Starting phenix.real_space_refine on Sun Mar 10 20:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aza_15757/03_2024/8aza_15757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aza_15757/03_2024/8aza_15757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aza_15757/03_2024/8aza_15757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aza_15757/03_2024/8aza_15757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aza_15757/03_2024/8aza_15757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aza_15757/03_2024/8aza_15757.pdb" } resolution = 3.15 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= -0.001 sd= 0.025 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 Zn 1 6.06 5 S 20 5.16 5 C 3204 2.51 5 N 872 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 183": "OE1" <-> "OE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4970 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 624 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "A" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2327 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 263} Chain breaks: 3 Chain: "B" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2018 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 229} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 336 SG CYS C 200 35.671 18.583 82.528 1.00273.60 S ATOM 359 SG CYS C 203 39.057 18.926 84.298 1.00305.23 S ATOM 564 SG CYS C 227 38.823 16.632 81.459 1.00267.04 S Time building chain proxies: 3.06, per 1000 atoms: 0.62 Number of scatterers: 4970 At special positions: 0 Unit cell: (71.949, 76.911, 95.932, 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) Zn 1 29.99 S 20 16.00 O 873 8.00 N 872 7.00 C 3204 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: 2.85 Conformation dependent library (CDL) restraints added in 802.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 220 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 227 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 203 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 200 " Number of angles added : 3 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 43.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'C' and resid 162 through 170 removed outlier: 3.570A pdb=" N ARG C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 117 through 136 removed outlier: 3.989A pdb=" N LEU A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.012A pdb=" N MET A 193 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 225 removed outlier: 4.066A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 4.093A pdb=" N MET A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 273 Processing helix chain 'A' and resid 282 through 295 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.847A pdb=" N ILE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 60 through 73 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.718A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 136 Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.541A pdb=" N LEU B 167 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 225 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 282 through 297 Proline residue: B 292 - end of helix removed outlier: 3.843A pdb=" N PHE B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.625A pdb=" N PHE B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 189 through 191 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 23 removed outlier: 4.777A pdb=" N ASP A 20 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 36 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 92 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 85 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU A 96 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 81 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.719A pdb=" N LEU A 143 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 26 removed outlier: 4.589A pdb=" N LEU B 21 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 34 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR B 23 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL B 32 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.639A pdb=" N GLY B 83 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 142 through 143 removed outlier: 3.825A pdb=" N LEU B 143 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 154 197 hydrogen bonds defined for protein. 