Starting phenix.real_space_refine on Sun Mar 10 16:05:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/03_2024/7pqg_13593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/03_2024/7pqg_13593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/03_2024/7pqg_13593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/03_2024/7pqg_13593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/03_2024/7pqg_13593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/03_2024/7pqg_13593.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 31 5.16 5 C 2134 2.51 5 N 522 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 38": "NH1" <-> "NH2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3251 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 955 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2296 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Time building chain proxies: 2.25, per 1000 atoms: 0.69 Number of scatterers: 3251 At special positions: 0 Unit cell: (61.488, 75.6, 99.792, 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 31 16.00 O 564 8.00 N 522 7.00 C 2134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 67.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.715A pdb=" N ASP B 90 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.610A pdb=" N TYR B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 44 removed outlier: 4.031A pdb=" N ASP A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.588A pdb=" N ALA A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 removed outlier: 3.686A pdb=" N MET A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.970A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix removed outlier: 3.785A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.475A pdb=" N ASP A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 210 removed outlier: 3.590A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.281A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.568A pdb=" N CYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.535A pdb=" N LEU A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.800A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.933A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 98 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 115 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.707A pdb=" N VAL B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 598 1.45 - 1.57: 1814 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 3324 Sorted by residual: bond pdb=" CG GLN A 293 " pdb=" CD GLN A 293 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" N LYS A 189 " pdb=" CA LYS A 189 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" C VAL A 187 " pdb=" N ILE A 188 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.26e-02 6.30e+03 1.21e+00 bond pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" N THR A 13 " pdb=" CA THR A 13 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.94e-01 ... (remaining 3319 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.11: 60 104.11 - 111.58: 1467 111.58 - 119.06: 1210 119.06 - 126.53: 1726 126.53 - 134.00: 43 Bond angle restraints: 4506 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 110.62 114.37 -3.75 1.02e+00 9.61e-01 1.35e+01 angle pdb=" N GLN A 293 " pdb=" CA GLN A 293 " pdb=" CB GLN A 293 " ideal model delta sigma weight residual 110.28 115.50 -5.22 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 110.62 114.01 -3.39 1.02e+00 9.61e-01 1.10e+01 angle pdb=" N GLN A 261 " pdb=" CA GLN A 261 " pdb=" C GLN A 261 " ideal model delta sigma weight residual 109.96 114.98 -5.02 1.58e+00 4.01e-01 1.01e+01 angle pdb=" N TYR A 186 " pdb=" CA TYR A 186 " pdb=" C TYR A 186 " ideal model delta sigma weight residual 113.50 109.63 3.87 1.23e+00 6.61e-01 9.89e+00 ... (remaining 4501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1809 17.01 - 34.02: 131 34.02 - 51.03: 22 51.03 - 68.04: 3 68.04 - 85.05: 3 Dihedral angle restraints: 1968 sinusoidal: 758 harmonic: 1210 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 164.83 -71.83 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CA LYS A 309 " pdb=" C LYS A 309 " pdb=" N PHE A 310 " pdb=" CA PHE A 310 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLU B 89 " pdb=" C GLU B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 1965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 335 0.037 - 0.074: 120 0.074 - 0.112: 50 0.112 - 0.149: 19 0.149 - 0.186: 3 Chirality restraints: 527 Sorted by residual: chirality pdb=" CB ILE A 88 " pdb=" CA ILE A 88 " pdb=" CG1 ILE A 88 " pdb=" CG2 ILE A 88 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA MET A 229 " pdb=" N MET A 229 " pdb=" C MET A 229 " pdb=" CB MET A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CG LEU A 79 " pdb=" CB LEU A 79 " pdb=" CD1 LEU A 79 " pdb=" CD2 LEU A 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 524 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 109 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 110 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 289 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C TYR A 289 " -0.033 2.00e-02 2.50e+03 pdb=" O TYR A 289 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A 290 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.011 2.00e-02 2.50e+03 1.33e-02 3.08e+00 pdb=" CG PHE A 36 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 389 2.74 - 3.28: 3900 3.28 - 3.82: 5577 3.82 - 4.36: 6655 4.36 - 4.90: 10332 Nonbonded interactions: 26853 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" OG1 THR A 127 " model vdw 2.204 2.440 nonbonded pdb=" O TRP B 53 " pdb=" NH2 ARG B 72 " model vdw 2.223 2.520 nonbonded pdb=" O LYS A 113 " pdb=" NH2 ARG A 249 " model vdw 2.225 2.520 nonbonded pdb=" OG SER B 7 " pdb=" OG SER B 21 " model vdw 2.247 2.440 nonbonded pdb=" O ILE A 168 " pdb=" OG1 THR A 171 " model vdw 2.252 2.440 ... (remaining 26848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 0.050 3324 Z= 0.271 Angle : 0.880 7.914 4506 Z= 0.481 Chirality : 0.049 0.186 527 Planarity : 0.006 0.049 551 Dihedral : 12.564 85.048 1195 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % 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 (0.41), residues: 419 helix: 0.44 (0.32), residues: 241 sheet: -3.49 (0.73), residues: 34 loop : -1.44 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 116 HIS 0.003 0.001 HIS A 54 PHE 0.031 0.003 PHE A 36 TYR 0.018 0.002 TYR A 69 ARG 0.013 0.002 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7405 (mmm160) REVERT: B 93 LEU cc_start: 0.8568 (tp) cc_final: 0.8307 (tp) REVERT: A 36 PHE cc_start: 0.8694 (m-80) cc_final: 0.8474 (m-80) REVERT: A 52 LYS cc_start: 0.8498 (mtmm) cc_final: 0.7612 (tppt) REVERT: A 108 PHE cc_start: 0.9052 (m-80) cc_final: 0.8737 (m-80) REVERT: A 129 LEU cc_start: 0.8905 (mm) cc_final: 0.8299 (mm) REVERT: A 133 MET cc_start: 0.8119 (mpp) cc_final: 0.7717 (mpp) REVERT: A 215 MET cc_start: 0.8918 (mpp) cc_final: 0.8576 (mpp) REVERT: A 234 PHE cc_start: 0.8544 (m-80) cc_final: 0.8226 (m-80) REVERT: A 288 LEU cc_start: 0.9295 (mt) cc_final: 