Starting phenix.real_space_refine on Sun Mar 10 19:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/03_2024/7ym8_33924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/03_2024/7ym8_33924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/03_2024/7ym8_33924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/03_2024/7ym8_33924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/03_2024/7ym8_33924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/03_2024/7ym8_33924.pdb" } resolution = 2.92 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= 0.109 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 26 5.16 5 C 2805 2.51 5 N 704 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 204": "OE1" <-> "OE2" Residue "A PHE 163": "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: 4287 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1238 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2108 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'J5C': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.98, per 1000 atoms: 0.70 Number of scatterers: 4287 At special positions: 0 Unit cell: (59.5375, 58.455, 138.56, 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 26 16.00 O 752 8.00 N 704 7.00 C 2805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " 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: 1.62 Conformation dependent library (CDL) restraints added in 801.9 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 51.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.666A pdb=" N CYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.708A pdb=" N ALA B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 133' Processing helix chain 'B' and resid 169 through 184 removed outlier: 4.243A pdb=" N PHE B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.722A pdb=" N ARG B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 53 removed outlier: 3.586A pdb=" N ILE A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.664A pdb=" N ILE A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 95 through 129 Processing helix chain 'A' and resid 141 through 159 Processing helix chain 'A' and resid 184 through 211 removed outlier: 5.603A pdb=" N LEU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.931A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 304 through 326 removed outlier: 3.775A pdb=" N PHE A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 341 removed outlier: 3.875A pdb=" N GLN A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58 removed outlier: 9.826A pdb=" N ALA B 87 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG B 17 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE B 89 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 19 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 91 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.585A pdb=" N SER D 115 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 705 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: 1.18 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 669 1.32 - 1.44: 1248 1.44 - 1.56: 2438 1.56 - 1.68: 1 1.68 - 1.81: 35 Bond restraints: 4391 Sorted by residual: bond pdb=" C9 J5C A 501 " pdb=" N13 J5C A 501 " ideal model delta sigma weight residual 1.277 1.463 -0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" C9 J5C A 501 " pdb=" N10 J5C A 501 " ideal model delta sigma weight residual 1.373 1.465 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C11 J5C A 501 " pdb=" C12 J5C A 501 " ideal model delta sigma weight residual 1.540 1.490 0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C5 J5C A 501 " pdb=" O15 J5C A 501 " ideal model delta sigma weight residual 1.356 1.400 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C MET A 292 " pdb=" N PRO A 293 " ideal model delta sigma weight residual 1.334 1.376 -0.043 2.34e-02 1.83e+03 3.31e+00 ... (remaining 4386 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.47: 67 105.47 - 112.62: 2230 112.62 - 119.78: 1532 119.78 - 126.93: 2101 126.93 - 134.08: 59 Bond angle restraints: 5989 Sorted by residual: angle pdb=" C ARG B 117 " pdb=" N THR B 118 " pdb=" CA THR B 118 " ideal model delta sigma weight residual 122.46 127.56 -5.10 1.41e+00 5.03e-01 1.31e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 117.34 -7.53 2.21e+00 2.05e-01 1.16e+01 angle pdb=" CA THR B 118 " pdb=" CB THR B 118 " pdb=" CG2 THR B 118 " ideal model delta sigma weight residual 110.50 115.96 -5.46 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N ASN A 322 " pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 113.16 117.48 -4.32 1.42e+00 4.96e-01 9.26e+00 angle pdb=" N10 J5C A 501 " pdb=" C9 J5C A 501 " pdb=" N13 J5C A 501 " ideal model delta sigma weight residual 116.22 107.31 8.91 