564 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: 1.12 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1581 1.34 - 1.46: 816 1.46 - 1.58: 2673 1.58 - 1.70: 1 1.70 - 1.82: 31 Bond restraints: 5102 Sorted by residual: bond pdb=" CB PRO C 181 " pdb=" CG PRO C 181 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.89e+00 bond pdb=" CA LEU A 309 " pdb=" C LEU A 309 " ideal model delta sigma weight residual 1.524 1.502 0.021 1.32e-02 5.74e+03 2.61e+00 bond pdb=" C LEU A 309 " pdb=" O LEU A 309 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.22e-02 6.72e+03 2.38e+00 bond pdb=" CG PRO C 181 " pdb=" CD PRO C 181 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 1.98e+00 bond pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 ... (remaining 5097 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.05: 212 107.05 - 113.80: 2835 113.80 - 120.54: 1989 120.54 - 127.29: 1795 127.29 - 134.04: 90 Bond angle restraints: 6921 Sorted by residual: angle pdb=" N ASP A 278 " pdb=" CA ASP A 278 " pdb=" C ASP A 278 " ideal model delta sigma weight residual 111.28 117.77 -6.49 1.09e+00 8.42e-01 3.54e+01 angle pdb=" C ASN A 276 " pdb=" N PRO A 277 " pdb=" CA PRO A 277 " ideal model delta sigma weight residual 119.87 124.81 -4.94 1.04e+00 9.25e-01 2.26e+01 angle pdb=" N PRO A 277 " pdb=" CA PRO A 277 " pdb=" C PRO A 277 " ideal model delta sigma weight residual 114.03 119.01 -4.98 1.23e+00 6.61e-01 1.64e+01 angle pdb=" CA PRO C 181 " pdb=" N PRO C 181 " pdb=" CD PRO C 181 " ideal model delta sigma weight residual 112.00 106.47 5.53 1.40e+00 5.10e-01 1.56e+01 angle pdb=" CA LYS B 61 " pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 ... (remaining 6916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2606 17.94 - 35.87: 339 35.87 - 53.81: 101 53.81 - 71.74: 20 71.74 - 89.68: 7 Dihedral angle restraints: 3073 sinusoidal: 1286 harmonic: 1787 Sorted by residual: dihedral pdb=" C ASP A 278 " pdb=" N ASP A 278 " pdb=" CA ASP A 278 " pdb=" CB ASP A 278 " ideal model delta harmonic sigma weight residual -122.60 -133.29 10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" N ASP A 278 " pdb=" C ASP A 278 " pdb=" CA ASP A 278 " pdb=" CB ASP A 278 " ideal model delta harmonic sigma weight residual 122.80 133.27 -10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CA MET A 98 " pdb=" C MET A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta harmonic sigma weight residual 180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 697 0.085 - 0.170: 58 0.170 - 0.254: 2 0.254 - 0.339: 1 0.339 - 0.424: 1 Chirality restraints: 759 Sorted by residual: chirality pdb=" CA ASP A 278 " pdb=" N ASP A 278 " pdb=" C ASP A 278 " pdb=" CB ASP A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CB VAL B 222 " pdb=" CA VAL B 222 " pdb=" CG1 VAL B 222 " pdb=" CG2 VAL B 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU A 279 " pdb=" N GLU A 279 " pdb=" C GLU A 279 " pdb=" CB GLU A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 756 not shown) Planarity restraints: 877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 280 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 281 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 180 " 0.063 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO C 181 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 308 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C GLN A 308 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN A 308 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 309 " 0.013 2.00e-02 2.50e+03 ... (remaining 874 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 525 2.74 - 3.28: 5526 3.28 - 3.82: 9009 3.82 - 4.36: 10348 4.36 - 4.90: 16487 Nonbonded interactions: 41895 Sorted by model distance: nonbonded pdb=" O VAL B 293 " pdb=" OG1 THR B 296 " model vdw 2.202 2.440 nonbonded pdb=" OE1 GLU A 196 " pdb=" OG SER A 207 " model vdw 2.238 2.440 nonbonded pdb=" O ASN A 234 " pdb=" NE2 GLN A 237 " model vdw 2.280 2.520 nonbonded pdb=" NH2 ARG A 247 " pdb=" O TRP A 273 " model vdw 2.303 2.520 nonbonded pdb=" NE2 HIS A 136 " pdb=" OD2 ASP A 211 " model vdw 2.308 2.520 ... (remaining 41890 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 