0.8965 (mt) REVERT: A 290 MET cc_start: 0.8966 (tmm) cc_final: 0.8710 (tmm) REVERT: A 291 ILE cc_start: 0.9400 (pt) cc_final: 0.8852 (pt) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1565 time to fit residues: 26.6649 Evaluate side-chains 118 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN B 39 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3324 Z= 0.258 Angle : 0.859 8.394 4506 Z= 0.448 Chirality : 0.051 0.188 527 Planarity : 0.005 0.033 551 Dihedral : 5.666 20.072 454 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.96 % Allowed : 12.89 % Favored : 85.15 % 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: -0.96 (0.41), residues: 419 helix: 0.38 (0.32), residues: 250 sheet: -2.68 (0.73), residues: 44 loop : -1.75 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.002 0.001 HIS A 54 PHE 0.025 0.003 PHE A 231 TYR 0.022 0.002 TYR A 289 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6078 (tmm-80) REVERT: A 36 PHE cc_start: 0.8601 (m-80) cc_final: 0.8388 (m-80) REVERT: A 38 ILE cc_start: 0.9619 (pt) cc_final: 0.9410 (pt) REVERT: A 108 PHE cc_start: 0.9047 (m-80) cc_final: 0.8615 (m-80) REVERT: A 112 MET cc_start: 0.7631 (ppp) cc_final: 0.6125 (ppp) REVERT: A 129 LEU cc_start: 0.8881 (mm) cc_final: 0.8136 (mm) REVERT: A 133 MET cc_start: 0.8150 (mpp) cc_final: 0.7914 (mpp) REVERT: A 182 GLN cc_start: 0.8804 (mm110) cc_final: 0.8558 (mm-40) REVERT: A 215 MET cc_start: 0.8797 (mpp) cc_final: 0.8468 (mpp) REVERT: A 221 HIS cc_start: 0.8018 (m-70) cc_final: 0.7403 (m-70) REVERT: A 234 PHE cc_start: 0.8614 (m-80) cc_final: 0.8281 (m-80) REVERT: A 264 GLN cc_start: 0.8848 (mp10) cc_final: 0.8612 (mp10) REVERT: A 291 ILE cc_start: 0.9392 (pt) cc_final: 0.8700 (pt) outliers start: 7 outliers final: 3 residues processed: 130 average time/residue: 0.1613 time to fit residues: 25.0989 Evaluate side-chains 118 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 GLN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN B 39 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3324 Z= 0.272 Angle : 0.851 8.466 4506 Z= 0.447 Chirality : 0.052 0.315 527 Planarity : 0.005 0.060 551 Dihedral : 5.531 20.349 454 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 30.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.64 % Allowed : 18.49 % Favored : 77.87 % 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: -1.17 (0.41), residues: 419 helix: 0.12 (0.32), residues: 253 sheet: -2.47 (0.80), residues: 44 loop : -1.80 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 56 HIS 0.003 0.001 HIS A 54 PHE 0.025 0.002 PHE A 128 TYR 0.026 0.002 TYR B 32 ARG 0.006 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.7648 (p90) cc_final: 0.7295 (p90) REVERT: B 38 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7701 (mmm-85) REVERT: B 76 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8498 (tptp) REVERT: B 83 MET cc_start: 0.7966 (ppp) cc_final: 0.7504 (ppp) REVERT: A 34 MET cc_start: 0.8773 (tmm) cc_final: 0.8503 (tmm) REVERT: A 35 LEU cc_start: 0.9380 (mt) cc_final: 0.9100 (mt) REVERT: A 104 LEU cc_start: 0.8554 (pt) cc_final: 0.7407 (pp) REVERT: A 108 PHE cc_start: 0.9061 (m-80) cc_final: 0.8532 (m-80) REVERT: A 112 MET cc_start: 0.7704 (ppp) cc_final: 0.6315 (ppp) REVERT: A 215 MET cc_start: 0.8642 (mpp) cc_final: 0.8362 (mpp) REVERT: A 234 PHE cc_start: 0.8658 (m-80) cc_final: 0.8278 (m-80) REVERT: A 290 MET cc_start: 0.8852 (tmm) cc_final: 0.8612 (tmm) REVERT: A 291 ILE cc_start: 0.9173 (pt) cc_final: 0.8908 (pt) REVERT: A 296 GLU cc_start: 0.8910 (pt0) cc_final: 