3.00e+00 1.11e-01 8.82e+00 ... (remaining 5984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.45: 2347 20.45 - 40.90: 199 40.90 - 61.34: 34 61.34 - 81.79: 8 81.79 - 102.24: 3 Dihedral angle restraints: 2591 sinusoidal: 976 harmonic: 1615 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 94 " pdb=" CB CYS D 94 " ideal model delta sinusoidal sigma weight residual 93.00 59.87 33.13 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA ILE A 325 " pdb=" C ILE A 325 " pdb=" N TYR A 326 " pdb=" CA TYR A 326 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CAR Y01 A 502 " pdb=" CAV Y01 A 502 " pdb=" CBC Y01 A 502 " pdb=" CAZ Y01 A 502 " ideal model delta sinusoidal sigma weight residual 55.40 -46.84 102.24 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 2588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 411 0.038 - 0.077: 191 0.077 - 0.115: 67 0.115 - 0.154: 16 0.154 - 0.192: 7 Chirality restraints: 692 Sorted by residual: chirality pdb=" CB VAL B 85 " pdb=" CA VAL B 85 " pdb=" CG1 VAL B 85 " pdb=" CG2 VAL B 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA THR B 118 " pdb=" N THR B 118 " pdb=" C THR B 118 " pdb=" CB THR B 118 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB ILE A 126 " pdb=" CA ILE A 126 " pdb=" CG1 ILE A 126 " pdb=" CG2 ILE A 126 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 689 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 81 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 327 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 286 " -0.038 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 287 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.032 5.00e-02 4.00e+02 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1415 2.84 - 3.36: 3748 3.36 - 3.87: 7189 3.87 - 4.39: 8184 4.39 - 4.90: 14266 Nonbonded interactions: 34802 Sorted by model distance: nonbonded pdb=" O LEU A 74 " pdb=" OG1 THR A 78 " model vdw 2.331 2.440 nonbonded pdb=" O ALA B 23 " pdb=" OG SER B 26 " model vdw 2.353 2.440 nonbonded pdb=" O SER D 83 " pdb=" OG SER D 83 " model vdw 2.369 2.440 nonbonded pdb=" NH2 ARG A 124 " pdb=" OG SER A 329 " model vdw 2.384 2.520 nonbonded pdb=" O GLN B 101 " pdb=" ND2 ASN B 105 " model vdw 2.396 2.520 ... (remaining 34797 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.800 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.360 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.186 4391 Z= 0.451 Angle : 0.860 8.907 5989 Z= 0.462 Chirality : 0.051 0.192 692 Planarity : 0.007 0.061 740 Dihedral : 16.010 102.240 1547 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: -3.62 (0.30), residues: 544 helix: -2.14 (0.24), residues: 271 sheet: -1.98 (0.50), residues: 100 loop : -2.68 (0.41), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 165 HIS 0.005 0.001 HIS B 191 PHE 0.017 0.002 PHE A 94 TYR 0.035 0.002 TYR D 37 ARG 0.005 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.430 Fit side-chains REVERT: B 17 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7150 (ttp-110) REVERT: B 21 LEU cc_start: 0.7899 (mt) cc_final: 0.7671 (mp) REVERT: B 204 GLU cc_start: 0.6596 (mp0) cc_final: 0.6389 (mp0) REVERT: A 61 THR cc_start: 0.8518 (m) cc_final: 0.8288 (p) REVERT: A 203 MET cc_start: 0.8882 (mmp) cc_final: 0.8631 (mmm) REVERT: D 105 TYR cc_start: 0.7753 (m-10) cc_final: 0.7372 (m-10) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 0.7558 time to fit residues: 59.1272 Evaluate side-chains 56 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS B 112 ASN B 211 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4391 Z= 0.235 Angle : 0.564 5.774 5989 Z= 0.291 Chirality : 0.042 0.136 692 Planarity : 0.005 0.044 740 Dihedral : 9.806 82.729 681 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.33 % Allowed : 14.19 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.34), residues: 544 helix: -0.32 (0.29), residues: 275 sheet: -1.60 (0.51), residues: 101 loop : -2.20 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 PHE 0.014 0.002 PHE A 94 TYR 0.019 0.002 TYR D 37 ARG 0.001 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.428 Fit side-chains REVERT: B 226 ASN cc_start: 0.7709 (m-40) cc_final: 0.7422 (t0) REVERT: A 61 THR cc_start: 0.8537 (m) cc_final: 0.8289 (p) REVERT: A 203 MET cc_start: 0.8914 (mmp) cc_final: 0.8679 (mmm) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.8093 time to fit residues: 54.6920 Evaluate side-chains 62 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4391 Z= 0.236 Angle : 0.558 8.199 5989 Z= 0.282 Chirality : 0.042 0.124 692 Planarity : 0.004 0.043 740 Dihedral : 8.644 64.159 679 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.02 % Allowed : 16.98 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.36), residues: 544 