90) cc_final: 0.6690 (p90) REVERT: D 223 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8021 (ttp80) outliers start: 16 outliers final: 2 residues processed: 108 average time/residue: 1.2292 time to fit residues: 141.3417 Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 266 GLN B 405 HIS C 46 GLN D 405 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8550 Z= 0.181 Angle : 0.525 6.475 11598 Z= 0.275 Chirality : 0.037 0.134 1216 Planarity : 0.006 0.100 1514 Dihedral : 5.035 81.500 1164 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.50 % Favored : 97.31 % Rotamer: Outliers : 1.23 % Allowed : 12.00 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.80 (0.27), residues: 1040 helix: 4.03 (0.28), residues: 254 sheet: 0.65 (0.29), residues: 316 loop : 0.00 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.002 0.001 HIS A 140 PHE 0.010 0.001 PHE D 354 TYR 0.011 0.001 TYR D 377 ARG 0.005 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7732 (ptm) REVERT: A 125 MET cc_start: 0.7573 (mmm) cc_final: 0.7292 (mmt) REVERT: A 151 ASP cc_start: 0.8149 (m-30) cc_final: 0.7815 (m-30) REVERT: B 32 TRP cc_start: 0.7326 (p90) cc_final: 0.6752 (p90) REVERT: B 223 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8039 (ttp80) REVERT: C 64 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7734 (ptm) REVERT: C 125 MET cc_start: 0.7574 (mmm) cc_final: 0.7281 (mmt) REVERT: C 151 ASP cc_start: 0.8152 (m-30) cc_final: 0.7818 (m-30) REVERT: D 32 TRP cc_start: 0.7303 (p90) cc_final: 0.6750 (p90) REVERT: D 223 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8061 (ttp80) outliers start: 11 outliers final: 7 residues processed: 112 average time/residue: 1.3153 time to fit residues: 157.0100 Evaluate side-chains 107 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 363 HIS C 46 GLN D 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8550 Z= 0.329 Angle : 0.569 6.955 11598 Z= 0.294 Chirality : 0.039 0.131 1216 Planarity : 0.006 0.101 1514 Dihedral : 5.153 79.709 1164 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.12 % Favored : 97.69 % Rotamer: Outliers : 2.47 % Allowed : 11.10 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.63 (0.27), residues: 1040 helix: 3.61 (0.29), residues: 254 sheet: 0.66 (0.29), residues: 320 loop : -0.02 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 26 HIS 0.004 0.001 HIS B 363 PHE 0.007 0.001 PHE B 351 TYR 0.014 0.002 TYR B 198 ARG 0.005 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: A 151 ASP cc_start: 0.8221 (m-30) cc_final: 0.7847 (m-30) REVERT: B 32 TRP cc_start: 0.7287 (p90) cc_final: 0.6948 (p90) REVERT: B 223 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8079 (ttp80) REVERT: C 132 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: C 151 ASP cc_start: 0.8219 (m-30) cc_final: 0.7845 (m-30) REVERT: D 32 TRP cc_start: 0.7327 (p90) cc_final: 0.6995 (p90) REVERT: D 223 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8102 (ttp80) outliers start: 22 outliers final: 9 residues processed: 120 average time/residue: 1.2407 time to fit residues: 158.1779 Evaluate side-chains 109 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.0020 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS C 46 GLN D 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8550 Z= 0.153 Angle : 0.483 6.551 11598 Z= 0.251 Chirality : 0.036 0.140 1216 Planarity : 0.006 0.108 1514 Dihedral : 4.816 75.246 1164 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.92 % Favored : 97.88 % Rotamer: Outliers : 1.79 % Allowed : 12.22 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.82 (0.27), residues: 1040 helix: 3.89 (0.28), residues: 254 sheet: 0.63 (0.28), residues: 336 loop : 0.14 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.007 0.001 PHE D 354 TYR 0.011 0.001 TYR B 377 ARG 0.012 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.8242 (m-30) cc_final: 0.7997 (m-30) REVERT: B 32 TRP cc_start: 0.7232 (p90) cc_final: 0.6863 (p90) REVERT: B 223 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8090 (ttp80) REVERT: C 151 ASP cc_start: 0.8241 (m-30) cc_final: 0.8003 (m-30) REVERT: D 32 TRP cc_start: 0.7281 (p90) cc_final: 0.6898 (p90) REVERT: D 223 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8139 (ttp80) REVERT: D 383 MET cc_start: 0.8205 (mtm) cc_final: 0.7956 (mtt) outliers start: 16 outliers final: 9 residues processed: 108 average time/residue: 1.2297 time to fit residues: 141.3354 Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 326 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.0000 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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: 0.7887 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8550 Z= 0.220 Angle : 0.506 6.131 11598 Z= 0.261 Chirality : 0.037 0.135 1216 Planarity : 0.006 0.101 1514 Dihedral : 4.849 73.535 1164 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.58 % Allowed : 12.11 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.78 (0.27), residues: 1040 helix: 3.77 (0.28), residues: 254 sheet: 0.60 (0.28), residues: 332 loop : 0.17 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 26 HIS 0.004 0.001 HIS B 152 PHE 0.008 0.001 PHE D 354 TYR 0.012 0.001 TYR B 198 ARG 0.021 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: A 151 ASP cc_start: 0.8202 (m-30) cc_final: 0.7943 (m-30) REVERT: B 32 TRP cc_start: 0.7224 (p90) cc_final: 0.6842 (p90) REVERT: B 223 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8130 (ttp80) REVERT: C 112 ARG cc_start: 0.6980 (mtm110) cc_final: 0.6741 (mtp85) REVERT: C 132 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7521 (tp30) REVERT: C 151 ASP cc_start: 0.8203 (m-30) cc_final: 0.7865 (m-30) REVERT: D 32 TRP cc_start: 0.7260 (p90) cc_final: 0.6883 (p90) REVERT: D 223 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8133 (ttp80) outliers start: 23 outliers final: 13 residues processed: 103 average time/residue: 1.1722 time to fit residues: 129.1810 Evaluate side-chains 106 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8550 Z= 0.240 Angle : 0.512 5.920 11598 Z= 0.264 Chirality : 0.037 0.135 1216 Planarity : 0.006 0.109 1514 Dihedral : 4.840 71.486 1164 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.40 % Favored : 97.50 % Rotamer: Outliers : 3.03 % Allowed : 11.66 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.77 (0.27), residues: 1040 helix: 3.72 (0.28), residues: 254 sheet: 0.54 (0.28), residues: 332 loop : 0.24 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 306 HIS 0.005 0.001 HIS B 363 PHE 0.008 0.001 PHE D 354 TYR 0.011 0.001 TYR D 197 ARG 0.014 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7536 (tp30) REVERT: A 151 ASP cc_start: 0.8149 (m-30) cc_final: 0.7896 (m-30) REVERT: B 32 TRP cc_start: 0.7260 (p90) cc_final: 0.6904 (p90) REVERT: B 223 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8082 (ttp80) REVERT: C 132 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7545 (tp30) REVERT: C 151 ASP cc_start: 0.8199 (m-30) cc_final: 0.7950 (m-30) REVERT: D 32 TRP cc_start: 0.7267 (p90) cc_final: 0.6884 (p90) REVERT: D 223 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8111 (ttp80) outliers start: 27 outliers final: 16 residues processed: 111 average time/residue: 1.1775 time to fit residues: 139.4566 Evaluate side-chains 107 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8550 Z= 0.189 Angle : 0.481 5.686 11598 Z= 0.248 Chirality : 0.036 0.134 1216 Planarity : 0.005 0.100 1514 Dihedral : 4.747 70.075 1164 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.58 % Allowed : 12.11 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.99 (0.27), residues: 1040 helix: 3.88 (0.28), residues: 254 sheet: 0.64 (0.28), residues: 336 loop : 0.42 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.005 0.001 HIS B 363 PHE 0.010 0.001 PHE D 354 TYR 0.015 0.001 TYR D 297 ARG 0.004 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6541 (mt-10) REVERT: A 132 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: A 151 ASP cc_start: 0.8195 (m-30) cc_final: 0.7957 (m-30) REVERT: B 32 TRP cc_start: 0.7283 (p90) cc_final: 0.6963 (p90) REVERT: B 223 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8034 (ttp80) REVERT: C 132 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: C 151 ASP cc_start: 0.8195 (m-30) cc_final: 0.7959 (m-30) REVERT: D 32 TRP cc_start: 0.7279 (p90) cc_final: 0.6981 (p90) REVERT: D 223 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8053 (ttp80) outliers start: 23 outliers final: 12 residues processed: 102 average time/residue: 1.2807 time to fit