8 through 49 or resid 59 through 171 or resid 206 through \ 228 or resid 247 through 314)) selection = chain 'B' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 5.590 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.760 Find NCS groups from input model: 0.260 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 5102 Z= 0.249 Angle : 0.758 9.671 6921 Z= 0.386 Chirality : 0.049 0.424 759 Planarity : 0.006 0.104 877 Dihedral : 17.832 89.676 1907 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.73 % Allowed : 33.39 % Favored : 65.87 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.00 % 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 (0.34), residues: 588 helix: -0.08 (0.33), residues: 247 sheet: -2.64 (0.61), residues: 63 loop : -0.15 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 220 HIS 0.004 0.001 HIS B 144 PHE 0.014 0.001 PHE A 229 TYR 0.013 0.001 TYR B 134 ARG 0.002 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8022 (ppp) cc_final: 0.7004 (ppp) REVERT: B 61 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8807 (tppt) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.1728 time to fit residues: 17.9515 Evaluate side-chains 72 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 223 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.0030 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN B 86 ASN B 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5102 Z= 0.223 Angle : 0.664 11.351 6921 Z= 0.321 Chirality : 0.044 0.154 759 Planarity : 0.005 0.071 877 Dihedral : 5.235 49.072 670 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.77 % Allowed : 30.83 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.62 (0.34), residues: 588 helix: 0.19 (0.33), residues: 252 sheet: -2.90 (0.56), residues: 65 loop : -0.15 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 118 HIS 0.003 0.001 HIS B 144 PHE 0.012 0.001 PHE A 229 TYR 0.018 0.002 TYR C 191 ARG 0.004 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7900 (mt) cc_final: 0.7686 (pt) REVERT: A 193 MET cc_start: 0.7933 (ppp) cc_final: 0.7270 (ppp) REVERT: A 276 ASN cc_start: 0.8507 (p0) cc_final: 0.8155 (p0) REVERT: B 265 MET cc_start: 0.8548 (mmt) cc_final: 0.8268 (mmt) outliers start: 26 outliers final: 12 residues processed: 92 average time/residue: 0.1424 time to fit residues: 17.7673 Evaluate side-chains 83 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 170 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5102 Z= 0.208 Angle : 0.644 9.852 6921 Z= 0.310 Chirality : 0.044 0.211 759 Planarity : 0.005 0.055 877 Dihedral : 4.732 46.483 664 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.40 % Allowed : 31.38 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.37 (0.35), residues: 588 helix: 0.42 (0.34), residues: 246 sheet: -2.63 (0.61), residues: 57 loop : -0.17 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 118 HIS 0.002 0.001 HIS B 261 PHE 0.012 0.001 PHE A 229 TYR 0.021 0.001 TYR C 191 ARG 0.003 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8062 (mt) cc_final: 0.7831 (pt) REVERT: A 193 MET cc_start: 0.7902 (ppp) cc_final: 0.7415 (ppp) REVERT: A 220 TRP cc_start: 0.6981 (OUTLIER) cc_final: 0.6664 (t60) REVERT: A 276 ASN cc_start: 0.8643 (p0) cc_final: 0.8409 (p0) REVERT: B 98 MET cc_start: 0.1996 (ptp) cc_final: 0.1477 (ptp) REVERT: B 265 MET cc_start: 0.8570 (mmt) cc_final: 0.8173 (mmt) outliers start: 24 outliers final: 10 residues processed: 87 average time/residue: 0.1411 time to fit residues: 16.7974 Evaluate side-chains 75 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 211 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.0000 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5102 Z= 0.213 Angle : 0.653 10.810 6921 Z= 0.311 Chirality : 0.044 0.179 759 Planarity : 0.005 0.047 877 Dihedral : 4.673 44.734 664 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.32 % Allowed : 30.09 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.32 (0.35), residues: 588 helix: 0.51 (0.34), residues: 245 sheet: -2.56 (0.63), residues: 57 loop : -0.19 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 118 HIS 0.002 0.001 HIS B 261 PHE 0.014 0.001 PHE A 229 TYR 0.014 0.001 TYR C 191 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 71 