Starting phenix.real_space_refine on Tue Feb 13 04:48:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/02_2024/8eqt_28545_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/02_2024/8eqt_28545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/02_2024/8eqt_28545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/02_2024/8eqt_28545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/02_2024/8eqt_28545_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/02_2024/8eqt_28545_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 4 5.49 5 S 16 5.16 5 C 2122 2.51 5 N 490 2.21 5 O 574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Time building chain proxies: 2.16, per 1000 atoms: 0.67 Number of scatterers: 3206 At special positions: 0 Unit cell: (63.3, 59.924, 91.152, 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) S 16 16.00 P 4 15.00 O 574 8.00 N 490 7.00 C 2122 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 - 3.50 Amino acid : False - 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: 1.28 Conformation dependent library (CDL) restraints added in 559.2 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 4 sheets defined 46.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 Processing helix chain 'A' and resid 68 through 99 removed outlier: 4.095A pdb=" N SER A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'B' and resid 43 through 62 Processing helix chain 'B' and resid 68 through 99 removed outlier: 4.095A pdb=" N SER B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 133 Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 6.214A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= C, first strand: chain 'B' and resid 155 through 160 removed outlier: 6.214A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 186 190 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 464 1.31 - 1.44: 1042 1.44 - 1.57: 1764 1.57 - 1.69: 8 1.69 - 1.82: 18 Bond restraints: 3296 Sorted by residual: bond pdb=" C10 PEE B 402 " pdb=" O2 PEE B 402 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C10 PEE A 402 " pdb=" O2 PEE A 402 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C30 PEE B 402 " pdb=" O3 PEE B 402 " ideal model delta sigma weight residual 1.327 1.410 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 3291 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 98 107.47 - 114.10: 1900 114.10 - 120.72: 1386 120.72 - 127.35: 1060 127.35 - 133.98: 44 Bond angle restraints: 4488 Sorted by residual: angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 110.27 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PEE B 402 " pdb=" P PEE B 402 " pdb=" O4P PEE B 402 " ideal model delta sigma weight residual 92.91 110.27 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.90 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O3P PEE A 402 " pdb=" P PEE A 402 " pdb=" O4P PEE A 402 " ideal model delta sigma weight residual 92.91 109.90 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 108.94 10.49 3.00e+00 1.11e-01 1.22e+01 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.38: 1822 29.38 - 58.76: 34 58.76 - 88.14: 10 88.14 - 117.52: 6 117.52 - 146.90: 6 Dihedral angle restraints: 1878 sinusoidal: 740 harmonic: 1138 Sorted by residual: dihedral pdb=" C4 PEE A 401 " pdb=" O4P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sinusoidal sigma weight residual -75.78 71.12 -146.90 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C4 PEE B 402 " pdb=" O4P PEE B 402 " pdb=" P PEE B 402 " pdb=" O2P PEE B 402 " ideal model delta sinusoidal sigma weight residual -75.78 71.12 -146.90 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -79.00 141.73 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 1875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 446 0.065 - 0.129: 54 0.129 - 0.193: 0 0.193 - 0.258: 0 0.258 - 0.322: 4 Chirality restraints: 504 Sorted by residual: chirality pdb=" C2 PEE B 402 " pdb=" C1 PEE B 402 " pdb=" C3 PEE B 402 " pdb=" O2 PEE B 402 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 