residues: 139.4066 Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 93 optimal weight: 0.1980 chunk 61 optimal weight: 0.5980 chunk 98 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 363 HIS D 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8550 Z= 0.138 Angle : 0.450 5.249 11598 Z= 0.234 Chirality : 0.035 0.137 1216 Planarity : 0.005 0.099 1514 Dihedral : 4.572 67.319 1164 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.57 % Allowed : 13.45 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.28), residues: 1040 helix: 4.08 (0.28), residues: 254 sheet: 0.79 (0.29), residues: 336 loop : 0.58 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 26 HIS 0.005 0.001 HIS B 363 PHE 0.010 0.001 PHE D 354 TYR 0.012 0.001 TYR B 377 ARG 0.004 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6558 (mt-10) REVERT: A 132 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: A 151 ASP cc_start: 0.8174 (m-30) cc_final: 0.7952 (m-30) REVERT: B 32 TRP cc_start: 0.7346 (p90) cc_final: 0.7016 (p90) REVERT: B 223 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7992 (ttp80) REVERT: C 49 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6509 (mt-10) REVERT: C 132 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: C 151 ASP cc_start: 0.8183 (m-30) cc_final: 0.7952 (m-30) REVERT: D 32 TRP cc_start: 0.7360 (p90) cc_final: 0.7057 (p90) REVERT: D 223 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8115 (ttp80) REVERT: D 253 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8503 (ptt-90) outliers start: 14 outliers final: 7 residues processed: 96 average time/residue: 1.2588 time to fit residues: 128.3871 Evaluate side-chains 92 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 253 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8550 Z= 0.344 Angle : 0.557 5.687 11598 Z= 0.284 Chirality : 0.039 0.136 1216 Planarity : 0.006 0.099 1514 Dihedral : 4.893 68.596 1164 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.57 % Allowed : 14.46 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.90 (0.27), residues: 1040 helix: 3.58 (0.28), residues: 254 sheet: 0.70 (0.29), residues: 330 loop : 0.42 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 306 HIS 0.005 0.001 HIS D 363 PHE 0.008 0.001 PHE B 381 TYR 0.014 0.002 TYR B 198 ARG 0.004 0.001 ARG C 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6549 (mt-10) REVERT: A 61 ARG cc_start: 0.7558 (mtp-110) cc_final: 0.7332 (mmt180) REVERT: A 132 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: A 151 ASP cc_start: 0.8094 (m-30) cc_final: 0.7848 (m-30) REVERT: B 32 TRP cc_start: 0.7372 (p90) cc_final: 0.7093 (p90) REVERT: B 223 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8091 (ttp80) REVERT: C 49 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6535 (mt-10) REVERT: C 132 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7571 (tp30) REVERT: C 151 ASP cc_start: 0.8088 (m-30) cc_final: 0.7837 (m-30) REVERT: D 32 TRP cc_start: 0.7320 (p90) cc_final: 0.7038 (p90) REVERT: D 223 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8121 (ttp80) REVERT: D 253 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (ptt90) outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 1.2881 time to fit residues: 151.6058 Evaluate side-chains 109 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.0370 chunk 34 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 0.0000 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.192639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145148 restraints weight = 8979.938| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.52 r_work: 0.3408 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8550 Z= 0.167 Angle : 0.478 5.407 11598 Z= 0.247 Chirality : 0.036 0.131 1216 Planarity : 0.005 0.098 1514 Dihedral : 4.718 68.300 1164 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.46 % Allowed : 14.80 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.27), residues: 1040 helix: 3.86 (0.28), residues: 254 sheet: 0.77 (0.29), residues: 334 loop : 0.56 (0.33), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.011 0.001 PHE D 354 TYR 0.013 0.001 TYR B 377 ARG 0.005 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3173.51 seconds wall clock time: 56 minutes 16.97 seconds (3376.97 seconds total)