helix: 0.40 (0.31), residues: 277 sheet: -1.32 (0.52), residues: 102 loop : -1.78 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 PHE 0.014 0.002 PHE A 94 TYR 0.021 0.002 TYR D 37 ARG 0.006 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.447 Fit side-chains REVERT: B 226 ASN cc_start: 0.7722 (m-40) cc_final: 0.7500 (t0) REVERT: A 36 LEU cc_start: 0.8112 (mt) cc_final: 0.7793 (tp) REVERT: A 61 THR cc_start: 0.8562 (m) cc_final: 0.8223 (p) REVERT: A 162 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7340 (tp) REVERT: A 203 MET cc_start: 0.8896 (mmp) cc_final: 0.8677 (mmm) REVERT: A 294 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 305 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7233 (tt0) outliers start: 13 outliers final: 4 residues processed: 69 average time/residue: 0.8453 time to fit residues: 61.4085 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4391 Z= 0.186 Angle : 0.525 6.716 5989 Z= 0.264 Chirality : 0.042 0.197 692 Planarity : 0.004 0.039 740 Dihedral : 7.374 63.658 679 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.02 % Allowed : 17.67 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.36), residues: 544 helix: 0.86 (0.31), residues: 276 sheet: -1.08 (0.52), residues: 100 loop : -1.66 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS A 56 PHE 0.011 0.001 PHE A 94 TYR 0.016 0.001 TYR D 53 ARG 0.002 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.479 Fit side-chains REVERT: B 182 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7335 (mp) REVERT: B 226 ASN cc_start: 0.7706 (m-40) cc_final: 0.7447 (t0) REVERT: A 36 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7815 (tp) REVERT: A 61 THR cc_start: 0.8559 (m) cc_final: 0.8215 (p) REVERT: A 203 MET cc_start: 0.8876 (mmp) cc_final: 0.8642 (mmm) REVERT: A 294 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7517 (mp) REVERT: A 305 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7280 (tt0) outliers start: 13 outliers final: 4 residues processed: 67 average time/residue: 0.9924 time to fit residues: 69.6215 Evaluate side-chains 65 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 21 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4391 Z= 0.157 Angle : 0.494 6.342 5989 Z= 0.250 Chirality : 0.041 0.124 692 Planarity : 0.004 0.038 740 Dihedral : 6.946 64.272 679 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.26 % Allowed : 17.67 % Favored : 79.07 % 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: -0.07 (0.37), residues: 544 helix: 1.19 (0.32), residues: 275 sheet: -0.93 (0.52), residues: 101 loop : -1.48 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 102 HIS 0.002 0.001 HIS A 56 PHE 0.010 0.001 PHE B 56 TYR 0.018 0.001 TYR D 53 ARG 0.005 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.468 Fit side-chains REVERT: B 182 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7205 (mp) REVERT: A 36 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7839 (tp) REVERT: A 67 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7697 (p0) REVERT: A 203 MET cc_start: 0.8872 (mmp) cc_final: 0.8607 (mmm) REVERT: A 294 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7468 (mp) REVERT: A 305 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7184 (tp30) outliers start: 14 outliers final: 3 residues processed: 69 average time/residue: 0.8833 time to fit residues: 64.1200 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4391 Z= 0.160 Angle : 0.494 5.813 5989 Z= 0.252 Chirality : 0.041 0.131 692 Planarity : 0.004 0.036 740 Dihedral : 6.961 64.020 679 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.02 % Allowed : 18.84 % Favored : 78.14 % 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: 0.08 (0.37), residues: 544 helix: 1.29 (0.32), residues: 275 sheet: -0.83 (0.52), residues: 101 loop : -1.37 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.002 0.001 HIS A 56 PHE 0.010 0.001 PHE B 56 TYR 0.022 0.001 TYR D 53 ARG 0.002 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.469 Fit side-chains REVERT: B 182 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7154 (mp) REVERT: A 36 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 67 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7690 (p0) REVERT: A 195 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 203 MET cc_start: 0.8871 (mmp) cc_final: 0.8592 (mmm) REVERT: A 305 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6987 (tt0) outliers start: 13 outliers final: 5 residues processed: 67 average time/residue: 0.8313 time to fit residues: 58.7518 Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4391 Z= 0.227 Angle : 0.530 5.853 5989 Z= 0.269 Chirality : 0.042 0.136 692 Planarity : 0.004 0.039 740 Dihedral : 7.078 63.161 679 