501 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 79 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C PHE B 79 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE B 79 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 80 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 79 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C PHE A 79 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 79 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 80 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 87 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C PHE A 87 " -0.021 2.00e-02 2.50e+03 pdb=" O PHE A 87 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 88 " 0.007 2.00e-02 2.50e+03 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 345 2.75 - 3.29: 3206 3.29 - 3.83: 5425 3.83 - 4.36: 6184 4.36 - 4.90: 10492 Nonbonded interactions: 25652 Sorted by model distance: nonbonded pdb=" O THR B 89 " pdb=" OG SER B 92 " model vdw 2.213 2.440 nonbonded pdb=" O THR A 89 " pdb=" OG SER A 92 " model vdw 2.213 2.440 nonbonded pdb=" O PRO B 42 " pdb=" OH TYR B 91 " model vdw 2.232 2.440 nonbonded pdb=" O PRO A 42 " pdb=" OH TYR A 91 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.248 2.440 ... (remaining 25647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 238 or (resid 401 through 402 and (name N or na \ me C1 or name C10 or name C11 or name C2 or name C3 or name C30 or name C31 or n \ ame C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )))) selection = (chain 'B' and (resid 40 through 238 or (resid 401 through 402 and (name N or na \ me C1 or name C10 or name C11 or name C2 or name C3 or name C30 or name C31 or n \ ame C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )))) } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.470 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.006 0.091 3296 Z= 0.438 Angle : 0.888 17.361 4488 Z= 0.355 Chirality : 0.046 0.322 504 Planarity : 0.004 0.026 530 Dihedral : 17.012 146.900 1150 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.40), residues: 374 helix: 1.18 (0.37), residues: 164 sheet: 0.65 (0.56), residues: 90 loop : -0.77 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.003 0.001 HIS A 204 PHE 0.005 0.001 PHE B 114 TYR 0.006 0.001 TYR B 156 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.386 Fit side-chains REVERT: A 89 THR cc_start: 0.9351 (m) cc_final: 0.9042 (p) REVERT: A 105 PHE cc_start: 0.9339 (m-80) cc_final: 0.9061 (m-80) REVERT: A 106 LEU cc_start: 0.8382 (pp) cc_final: 0.8128 (tp) REVERT: A 134 ARG cc_start: 0.8323 (tpt170) cc_final: 0.6923 (ttt180) REVERT: A 136 LYS cc_start: 0.8499 (pttt) cc_final: 0.8201 (pttt) REVERT: A 154 TYR cc_start: 0.8408 (t80) cc_final: 0.7536 (t80) REVERT: A 183 ASP cc_start: 0.9086 (p0) cc_final: 0.8709 (p0) REVERT: B 89 THR cc_start: 0.9350 (m) cc_final: 0.9042 (p) REVERT: B 105 PHE cc_start: 0.9337 (m-80) cc_final: 0.9058 (m-80) REVERT: B 106 LEU cc_start: 0.8384 (pp) cc_final: 0.8127 (tp) REVERT: B 134 ARG cc_start: 0.8321 (tpt170) cc_final: 0.6922 (ttt180) REVERT: B 136 LYS cc_start: 0.8499 (pttt) cc_final: 0.8199 (pttt) REVERT: B 154 TYR cc_start: 0.8403 (t80) cc_final: 0.7533 (t80) REVERT: B 183 ASP cc_start: 0.9088 (p0) cc_final: 0.8717 (p0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1557 time to fit residues: 32.8514 Evaluate side-chains 82 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 57 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3296 Z= 0.229 Angle : 0.515 4.786 4488 Z= 0.281 Chirality : 0.039 0.128 504 Planarity : 0.005 0.022 530 Dihedral : 17.917 147.056 480 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.05 % Allowed : 16.76 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.41), residues: 374 helix: 2.16 (0.38), residues: 166 sheet: 0.62 (0.56), residues: 90 loop : -0.98 (0.45), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 193 HIS 0.007 0.002 HIS A 78 PHE 0.025 0.002 PHE A 230 TYR 0.007 0.001 TYR A 154 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.392 