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8197 (mt) cc_final: 0.7971 (pt) REVERT: A 193 MET cc_start: 0.7863 (ppp) cc_final: 0.7425 (ppp) REVERT: A 220 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.6646 (t60) REVERT: B 98 MET cc_start: 0.2155 (OUTLIER) cc_final: 0.1850 (ptp) REVERT: B 265 MET cc_start: 0.8584 (mmt) cc_final: 0.8156 (mmt) outliers start: 29 outliers final: 12 residues processed: 91 average time/residue: 0.1319 time to fit residues: 16.6236 Evaluate side-chains 79 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5102 Z= 0.386 Angle : 0.777 10.058 6921 Z= 0.380 Chirality : 0.048 0.177 759 Planarity : 0.006 0.062 877 Dihedral : 5.037 40.063 664 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 36.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.50 % Allowed : 30.28 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.34), residues: 588 helix: 0.11 (0.33), residues: 248 sheet: -2.68 (0.59), residues: 60 loop : -0.39 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 220 HIS 0.007 0.001 HIS B 261 PHE 0.011 0.002 PHE A 229 TYR 0.017 0.002 TYR C 191 ARG 0.005 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 70 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8299 (mt) cc_final: 0.8080 (pt) REVERT: A 220 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6718 (t60) REVERT: A 275 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8220 (mm-40) REVERT: B 21 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9364 (tt) REVERT: B 98 MET cc_start: 0.2137 (OUTLIER) cc_final: 0.1601 (ptp) REVERT: B 265 MET cc_start: 0.8762 (mmt) cc_final: 0.8145 (mmt) outliers start: 30 outliers final: 16 residues processed: 89 average time/residue: 0.1256 time to fit residues: 15.7123 Evaluate side-chains 84 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 0.0050 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5102 Z= 0.209 Angle : 0.707 11.482 6921 Z= 0.334 Chirality : 0.046 0.279 759 Planarity : 0.005 0.074 877 Dihedral : 4.417 18.384 662 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.04 % Allowed : 31.74 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.51 (0.34), residues: 588 helix: 0.37 (0.34), residues: 246 sheet: -2.26 (0.64), residues: 57 loop : -0.43 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 220 HIS 0.003 0.001 HIS B 159 PHE 0.013 0.001 PHE A 229 TYR 0.016 0.001 TYR B 134 ARG 0.002 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8344 (mt) cc_final: 0.8004 (pt) REVERT: A 220 TRP cc_start: 0.7072 (OUTLIER) cc_final: 0.6618 (t60) REVERT: A 275 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: B 98 MET cc_start: 0.2117 (OUTLIER) cc_final: 0.1398 (ptp) REVERT: B 265 MET cc_start: 0.8669 (mmt) cc_final: 0.8154 (mmm) outliers start: 22 outliers final: 13 residues processed: 85 average time/residue: 0.1409 time to fit residues: 16.4590 Evaluate side-chains 82 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5102 Z= 0.273 Angle : 0.747 15.309 6921 Z= 0.353 Chirality : 0.046 0.240 759 Planarity : 0.006 0.074 877 Dihedral : 4.461 18.257 662 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.14 % Allowed : 31.38 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.58 (0.34), residues: 588 helix: 0.25 (0.34), residues: 245 sheet: -2.30 (0.62), residues: 62 loop : -0.34 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 118 HIS 0.004 0.001 HIS B 261 PHE 0.012 0.001 PHE A 229 TYR 0.018 0.002 TYR A 134 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 67 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8393 (mt) cc_final: 0.8140 (pt) REVERT: A 138 MET cc_start: 0.7795 (mmp) cc_final: 0.7340 (mmp) REVERT: A 193 MET cc_start: 0.7875 (ppp) cc_final: 0.7656 (ppp) REVERT: A 220 TRP cc_start: 0.7160 (OUTLIER) cc_final: 0.6716 (t60) REVERT: A 275 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8326 (mm-40) REVERT: B 93 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7988 (mp) REVERT: B 265 MET cc_start: 0.8704 (mmt) cc_final: 0.8082 (mmt) outliers start: 28 outliers final: 19 residues processed: 84 average time/residue: 0.1349 time to fit residues: 15.7406 Evaluate side-chains 86 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5102 Z= 0.210 Angle : 0.732 15.856 6921 Z= 0.342 Chirality : 0.045 0.186 759 Planarity : 0.006 0.082 877 Dihedral : 4.348 