0.8518 (pt0) outliers start: 13 outliers final: 7 residues processed: 135 average time/residue: 0.1526 time to fit residues: 24.8557 Evaluate side-chains 124 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.249 Angle : 0.867 11.137 4506 Z= 0.440 Chirality : 0.051 0.291 527 Planarity : 0.005 0.028 551 Dihedral : 5.474 20.618 454 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.92 % Allowed : 20.17 % Favored : 75.91 % 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: -1.12 (0.42), residues: 419 helix: 0.20 (0.32), residues: 252 sheet: -2.37 (0.80), residues: 44 loop : -1.91 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 56 HIS 0.002 0.001 HIS A 54 PHE 0.051 0.003 PHE A 36 TYR 0.020 0.001 TYR B 32 ARG 0.004 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: B 46 GLU cc_start: 0.8749 (pp20) cc_final: 0.8478 (pp20) REVERT: B 76 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8521 (tptp) REVERT: B 83 MET cc_start: 0.8013 (ppp) cc_final: 0.7462 (ppp) REVERT: B 93 LEU cc_start: 0.8635 (tp) cc_final: 0.7586 (tp) REVERT: A 34 MET cc_start: 0.8772 (tmm) cc_final: 0.8477 (tmm) REVERT: A 35 LEU cc_start: 0.9357 (mt) cc_final: 0.8994 (mt) REVERT: A 104 LEU cc_start: 0.8716 (pt) cc_final: 0.7374 (pp) REVERT: A 108 PHE cc_start: 0.9054 (m-80) cc_final: 0.8495 (m-80) REVERT: A 112 MET cc_start: 0.7730 (ppp) cc_final: 0.6336 (ppp) REVERT: A 215 MET cc_start: 0.8558 (mpp) cc_final: 0.8164 (mpp) REVERT: A 234 PHE cc_start: 0.8601 (m-80) cc_final: 0.8180 (m-80) REVERT: A 290 MET cc_start: 0.8965 (tmm) cc_final: 0.8661 (tmm) REVERT: A 291 ILE cc_start: 0.9201 (pt) cc_final: 0.8866 (pt) REVERT: A 296 GLU cc_start: 0.8879 (pt0) cc_final: 0.8536 (pt0) outliers start: 14 outliers final: 8 residues processed: 129 average time/residue: 0.1587 time to fit residues: 24.4140 Evaluate side-chains 123 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.251 Angle : 0.878 10.516 4506 Z= 0.449 Chirality : 0.053 0.376 527 Planarity : 0.005 0.035 551 Dihedral : 5.452 21.084 454 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.64 % Allowed : 24.09 % Favored : 72.27 % 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: -1.16 (0.41), residues: 419 helix: 0.11 (0.32), residues: 251 sheet: -2.28 (0.80), residues: 44 loop : -1.80 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.002 0.001 HIS A 221 PHE 0.046 0.003 PHE A 36 TYR 0.025 0.002 TYR B 32 ARG 0.004 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: B 76 LYS cc_start: 0.8901 (mtmm) cc_final: 0.8525 (tptp) REVERT: B 83 MET cc_start: 0.7978 (ppp) cc_final: 0.6851 (ppp) REVERT: B 93 LEU cc_start: 0.8763 (tp) cc_final: 0.7879 (tp) REVERT: A 31 LEU cc_start: 0.9594 (mt) cc_final: 0.9342 (mt) REVERT: A 34 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8437 (tmm) REVERT: A 35 LEU cc_start: 0.9319 (mt) cc_final: 0.8945 (mt) REVERT: A 104 LEU cc_start: 0.8619 (pt) cc_final: 0.7327 (pp) REVERT: A 108 PHE cc_start: 0.9077 (m-80) cc_final: 0.8614 (m-80) REVERT: A 112 MET cc_start: 0.7796 (ppp) cc_final: 0.6416 (ppp) REVERT: A 147 ASP cc_start: 0.8597 (m-30) cc_final: 0.8133 (p0) REVERT: A 215 MET cc_start: 0.8600 (mpp) cc_final: 0.8178 (mpp) REVERT: A 234 PHE cc_start: 0.8589 (m-80) cc_final: 0.8197 (m-80) REVERT: A 290 MET cc_start: 0.8950 (tmm) cc_final: 0.8641 (tmm) REVERT: A 291 ILE cc_start: 0.9168 (pt) cc_final: 0.8769 (pt) outliers start: 13 outliers final: 7 residues processed: 124 average time/residue: 0.1597 time to fit residues: 23.5387 Evaluate side-chains 123 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.0570 chunk 22 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.230 Angle : 0.912 11.856 4506 Z= 0.455 Chirality : 0.052 0.306 527 Planarity : 0.005 0.034 551 Dihedral : 5.407 20.921 454 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 29.