Fit side-chains REVERT: A 134 ARG cc_start: 0.7978 (tpt170) cc_final: 0.7476 (ttt180) REVERT: A 136 LYS cc_start: 0.8657 (pttt) cc_final: 0.8430 (pttt) REVERT: A 154 TYR cc_start: 0.8380 (t80) cc_final: 0.7713 (t80) REVERT: A 194 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 211 TYR cc_start: 0.7941 (m-80) cc_final: 0.7643 (m-80) REVERT: A 213 GLN cc_start: 0.9164 (tt0) cc_final: 0.8955 (tt0) REVERT: A 233 TYR cc_start: 0.9494 (m-80) cc_final: 0.8821 (m-80) REVERT: B 134 ARG cc_start: 0.7976 (tpt170) cc_final: 0.7475 (ttt180) REVERT: B 136 LYS cc_start: 0.8653 (pttt) cc_final: 0.8426 (pttt) REVERT: B 154 TYR cc_start: 0.8381 (t80) cc_final: 0.7714 (t80) REVERT: B 194 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8299 (mt-10) REVERT: B 211 TYR cc_start: 0.7943 (m-80) cc_final: 0.7643 (m-80) REVERT: B 213 GLN cc_start: 0.9165 (tt0) cc_final: 0.8958 (tt0) REVERT: B 233 TYR cc_start: 0.9493 (m-80) cc_final: 0.8811 (m-80) outliers start: 14 outliers final: 12 residues processed: 106 average time/residue: 0.1654 time to fit residues: 20.8589 Evaluate side-chains 93 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3296 Z= 0.253 Angle : 0.469 4.592 4488 Z= 0.259 Chirality : 0.039 0.123 504 Planarity : 0.005 0.021 530 Dihedral : 17.147 145.072 480 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 6.07 % Allowed : 17.05 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.43), residues: 374 helix: 2.22 (0.42), residues: 166 sheet: 0.56 (0.56), residues: 86 loop : -1.09 (0.43), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.004 0.002 HIS A 78 PHE 0.014 0.002 PHE A 230 TYR 0.006 0.001 TYR B 160 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8655 (mp0) cc_final: 0.8304 (mp0) REVERT: A 134 ARG cc_start: 0.8091 (tpt170) cc_final: 0.7535 (ttt180) REVERT: A 136 LYS cc_start: 0.8691 (pttt) cc_final: 0.8446 (pttt) REVERT: A 155 ASP cc_start: 0.8000 (p0) cc_final: 0.7419 (p0) REVERT: A 194 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 199 ASP cc_start: 0.8727 (p0) cc_final: 0.8445 (p0) REVERT: A 211 TYR cc_start: 0.7922 (m-80) cc_final: 0.7642 (m-80) REVERT: B 102 GLU cc_start: 0.8649 (mp0) cc_final: 0.8297 (mp0) REVERT: B 134 ARG cc_start: 0.8089 (tpt170) cc_final: 0.7535 (ttt180) REVERT: B 136 LYS cc_start: 0.8688 (pttt) cc_final: 0.8444 (pttt) REVERT: B 155 ASP cc_start: 0.8001 (p0) cc_final: 0.7417 (p0) REVERT: B 194 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 199 ASP cc_start: 0.8723 (p0) cc_final: 0.8442 (p0) REVERT: B 211 TYR cc_start: 0.7924 (m-80) cc_final: 0.7642 (m-80) outliers start: 21 outliers final: 19 residues processed: 96 average time/residue: 0.1738 time to fit residues: 19.8953 Evaluate side-chains 100 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS B 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3296 Z= 0.179 Angle : 0.440 5.379 4488 Z= 0.244 Chirality : 0.038 0.125 504 Planarity : 0.004 0.021 530 Dihedral : 16.502 154.482 480 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.34 % Allowed : 21.39 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.42), residues: 374 helix: 2.28 (0.41), residues: 166 sheet: 0.42 (0.55), residues: 86 loop : -1.29 (0.43), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS B 78 PHE 0.012 0.002 PHE A 230 TYR 0.005 0.001 TYR B 160 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.375 Fit side-chains REVERT: A 134 ARG cc_start: 0.8131 (tpt170) cc_final: 0.7739 (ttt180) REVERT: A 136 LYS cc_start: 0.8707 (pttt) cc_final: 0.8474 (pttt) REVERT: A 154 TYR cc_start: 0.8425 (t80) cc_final: 0.8120 (t80) REVERT: A 155 ASP cc_start: 0.7978 (p0) cc_final: 0.7328 (p0) REVERT: A 183 ASP cc_start: 0.8907 (p0) cc_final: 0.8703 (p0) REVERT: A 194 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 134 ARG cc_start: 0.8140 (tpt170) cc_final: 0.7736 (ttt180) REVERT: B 136 LYS cc_start: 0.8705 (pttt) cc_final: 0.8472 (pttt) REVERT: B 154 TYR cc_start: 0.8424 (t80) cc_final: 0.8120 (t80) REVERT: B 155 ASP cc_start: 0.7980 (p0) cc_final: 0.7326 (p0) REVERT: B 183 ASP