Starting phenix.real_space_refine on Thu Nov 14 07:24:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/11_2024/8ey2_28666.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/11_2024/8ey2_28666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/11_2024/8ey2_28666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/11_2024/8ey2_28666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/11_2024/8ey2_28666.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/11_2024/8ey2_28666.cif" } resolution = 3.5 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= 1.000 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 46 5.16 5 C 3108 2.51 5 N 836 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Time building chain proxies: 6.50, per 1000 atoms: 1.32 Number of scatterers: 4908 At special positions: 0 Unit cell: (72.483, 86.849, 74.442, 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 46 16.00 O 918 8.00 N 836 7.00 C 3108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 1.2 seconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 27.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.549A pdb=" N MET B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 118 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.949A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.120A pdb=" N LYS B 102 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR B 118 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.904A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1612 1.34 - 1.46: 1160 1.46 - 1.58: 2176 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 5016 Sorted by residual: bond pdb=" CG LEU B 32 " pdb=" CD1 LEU B 32 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB MET A 264 " pdb=" CG MET A 264 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.04e-01 bond pdb=" CG LEU B 272 " pdb=" CD1 LEU B 272 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CG LEU C -1 " pdb=" CD2 LEU C -1 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.95e-01 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.59e-01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 6682 1.94 - 3.88: 119 3.88 - 5.82: 6 5.82 - 7.75: 1 7.75 - 9.69: 2 Bond angle restraints: 6810 Sorted by residual: angle pdb=" N VAL B 13 " pdb=" CA VAL B 13 " pdb=" C VAL B 13 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N VAL A 13 " pdb=" CA VAL A 13 " pdb=" C VAL A 13 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA LEU C -1 " pdb=" CB LEU C -1 " pdb=" CG LEU C -1 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.67e+00 angle pdb=" CA LEU D -1 " pdb=" CB LEU D -1 " pdb=" CG LEU D -1 " ideal model delta sigma weight residual 116.30 125.27 -8.97 3.50e+00 8.16e-02 6.57e+00 angle pdb=" C VAL C -2 " pdb=" N LEU C -1 " pdb=" CA LEU C -1 " ideal model delta sigma weight residual 121.26 124.71 -3.45 1.59e+00 3.96e-01 4.70e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 2616 14.12 - 28.24: 240 28.24 - 42.35: 88 42.35 - 56.47: 12 56.47 - 70.59: 6 Dihedral angle restraints: 2962 sinusoidal: 1142 harmonic: 1820 Sorted by residual: dihedral pdb=" CA GLN C 0 " pdb=" C GLN C 0 " pdb=" N SER C 1 " pdb=" CA SER C 1 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C -1 " pdb=" C LEU C -1 " pdb=" N GLN C 0 " pdb=" CA GLN C 0 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA THR B 175 " pdb=" C THR B 175 " pdb=" N ASP B 176 " pdb=" CA ASP B 176 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 447 0.031 - 0.062: 218 0.062 - 0.093: 74 0.093 - 0.123: 27 0.123 - 0.154: 2 Chirality restraints: 768 Sorted by residual: chirality pdb=" CG LEU D -1 " pdb=" CB LEU D -1 " pdb=" CD1 LEU D -1 " pdb=" CD2 LEU D -1 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA VAL C -2 " pdb=" N VAL C -2 " pdb=" C VAL C -2 " pdb=" CB VAL