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.20 % Allowed : 25.77 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.41), residues: 419 helix: 0.04 (0.31), residues: 253 sheet: -2.35 (0.78), residues: 44 loop : -1.97 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.005 0.002 HIS A 221 PHE 0.046 0.003 PHE A 36 TYR 0.019 0.002 TYR B 32 ARG 0.004 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7494 (mmm160) cc_final: 0.6822 (mmm160) REVERT: B 38 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7482 (mmm-85) REVERT: B 67 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7973 (mtp-110) REVERT: B 76 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8539 (tptp) REVERT: B 80 TYR cc_start: 0.8238 (t80) cc_final: 0.7391 (t80) REVERT: B 82 GLN cc_start: 0.7956 (tp40) cc_final: 0.7172 (tp40) REVERT: B 93 LEU cc_start: 0.8738 (tp) cc_final: 0.7768 (tp) REVERT: A 31 LEU cc_start: 0.9584 (mt) cc_final: 0.9340 (mt) REVERT: A 34 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8458 (tmm) REVERT: A 35 LEU cc_start: 0.9292 (mt) cc_final: 0.8942 (mt) REVERT: A 108 PHE cc_start: 0.9039 (m-80) cc_final: 0.8770 (m-80) REVERT: A 112 MET cc_start: 0.7778 (ppp) cc_final: 0.6475 (ppp) REVERT: A 147 ASP cc_start: 0.8576 (m-30) cc_final: 0.8129 (p0) REVERT: A 182 GLN cc_start: 0.8784 (mm110) cc_final: 0.8485 (mm-40) REVERT: A 215 MET cc_start: 0.8493 (mpp) cc_final: 0.8124 (mpp) REVERT: A 234 PHE cc_start: 0.8572 (m-80) cc_final: 0.8201 (m-80) REVERT: A 290 MET cc_start: 0.8951 (tmm) cc_final: 0.8661 (tmm) REVERT: A 291 ILE cc_start: 0.9168 (pt) cc_final: 0.8942 (pt) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.1618 time to fit residues: 24.4189 Evaluate side-chains 126 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3324 Z= 0.233 Angle : 0.930 11.524 4506 Z= 0.467 Chirality : 0.053 0.330 527 Planarity : 0.005 0.040 551 Dihedral : 5.368 20.656 454 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 30.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.92 % Allowed : 28.01 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.41), residues: 419 helix: 0.14 (0.32), residues: 253 sheet: -2.37 (0.76), residues: 44 loop : -1.99 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.013 0.005 HIS A 221 PHE 0.046 0.003 PHE A 36 TYR 0.018 0.001 TYR B 32 ARG 0.004 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7455 (mmm160) cc_final: 0.7093 (mmm160) REVERT: B 76 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8558 (tptp) REVERT: B 80 TYR cc_start: 0.8232 (t80) cc_final: 0.7726 (t80) REVERT: B 93 LEU cc_start: 0.8731 (tp) cc_final: 0.8383 (tp) REVERT: A 31 LEU cc_start: 0.9585 (mt) cc_final: 0.9152 (pp) REVERT: A 34 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8504 (tmm) REVERT: A 35 LEU cc_start: 0.9312 (mt) cc_final: 0.8944 (mt) REVERT: A 47 GLU cc_start: 0.9057 (pm20) cc_final: 0.8549 (pm20) REVERT: A 108 PHE cc_start: 0.9055 (m-80) cc_final: 0.8761 (m-80) REVERT: A 112 MET cc_start: 0.7765 (ppp) cc_final: 0.6463 (ppp) REVERT: A 147 ASP cc_start: 0.8564 (m-30) cc_final: 0.8075 (p0) REVERT: A 182 GLN cc_start: 0.8755 (mm110) cc_final: 0.8439 (mm-40) REVERT: A 215 MET cc_start: 0.8535 (mpp) cc_final: 0.8189 (mpp) REVERT: A 221 HIS cc_start: 0.7780 (m-70) cc_final: 0.7511 (m-70) REVERT: A 234 PHE cc_start: 0.8658 (m-80) cc_final: 0.8191 (m-80) REVERT: A 274 PHE cc_start: 0.8165 (m-80) cc_final: 0.7613 (t80) outliers start: 14 outliers final: 10 residues processed: 124 average time/residue: 0.1640 time to fit residues: 24.1693 Evaluate side-chains 128 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.245 Angle : 0.943 11.426 4506 Z= 0.470 Chirality : 0.054 0.312 527 Planarity : 0.005 0.036 551 Dihedral : 5.378 20.402 454 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 32.