cc_start: 0.8917 (p0) cc_final: 0.8707 (p0) REVERT: B 194 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 226 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 227 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7531 (m90) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.1549 time to fit residues: 20.7045 Evaluate side-chains 86 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 144 ASN B 78 HIS B 144 ASN B 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3296 Z= 0.152 Angle : 0.429 4.555 4488 Z= 0.241 Chirality : 0.038 0.131 504 Planarity : 0.004 0.020 530 Dihedral : 16.416 157.106 480 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.76 % Allowed : 20.81 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.42), residues: 374 helix: 2.37 (0.40), residues: 168 sheet: 0.68 (0.53), residues: 84 loop : -1.44 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.002 0.001 HIS A 150 PHE 0.010 0.001 PHE B 56 TYR 0.005 0.001 TYR B 160 ARG 0.000 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8103 (tpt170) cc_final: 0.7742 (ttt180) REVERT: A 136 LYS cc_start: 0.8703 (pttt) cc_final: 0.8472 (pttt) REVERT: A 154 TYR cc_start: 0.8425 (t80) cc_final: 0.8108 (t80) REVERT: A 155 ASP cc_start: 0.8018 (p0) cc_final: 0.7376 (p0) REVERT: A 194 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8253 (mt-10) REVERT: A 198 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7685 (mmtm) REVERT: A 226 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 227 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.7830 (m-70) REVERT: B 134 ARG cc_start: 0.8103 (tpt170) cc_final: 0.7740 (ttt180) REVERT: B 136 LYS cc_start: 0.8698 (pttt) cc_final: 0.8467 (pttt) REVERT: B 154 TYR cc_start: 0.8423 (t80) cc_final: 0.8110 (t80) REVERT: B 155 ASP cc_start: 0.8015 (p0) cc_final: 0.7375 (p0) REVERT: B 194 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8264 (mt-10) REVERT: B 198 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7682 (mmtm) outliers start: 13 outliers final: 12 residues processed: 89 average time/residue: 0.1718 time to fit residues: 18.1400 Evaluate side-chains 88 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 229 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS B 78 HIS B 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3296 Z= 0.165 Angle : 0.424 4.585 4488 Z= 0.238 Chirality : 0.038 0.127 504 Planarity : 0.004 0.020 530 Dihedral : 16.244 159.394 480 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.20 % Allowed : 18.50 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.42), residues: 374 helix: 2.50 (0.41), residues: 168 sheet: 0.43 (0.53), residues: 86 loop : -1.24 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.003 0.001 HIS B 227 PHE 0.012 0.001 PHE A 43 TYR 0.004 0.001 TYR B 160 ARG 0.000 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.390 Fit side-chains REVERT: A 134 ARG cc_start: 0.8151 (tpt170) cc_final: 0.7731 (ttp-170) REVERT: A 136 LYS cc_start: 0.8710 (pttt) cc_final: 0.8481 (pttt) REVERT: A 154 TYR cc_start: 0.8447 (t80) cc_final: 0.8105 (t80) REVERT: A 155 ASP cc_start: 0.8000 (p0) cc_final: 0.7343 (p0) REVERT: A 194 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8258 (mt-10) REVERT: B 134 ARG cc_start: 0.8151 (tpt170) cc_final: 0.7729 (ttp-170) REVERT: B 136 LYS cc_start: 0.8706 (pttt) cc_final: 0.8478 (pttt) REVERT: B 154 TYR cc_start: 0.8443 (t80) cc_final: 0.8103 (t80) REVERT: B 155 ASP cc_start: 0.7998 (p0) cc_final: 0.7341 (p0) REVERT: B 194 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 226 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 227 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.7566 (m90) outliers start: 18 outliers final: 17 residues processed: 97 average time/residue: 0.1705 time to fit residues: 19.6114 Evaluate side-chains 94 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 36 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 144 ASN B 78 HIS B 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3296 Z= 0.142 Angle : 0.424 5.540 