C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 765 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 51 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 52 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 51 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 3 " 0.011 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 3 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 3 " 0.002 2.00e-02 2.50e+03 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 134 2.70 - 3.25: 4949 3.25 - 3.80: 8026 3.80 - 4.35: 10191 4.35 - 4.90: 17041 Nonbonded interactions: 40341 Sorted by model distance: nonbonded pdb=" OG1 THR A 292 " pdb=" OD2 ASP A 295 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR B 292 " pdb=" OD2 ASP B 295 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR A 209 " pdb=" OG SER A 254 " model vdw 2.177 3.040 nonbonded pdb=" O THR A 26 " pdb=" OG SER C 1 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR B 45 " pdb=" OD1 ASP B 48 " model vdw 2.217 3.040 ... (remaining 40336 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' and (resid 1 through 116 or resid 118 through 306)) selection = (chain 'B' and (resid 1 through 116 or resid 118 through 306)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.720 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 19.370 Find NCS groups from input model: 0.170 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5016 Z= 0.189 Angle : 0.600 9.693 6810 Z= 0.315 Chirality : 0.042 0.154 768 Planarity : 0.005 0.055 884 Dihedral : 13.039 70.588 1798 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.29 (0.35), residues: 628 helix: 1.88 (0.44), residues: 150 sheet: -1.02 (0.54), residues: 102 loop : -0.82 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 218 HIS 0.007 0.001 HIS A 41 PHE 0.026 0.001 PHE D 3 TYR 0.024 0.002 TYR A 239 ARG 0.002 0.000 ARG D 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8298 (p0) cc_final: 0.7777 (p0) REVERT: A 49 MET cc_start: 0.5976 (mmt) cc_final: 0.5328 (tpp) REVERT: A 100 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8622 (mtpp) REVERT: A 121 SER cc_start: 0.8685 (m) cc_final: 0.8476 (p) REVERT: A 214 ASN cc_start: 0.8538 (t0) cc_final: 0.8086 (t0) REVERT: A 232 LEU cc_start: 0.7767 (mt) cc_final: 0.7127 (mp) REVERT: A 286 LEU cc_start: 0.8563 (mt) cc_final: 0.8051 (pt) REVERT: C 4 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7848 (ttp80) REVERT: B 34 ASP cc_start: 0.8166 (p0) cc_final: 0.7786 (p0) REVERT: B 121 SER cc_start: 0.8664 (m) cc_final: 0.8438 (p) REVERT: B 214 ASN cc_start: 0.8604 (t0) cc_final: 0.8103 (t0) REVERT: B 232 LEU cc_start: 0.7754 (mt) cc_final: 0.7142 (mp) REVERT: B 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8058 (pt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1786 time to fit residues: 38.9049 Evaluate side-chains 136 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5016 Z= 0.200 Angle : 0.662 9.415 6810 Z= 0.337 Chirality : 0.043 0.200 768 Planarity : 0.005 0.045 884 Dihedral : 5.121 20.673 680 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.65 % Allowed : 11.90 % Favored : 86.45 % 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: -0.75 (0.33), residues: 628 helix: 0.71 (0.38), residues: 168 sheet: -0.98 (0.53), residues: 102 loop : -0.92 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 218 HIS 0.009 0.001 HIS B 41 PHE 0.015 0.001 PHE D 3 TYR 0.010 0.002 TYR A 239 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8261 (p0) cc_final: 0.7716 (p0) REVERT: A 49 MET cc_start: 0.5903 (mmt) cc_final: 0.4311 (mmm) REVERT: A 214 ASN cc_start: 0.8612 (t0) cc_final: 0.8214 (t0) REVERT: A 286 LEU cc_start: 0.8533 (mt) cc_final: 0.8047 (pt) REVERT: C 4 ARG cc_start: 0.8283 (ttt90) cc_final: 0.7841 (ttp80) REVERT: B 34 ASP cc_start: 0.8152 (p0) cc_final: 0.7727 (p0) REVERT: B 214 ASN cc_start: 0.8766 (t0) cc_final: 0.8461 (t0) REVERT: B 286 LEU cc_start: 0.8532 (mt) cc_final: 0.8030 (pt) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.1578 time to fit residues: 27.4806 Evaluate side-chains 128 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5016 Z= 0.185 Angle : 0.621 6.788 6810 Z= 0.317 Chirality : 0.042 0.146 768 Planarity : 0.004 0.039 884 Dihedral : 5.069 20.857 680 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.20 % Allowed : 14.65 % Favored : 83.15 % 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: -1.01 (0.32), residues: 628 helix: 0.45 (0.37), residues: 172 sheet: -1.57 (0.55), residues: 78 loop : -1.00 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 218 HIS 0.008 0.001 HIS B 41 PHE 0.011 0.001 PHE B 181 TYR 0.022 0.002 TYR B 161 ARG 0.002 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8223 (p0) cc_final: 0.7672 (p0) REVERT: A 49 MET cc_start: 0.6085 (mmt) cc_final: 0.5651 (tpp) REVERT: A 214 ASN cc_start: 0.8625 (t0) cc_final: 0.8215 (t0) REVERT: A 286 LEU cc_start: 0.8519 (mt) cc_final: 0.7998 (pt) REVERT: C 4 ARG cc_start: 0.8358 (ttt90) cc_final: 0.7897 (ttp80) REVERT: B 34 ASP cc_start: 0.8164 (p0) cc_final: 0.7723 (p0) REVERT: B 286 LEU cc_start: 0.8434 (mt) cc_final: 0.7936 (pt) outliers start: 12 outliers final: 9 residues processed: 116 average time/residue: 0.1833 time to fit residues: 27.3740 Evaluate side-chains 122 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5016 Z= 0.233 Angle : 0.613 8.003 6810 Z= 0.316 Chirality : 0.042 0.131 768 Planarity : 0.005 0.038 884 Dihedral : 5.043 22.623 680 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.38 % Allowed : 15.02 % Favored : 82.60 % 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: -0.71 (0.33), residues: 628 helix: 0.92 (0.39), residues: 172 sheet: -2.20 (0.65), residues: 56 loop : -0.83 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 218 HIS 0.008 0.001 HIS B 41 PHE 0.013 0.001 PHE B 181 TYR 0.034 0.002 TYR B 161 ARG 0.002 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8231 (p0) cc_final: 0.7808 (p0) REVERT: A 214 ASN cc_start: 0.8670 (t0) cc_final: 0.8262 (t0) REVERT: A 286 LEU cc_start: 0.8528 (mt) cc_final: 0.8028 (pt) REVERT: C 4 ARG cc_start: 0.8503 (ttt90) cc_final: 0.7968 (ttp80) REVERT: B 34 ASP cc_start: 0.8199 (p0) cc_final: 0.7803 (p0) REVERT: B 286 LEU cc_start: 0.8451 (mt) cc_final: 0.7967 (pt) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.1499 time to fit residues: 23.4898 Evaluate side-chains 121 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 5016 Z= 0.438 Angle : 0.744 10.628 6810 Z= 0.384 Chirality : 0.046 0.197 768 Planarity : 0.005 0.037 884 Dihedral : 5.562 26.972 680 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.56 % Allowed : 17.58 % Favored : 79.85 % 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: -0.66 (0.33), residues: 628 helix: 1.07 (0.40), residues: 156 sheet: -1.39 (0.59), residues: 80 loop : -0.85 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.012 0.002 HIS A 41 PHE 0.012 0.002 PHE B 219 TYR 0.033 0.003 TYR A 161 ARG 0.004 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8767 (t0) cc_final: 0.8552 (t0) REVERT: A 214 ASN cc_start: 0.8753 (t0) cc_final: 0.8297 (t0) REVERT: A 286 LEU cc_start: 0.8564 (mt) cc_final: 0.8148 (pt) REVERT: C 4 ARG cc_start: 0.8640 (ttt90) cc_final: 0.8038 (ttp80) REVERT: B 34 ASP cc_start: 0.8263 (p0) cc_final: 0.7821 (p0) REVERT: B 95 ASN cc_start: 0.8629 (t0) cc_final: 0.8328 (t0) REVERT: B 286 LEU cc_start: 0.8530 (mt) cc_final: 0.8095 (pt) outliers start: 14 outliers final: 13 residues processed: 120 average time/residue: 0.1357 time to fit residues: 21.8990 Evaluate side-chains 122 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 