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.48 % Allowed : 29.97 % Favored : 65.55 % 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: -1.13 (0.41), residues: 419 helix: 0.17 (0.32), residues: 253 sheet: -2.29 (0.76), residues: 44 loop : -1.90 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 105 HIS 0.001 0.000 HIS A 54 PHE 0.046 0.003 PHE A 36 TYR 0.018 0.001 TYR B 32 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7352 (mmm160) cc_final: 0.6946 (mmm160) REVERT: B 67 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7854 (mtp-110) REVERT: B 76 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8567 (tptp) REVERT: B 80 TYR cc_start: 0.8222 (t80) cc_final: 0.7721 (t80) REVERT: B 83 MET cc_start: 0.7022 (ppp) cc_final: 0.6777 (ppp) REVERT: A 31 LEU cc_start: 0.9586 (mt) cc_final: 0.9350 (mt) REVERT: A 34 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8549 (tmm) REVERT: A 35 LEU cc_start: 0.9300 (mt) cc_final: 0.8959 (mt) REVERT: A 50 LYS cc_start: 0.9062 (mppt) cc_final: 0.8763 (mppt) REVERT: A 108 PHE cc_start: 0.9053 (m-80) cc_final: 0.8750 (m-80) REVERT: A 112 MET cc_start: 0.7728 (ppp) cc_final: 0.6444 (ppp) REVERT: A 147 ASP cc_start: 0.8570 (m-30) cc_final: 0.8084 (p0) REVERT: A 182 GLN cc_start: 0.8769 (mm110) cc_final: 0.8431 (mm-40) REVERT: A 215 MET cc_start: 0.8560 (mpp) cc_final: 0.8291 (mpp) REVERT: A 221 HIS cc_start: 0.7901 (m-70) cc_final: 0.7631 (m-70) REVERT: A 234 PHE cc_start: 0.8625 (m-80) cc_final: 0.8130 (m-80) REVERT: A 274 PHE cc_start: 0.8172 (m-80) cc_final: 0.7592 (t80) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.1628 time to fit residues: 24.2360 Evaluate side-chains 126 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3324 Z= 0.245 Angle : 0.950 11.348 4506 Z= 0.473 Chirality : 0.055 0.320 527 Planarity : 0.005 0.034 551 Dihedral : 5.355 20.422 454 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 32.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.20 % Allowed : 30.53 % Favored : 65.27 % 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: -1.02 (0.41), residues: 419 helix: 0.23 (0.32), residues: 253 sheet: -2.17 (0.75), residues: 44 loop : -1.80 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 116 HIS 0.001 0.000 HIS A 54 PHE 0.050 0.003 PHE A 36 TYR 0.025 0.002 TYR B 95 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7264 (mmm160) cc_final: 0.6464 (mmm160) REVERT: B 76 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8557 (tptp) REVERT: B 80 TYR cc_start: 0.8255 (t80) cc_final: 0.7407 (t80) REVERT: B 82 GLN cc_start: 0.7755 (tp40) cc_final: 0.7045 (tp40) REVERT: B 84 ASP cc_start: 0.7804 (p0) cc_final: 0.7187 (p0) REVERT: B 93 LEU cc_start: 0.8791 (tp) cc_final: 0.8457 (tp) REVERT: A 31 LEU cc_start: 0.9580 (mt) cc_final: 0.9217 (pp) REVERT: A 34 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8549 (tmm) REVERT: A 35 LEU cc_start: 0.9312 (mt) cc_final: 0.8968 (mt) REVERT: A 50 LYS cc_start: 0.9063 (mppt) cc_final: 0.8768 (mppt) REVERT: A 108 PHE cc_start: 0.9022 (m-80) cc_final: 0.8730 (m-80) REVERT: A 112 MET