4488 Z= 0.240 Chirality : 0.037 0.126 504 Planarity : 0.004 0.020 530 Dihedral : 16.011 159.653 480 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.78 % Allowed : 17.63 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.42), residues: 374 helix: 2.58 (0.40), residues: 168 sheet: 0.47 (0.53), residues: 86 loop : -1.23 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.002 0.001 HIS B 227 PHE 0.012 0.001 PHE A 43 TYR 0.004 0.001 TYR B 160 ARG 0.000 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.387 Fit side-chains REVERT: A 134 ARG cc_start: 0.8148 (tpt170) cc_final: 0.7729 (ttp-170) REVERT: A 136 LYS cc_start: 0.8708 (pttt) cc_final: 0.8481 (pttt) REVERT: A 154 TYR cc_start: 0.8449 (t80) cc_final: 0.8109 (t80) REVERT: A 155 ASP cc_start: 0.8057 (p0) cc_final: 0.7393 (p0) REVERT: A 194 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8298 (mt-10) REVERT: A 198 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7793 (pttt) REVERT: A 226 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 227 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.7761 (m-70) REVERT: B 134 ARG cc_start: 0.8149 (tpt170) cc_final: 0.7727 (ttp-170) REVERT: B 136 LYS cc_start: 0.8703 (pttt) cc_final: 0.8477 (pttt) REVERT: B 154 TYR cc_start: 0.8446 (t80) cc_final: 0.8109 (t80) REVERT: B 155 ASP cc_start: 0.8056 (p0) cc_final: 0.7390 (p0) REVERT: B 194 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 198 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7909 (pttt) REVERT: B 226 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 227 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.7727 (m-70) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.1638 time to fit residues: 19.8617 Evaluate side-chains 91 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3296 Z= 0.163 Angle : 0.424 4.803 4488 Z= 0.238 Chirality : 0.037 0.129 504 Planarity : 0.004 0.020 530 Dihedral : 15.975 162.948 480 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.78 % Allowed : 17.05 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.43), residues: 374 helix: 2.65 (0.41), residues: 168 sheet: 0.49 (0.53), residues: 86 loop : -1.15 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.002 0.001 HIS B 78 PHE 0.011 0.001 PHE A 43 TYR 0.004 0.001 TYR B 160 ARG 0.000 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8181 (tpt170) cc_final: 0.7774 (ttp-170) REVERT: A 136 LYS cc_start: 0.8733 (pttt) cc_final: 0.8503 (pttt) REVERT: A 154 TYR cc_start: 0.8455 (t80) cc_final: 0.8092 (t80) REVERT: A 155 ASP cc_start: 0.8089 (p0) cc_final: 0.7422 (p0) REVERT: A 194 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 198 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7610 (mmtm) REVERT: A 227 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7924 (m-70) REVERT: B 134 ARG cc_start: 0.8182 (tpt170) cc_final: 0.7772 (ttp-170) REVERT: B 136 LYS cc_start: 0.8728 (pttt) cc_final: 0.8498 (pttt) REVERT: B 154 TYR cc_start: 0.8450 (t80) cc_final: 0.8095 (t80) REVERT: B 155 ASP cc_start: 0.8091 (p0) cc_final: 0.7426 (p0) REVERT: B 194 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 198 LYS cc_start: 0.8483 (mtmt) cc_final: 0.7813 (mmtm) outliers start: 20 outliers final: 19 residues processed: 102 average time/residue: 0.1623 time to fit residues: 20.1262 Evaluate side-chains 98 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 17 optimal weight: 0.0020 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 57 GLN B 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3296 Z= 0.146 Angle : 0.448 6.734 4488 Z= 0.250 Chirality : 0.037 0.128 504 Planarity : 0.004 0.020 530 Dihedral : 15.845 163.052 480 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.20 % Allowed : 18.50 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.43), residues: 374 helix: 2.66 (0.41), residues: 168 sheet: 0.58 (0.53), residues: 86 loop : -1.14 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.002 0.001 HIS B 78 PHE 0.012 0.001 PHE A 43 TYR 0.004 0.001 TYR A 91 ARG 0.000 