18.017 662 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.04 % Allowed : 32.48 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.55 (0.34), residues: 588 helix: 0.20 (0.33), residues: 246 sheet: -2.05 (0.69), residues: 53 loop : -0.39 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 220 HIS 0.003 0.001 HIS B 159 PHE 0.012 0.001 PHE A 229 TYR 0.016 0.001 TYR B 134 ARG 0.002 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8397 (mt) cc_final: 0.8043 (pt) REVERT: A 138 MET cc_start: 0.7819 (mmp) cc_final: 0.7392 (mmp) REVERT: A 220 TRP cc_start: 0.7282 (OUTLIER) cc_final: 0.6831 (t60) REVERT: A 275 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7907 (mm-40) REVERT: B 98 MET cc_start: 0.1407 (ptp) cc_final: 0.1021 (ptp) REVERT: B 265 MET cc_start: 0.8699 (mmt) cc_final: 0.8183 (mmm) outliers start: 22 outliers final: 19 residues processed: 81 average time/residue: 0.1305 time to fit residues: 14.7941 Evaluate side-chains 86 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.0040 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5102 Z= 0.216 Angle : 0.735 16.455 6921 Z= 0.344 Chirality : 0.045 0.170 759 Planarity : 0.006 0.085 877 Dihedral : 4.268 19.398 662 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.85 % Allowed : 32.84 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.44 (0.35), residues: 588 helix: 0.26 (0.33), residues: 244 sheet: -2.26 (0.64), residues: 62 loop : -0.14 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 220 HIS 0.003 0.001 HIS B 159 PHE 0.014 0.001 PHE A 229 TYR 0.017 0.001 TYR B 134 ARG 0.002 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8386 (mt) cc_final: 0.8042 (pt) REVERT: A 138 MET cc_start: 0.7862 (mmp) cc_final: 0.7511 (mmp) REVERT: A 220 TRP cc_start: 0.7287 (OUTLIER) cc_final: 0.6802 (t60) REVERT: A 275 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7942 (mm-40) REVERT: B 98 MET cc_start: 0.1551 (ptp) cc_final: 0.1340 (ptp) REVERT: B 265 MET cc_start: 0.8642 (mmt) cc_final: 0.8123 (mmm) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.1301 time to fit residues: 14.5756 Evaluate side-chains 86 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5102 Z= 0.216 Angle : 0.733 16.865 6921 Z= 0.343 Chirality : 0.045 0.170 759 Planarity : 0.006 0.084 877 Dihedral : 4.256 20.469 662 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.40 % Allowed : 32.11 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.39 (0.35), residues: 588 helix: 0.22 (0.33), residues: 246 sheet: -2.18 (0.71), residues: 52 loop : -0.14 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 220 HIS 0.003 0.001 HIS B 159 PHE 0.014 0.001 PHE A 229 TYR 0.016 0.001 TYR B 134 ARG 0.003 0.000 ARG A 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 67 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8426 (mt) cc_final: 0.8074 (pt) REVERT: A 138 MET cc_start: 0.7945 (mmp) cc_final: 0.7611 (mmp) REVERT: A 220 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.6867 (t60) REVERT: A 275 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: B 93 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7858 (mp) REVERT: B 98 MET cc_start: 0.1486 (ptp) cc_final: 0.1263 (ptp) REVERT: B 265 MET cc_start: 0.8656 (mmt) cc_final: 0.8130 (mmm) outliers start: 24 outliers final: 19 residues processed: 84 average time/residue: 0.1312 time to fit residues: 15.4336 Evaluate side-chains 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.111883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.092144 restraints weight = 20851.792| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 7.02 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5102 Z= 0.224 Angle : 0.732 16.768 6921 Z= 0.343 Chirality : 0.045 0.165 759 Planarity : 0.006 0.080 877 Dihedral : 4.290 21.425 662 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.22 % Allowed : 32.48 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.39 (0.35), residues: 588 helix: 0.27 (0.34), residues: 244 sheet: -2.23 (0.65), residues: 62 loop : -0.08 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 220 HIS 0.004 0.001 HIS B 159 PHE 0.012 0.001 PHE A 229 TYR 0.015 0.001 TYR B 134 ARG 0.003 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1460.44 seconds wall clock time: 27 minutes 11.88 seconds (1631.88 seconds total)