cc_start: 0.7770 (ppp) cc_final: 0.6562 (ppp) REVERT: A 147 ASP cc_start: 0.8561 (m-30) cc_final: 0.8077 (p0) REVERT: A 182 GLN cc_start: 0.8758 (mm110) cc_final: 0.8427 (mm-40) REVERT: A 215 MET cc_start: 0.8554 (mpp) cc_final: 0.8248 (mpp) REVERT: A 221 HIS cc_start: 0.7952 (m-70) cc_final: 0.7687 (m-70) REVERT: A 234 PHE cc_start: 0.8631 (m-80) cc_final: 0.8123 (m-80) REVERT: A 274 PHE cc_start: 0.8116 (m-80) cc_final: 0.7543 (t80) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.1626 time to fit residues: 23.1487 Evaluate side-chains 131 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.0270 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.246 Angle : 0.981 11.839 4506 Z= 0.484 Chirality : 0.055 0.346 527 Planarity : 0.005 0.032 551 Dihedral : 5.372 20.180 454 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 31.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.36 % Allowed : 31.37 % Favored : 65.27 % 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: -0.99 (0.41), residues: 419 helix: 0.24 (0.32), residues: 253 sheet: -2.11 (0.75), residues: 44 loop : -1.81 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 116 HIS 0.001 0.000 HIS A 54 PHE 0.050 0.003 PHE A 36 TYR 0.018 0.002 TYR B 32 ARG 0.004 0.001 ARG B 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8535 (tptp) REVERT: B 80 TYR cc_start: 0.8182 (t80) cc_final: 0.7333 (t80) REVERT: B 82 GLN cc_start: 0.7591 (tp40) cc_final: 0.6645 (tp40) REVERT: A 31 LEU cc_start: 0.9581 (mt) cc_final: 0.9202 (pp) REVERT: A 34 MET cc_start: 0.8950 (tmm) cc_final: 0.8400 (tmm) REVERT: A 35 LEU cc_start: 0.9330 (mt) cc_final: 0.8979 (mt) REVERT: A 38 ILE cc_start: 0.9266 (pt) cc_final: 0.9047 (pt) REVERT: A 50 LYS cc_start: 0.9061 (mppt) cc_final: 0.8744 (mppt) REVERT: A 108 PHE cc_start: 0.8981 (m-80) cc_final: 0.8700 (m-80) REVERT: A 112 MET cc_start: 0.7786 (ppp) cc_final: 0.6593 (ppp) REVERT: A 147 ASP cc_start: 0.8559 (m-30) cc_final: 0.8012 (p0) REVERT: A 182 GLN cc_start: 0.8707 (mm110) cc_final: 0.8391 (mm-40) REVERT: A 215 MET cc_start: 0.8503 (mpp) cc_final: 0.8192 (mpp) REVERT: A 221 HIS cc_start: 0.8008 (m-70) cc_final: 0.7717 (m-70) REVERT: A 234 PHE cc_start: 0.8607 (m-80) cc_final: 0.8127 (m-80) REVERT: A 274 PHE cc_start: 0.8105 (m-80) cc_final: 0.7537 (t80) outliers start: 12 outliers final: 11 residues processed: 128 average time/residue: 0.1642 time to fit residues: 25.2303 Evaluate side-chains 134 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 293 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.077960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.065110 restraints weight = 14370.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067033 restraints weight = 9950.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.068457 restraints weight = 7416.379| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3324 Z= 0.278 Angle : 1.012 15.790 4506 Z= 0.498 Chirality : 0.056 0.334 527 Planarity : 0.005 0.039 551 Dihedral : 5.503 20.620 454 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 35.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.64 % Allowed : 31.93 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.41), residues: 419 helix: 0.33 (0.33), residues: 253 sheet: -1.97 (0.80), residues: 35 loop : -2.00 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 105 HIS 0.001 0.001 HIS A 54 PHE 0.048 0.003 PHE A 36 TYR 0.018 0.002 TYR A 289 ARG 0.006 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.27 seconds wall clock time: 22 minutes 29.41 seconds (1349.41 seconds total)