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.312 Fit side-chains REVERT: A 134 ARG cc_start: 0.8167 (tpt170) cc_final: 0.7750 (ttp-170) REVERT: A 136 LYS cc_start: 0.8722 (pttt) cc_final: 0.8507 (pttt) REVERT: A 154 TYR cc_start: 0.8456 (t80) cc_final: 0.8101 (t80) REVERT: A 155 ASP cc_start: 0.8089 (p0) cc_final: 0.7429 (p0) REVERT: A 194 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 198 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7854 (pttt) REVERT: A 226 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 227 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7744 (m-70) REVERT: B 134 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7745 (ttp-170) REVERT: B 136 LYS cc_start: 0.8718 (pttt) cc_final: 0.8504 (pttt) REVERT: B 154 TYR cc_start: 0.8438 (t80) cc_final: 0.8088 (t80) REVERT: B 155 ASP cc_start: 0.8106 (p0) cc_final: 0.7446 (p0) REVERT: B 194 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 198 LYS cc_start: 0.8485 (mtmt) cc_final: 0.7999 (pttt) REVERT: B 226 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 227 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.7806 (m-70) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.1524 time to fit residues: 17.7385 Evaluate side-chains 94 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 12 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3296 Z= 0.139 Angle : 0.448 6.508 4488 Z= 0.251 Chirality : 0.038 0.127 504 Planarity : 0.004 0.020 530 Dihedral : 15.695 163.533 480 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.62 % Allowed : 19.65 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.42), residues: 374 helix: 2.50 (0.41), residues: 168 sheet: 0.62 (0.53), residues: 86 loop : -1.13 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 128 HIS 0.002 0.001 HIS B 204 PHE 0.013 0.001 PHE A 43 TYR 0.010 0.001 TYR A 91 ARG 0.000 0.000 ARG B 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.385 Fit side-chains REVERT: A 134 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7774 (ttp-170) REVERT: A 136 LYS cc_start: 0.8727 (pttt) cc_final: 0.8515 (pttt) REVERT: A 154 TYR cc_start: 0.8412 (t80) cc_final: 0.8059 (t80) REVERT: A 155 ASP cc_start: 0.8092 (p0) cc_final: 0.7446 (p0) REVERT: A 194 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 198 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7960 (pttt) REVERT: A 226 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 227 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7773 (m-70) REVERT: B 134 ARG cc_start: 0.8202 (tpt170) cc_final: 0.7771 (ttp-170) REVERT: B 136 LYS cc_start: 0.8723 (pttt) cc_final: 0.8511 (pttt) REVERT: B 154 TYR cc_start: 0.8404 (t80) cc_final: 0.8058 (t80) REVERT: B 155 ASP cc_start: 0.8118 (p0) cc_final: 0.7474 (p0) REVERT: B 194 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8306 (mt-10) REVERT: B 198 LYS cc_start: 0.8495 (mtmt) cc_final: 0.7991 (pttt) REVERT: B 226 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 227 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7668 (m90) outliers start: 16 outliers final: 14 residues processed: 114 average time/residue: 0.1574 time to fit residues: 21.4881 Evaluate side-chains 101 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.073820 restraints weight = 6642.782| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.10 r_work: 0.2787 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3296 Z= 0.175 Angle : 0.480 6.222 4488 Z= 0.265 Chirality : 0.038 0.129 504 Planarity : 0.004 0.020 530 Dihedral : 15.761 164.784 480 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.62 % Allowed : 22.54 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.43), residues: 374 helix: 2.50 (0.41), residues: 168 sheet: 0.62 (0.54), residues: 86 loop : -1.05 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.005 0.001 HIS B 227 PHE 0.011 0.001 PHE A 43 TYR 0.004 0.001 TYR A 160 ARG 0.000 0.000 ARG B 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.73 seconds wall clock time: 25 minutes 16.07 seconds (1516.07 seconds total)