265 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5016 Z= 0.202 Angle : 0.643 9.837 6810 Z= 0.331 Chirality : 0.043 0.248 768 Planarity : 0.004 0.036 884 Dihedral : 5.296 25.246 680 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.20 % Allowed : 18.32 % Favored : 79.49 % 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: -0.90 (0.32), residues: 628 helix: 0.77 (0.39), residues: 172 sheet: -2.44 (0.63), residues: 56 loop : -0.94 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 218 HIS 0.007 0.001 HIS A 41 PHE 0.010 0.001 PHE A 181 TYR 0.031 0.002 TYR A 161 ARG 0.001 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8232 (p0) cc_final: 0.7799 (p0) REVERT: A 95 ASN cc_start: 0.8698 (t0) cc_final: 0.8397 (t0) REVERT: A 119 ASN cc_start: 0.8021 (t0) cc_final: 0.7789 (t0) REVERT: A 214 ASN cc_start: 0.8701 (t0) cc_final: 0.8285 (t0) REVERT: A 264 MET cc_start: 0.7128 (ptp) cc_final: 0.6925 (ptp) REVERT: A 286 LEU cc_start: 0.8516 (mt) cc_final: 0.8089 (pt) REVERT: C 4 ARG cc_start: 0.8627 (ttt90) cc_final: 0.8003 (ttp80) REVERT: B 34 ASP cc_start: 0.8226 (p0) cc_final: 0.7823 (p0) REVERT: B 95 ASN cc_start: 0.8523 (t0) cc_final: 0.8181 (t0) REVERT: B 119 ASN cc_start: 0.8060 (t0) cc_final: 0.7799 (t0) REVERT: B 286 LEU cc_start: 0.8518 (mt) cc_final: 0.8069 (pt) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.1368 time to fit residues: 23.0325 Evaluate side-chains 121 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5016 Z= 0.188 Angle : 0.634 9.656 6810 Z= 0.328 Chirality : 0.043 0.195 768 Planarity : 0.004 0.036 884 Dihedral : 5.277 24.146 680 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.38 % Allowed : 19.41 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.33), residues: 628 helix: 0.88 (0.39), residues: 172 sheet: -2.43 (0.63), residues: 56 loop : -0.97 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.006 0.001 HIS A 41 PHE 0.010 0.001 PHE A 181 TYR 0.031 0.002 TYR A 161 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8241 (p0) cc_final: 0.7828 (p0) REVERT: A 95 ASN cc_start: 0.8706 (t0) cc_final: 0.8485 (t0) REVERT: A 119 ASN cc_start: 0.8048 (t0) cc_final: 0.7797 (t0) REVERT: A 214 ASN cc_start: 0.8676 (t0) cc_final: 0.8255 (t0) REVERT: A 286 LEU cc_start: 0.8489 (mt) cc_final: 0.8062 (pt) REVERT: C 4 ARG cc_start: 0.8624 (ttt90) cc_final: 0.8063 (ttp80) REVERT: D 4 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7808 (ptm160) REVERT: B 95 ASN cc_start: 0.8510 (t0) cc_final: 0.8286 (t0) REVERT: B 270 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: B 286 LEU cc_start: 0.8540 (mt) cc_final: 0.8120 (pt) outliers start: 13 outliers final: 10 residues processed: 120 average time/residue: 0.1254 time to fit residues: 20.5296 Evaluate side-chains 117 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 270 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5016 Z= 0.255 Angle : 0.701 12.460 6810 Z= 0.355 Chirality : 0.044 0.177 768 Planarity : 0.004 0.036 884 Dihedral : 5.483 28.654 680 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.38 % Allowed : 19.78 % Favored : 77.84 % 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: -0.95 (0.33), residues: 628 helix: 0.73 (0.39), residues: 172 sheet: -2.43 (0.63), residues: 56 loop : -0.98 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.008 0.001 HIS B 41 PHE 0.012 0.001 PHE B 181 TYR 0.029 0.002 TYR A 161 ARG 0.001 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8258 (p0) cc_final: 0.7825 (p0) REVERT: A 119 ASN cc_start: 0.8087 (t0) cc_final: 0.7882 (t0) REVERT: A 286 LEU cc_start: 0.8502 (mt) cc_final: 0.8103 (pt) REVERT: C 4 ARG cc_start: 0.8638 (ttt90) cc_final: 0.8000 (ttp80) REVERT: B 34 ASP cc_start: 0.8182 (p0) cc_final: 0.7799 (p0) REVERT: B 270 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: B 286 LEU cc_start: 0.8541 (mt) cc_final: 0.8112 (pt) outliers start: 13 outliers final: 10 residues processed: 117 average time/residue: 0.1335 time to fit residues: 21.2313 Evaluate side-chains 120 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 270 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5016 Z= 0.195 Angle : 0.676 11.941 6810 Z= 0.343 Chirality : 0.043 0.169 768 Planarity : 0.004 0.037 884 Dihedral : 5.348 29.814 680 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.01 % Allowed : 20.88 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.33), residues: 628 helix: 0.85 (0.39), residues: 172 sheet: -2.37 (0.63), residues: 56 loop : -0.96 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.006 0.001 HIS A 41 PHE 0.014 0.001 PHE B 181 TYR 0.030 0.002 TYR A 161 ARG 0.001 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8252 (p0) cc_final: 0.7849 (p0) REVERT: A 214 ASN cc_start: 0.8615 (t0) cc_final: 0.8198 (t0) REVERT: A 264 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6003 (ptp) REVERT: A 286 LEU cc_start: 0.8452 (mt) cc_final: 0.8066 (pt) REVERT: C 4 ARG cc_start: 0.8650 (ttt90) cc_final: 0.8009 (ttp80) REVERT: D -1 LEU cc_start: 0.7641 (tt) cc_final: 0.7309 (tt) REVERT: B 34 ASP cc_start: 0.8167 (p0) cc_final: 0.7774 (p0) REVERT: B 49 MET cc_start: 0.6471 (mmt) cc_final: 0.4955 (mmt) REVERT: B 286 LEU cc_start: 0.8549 (mt) cc_final: 0.8135 (pt) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.1310 time to fit residues: 20.5179 Evaluate side-chains 112 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.0020 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5016 Z= 0.184 Angle : 0.662 11.873 6810 Z= 0.341 Chirality : 0.042 0.166 768 Planarity : 0.004 0.037 884 Dihedral : 5.386 33.185 680 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.83 % Allowed : 21.79 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.33), residues: 628 helix: 0.83 (0.39), residues: 172 sheet: -2.32 (0.62), residues: 56 loop : -1.07 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 207 HIS 0.006 0.001 HIS A 41 PHE 0.014 0.001 PHE B 181 TYR 0.030 0.002 TYR A 161 ARG 0.001 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8262 (p0) cc_final: 0.7874 (p0) REVERT: A 214 ASN cc_start: 0.8624 (t0) cc_final: 0.8222 (t0) REVERT: A 286 LEU cc_start: 0.8436 (mt) cc_final: 0.8070 (pt) REVERT: C 4 ARG cc_start: 0.8638 (ttt90) cc_final: 0.7838 (ttp80) REVERT: B 34 ASP cc_start: 0.8189 (p0) cc_final: 0.7801 (p0) REVERT: B 286 LEU cc_start: 0.8552 (mt) cc_final: 0.8137 (pt) outliers start: 10 outliers final: 10 residues processed: 112 average time/residue: 0.1395 time to fit residues: 21.0117 Evaluate side-chains 113 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 0.0050 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.139677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119171 restraints weight = 12891.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.124513 restraints weight = 5287.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127918 restraints weight = 2960.418| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5016 Z= 0.178 Angle : 0.671 11.641 6810 Z= 0.344 Chirality : 0.043 0.163 768 Planarity : 0.004 0.037 884 Dihedral : 5.394 34.945 680 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.65 % Allowed : 22.16 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.98 (0.32), residues: 628 helix: 0.92 (0.39), residues: 172 sheet: -2.33 (0.61), residues: 56 loop : -1.14 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 207 HIS 0.015 0.002 HIS B 41 PHE 0.015 0.001 PHE B 181 TYR 0.029 0.002 TYR A 161 ARG 0.001 0.000 ARG C 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.39 seconds wall clock time: 27 minutes 15.13 seconds (1635.13 seconds total)