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.26 % Allowed : 18.60 % Favored : 78.14 % 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: -0.06 (0.37), residues: 544 helix: 1.03 (0.31), residues: 281 sheet: -0.85 (0.52), residues: 101 loop : -1.28 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 PHE 0.012 0.001 PHE A 94 TYR 0.025 0.001 TYR D 53 ARG 0.002 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.442 Fit side-chains REVERT: B 182 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7273 (mp) REVERT: A 67 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7677 (p0) REVERT: A 203 MET cc_start: 0.8872 (mmp) cc_final: 0.8668 (mmm) REVERT: A 294 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7528 (mp) REVERT: A 305 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7045 (tp30) outliers start: 14 outliers final: 4 residues processed: 66 average time/residue: 0.9037 time to fit residues: 62.7063 Evaluate side-chains 65 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4391 Z= 0.213 Angle : 0.520 5.654 5989 Z= 0.265 Chirality : 0.042 0.145 692 Planarity : 0.004 0.037 740 Dihedral : 7.074 63.490 679 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.26 % Allowed : 19.30 % Favored : 77.44 % 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: -0.01 (0.37), residues: 544 helix: 1.08 (0.32), residues: 279 sheet: -0.74 (0.53), residues: 97 loop : -1.28 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS B 191 PHE 0.011 0.001 PHE A 94 TYR 0.024 0.001 TYR D 53 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.424 Fit side-chains REVERT: B 35 MET cc_start: 0.6251 (mtp) cc_final: 0.5979 (ttp) REVERT: B 182 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A 67 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7689 (p0) REVERT: A 203 MET cc_start: 0.8864 (mmp) cc_final: 0.8628 (mmm) REVERT: A 294 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7531 (mp) REVERT: A 305 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7068 (tp30) outliers start: 14 outliers final: 5 residues processed: 66 average time/residue: 0.9106 time to fit residues: 63.1304 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4391 Z= 0.202 Angle : 0.513 5.363 5989 Z= 0.263 Chirality : 0.041 0.143 692 Planarity : 0.004 0.038 740 Dihedral : 6.969 63.658 679 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.02 % Allowed : 19.53 % Favored : 77.44 % 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: 0.06 (0.37), residues: 544 helix: 1.15 (0.32), residues: 279 sheet: -0.71 (0.53), residues: 97 loop : -1.28 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.002 0.001 HIS A 56 PHE 0.011 0.001 PHE A 94 TYR 0.023 0.001 TYR D 53 ARG 0.002 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.453 Fit side-chains REVERT: B 35 MET cc_start: 0.6599 (mtp) cc_final: 0.6385 (ttp) REVERT: B 182 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 67 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7675 (p0) REVERT: A 167 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.5693 (mt0) REVERT: A 203 MET cc_start: 0.8866 (mmp) cc_final: 0.8631 (mmm) REVERT: A 294 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 305 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7044 (tp30) outliers start: 13 outliers final: 5 residues processed: 64 average time/residue: 0.8957 time to fit residues: 60.2830 Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4391 Z= 0.195 Angle : 0.507 5.159 5989 Z= 0.260 Chirality : 0.041 0.145 692 Planarity : 0.004 0.037 740 Dihedral : 6.966 63.689 679 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.33 % Allowed : 20.23 % Favored : 77.44 % 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: 0.09 (0.37), residues: 544 helix: 1.17 (0.32), residues: 280 sheet: -0.70 (0.53), residues: 97 loop : -1.28 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.002 0.001 HIS A 56 PHE 0.011 0.001 PHE B 56 TYR 0.023 0.001 TYR D 53 ARG 0.003 0.000 ARG B 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.464 Fit side-chains REVERT: B 182 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7279 (mp) REVERT: A 67 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7670 (p0) REVERT: A 167 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5691 (mt0) REVERT: A 203 MET cc_start: 0.8865 (mmp) cc_final: 0.8619 (mmm) REVERT: A 294 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7526 (mp) REVERT: A 305 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6949 (tt0) outliers start: 10 outliers final: 4 residues processed: 62 average time/residue: 0.9268 time to fit residues: 60.3566 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.0050 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 34 optimal weight: 0.0570 overall best weight: 0.3312 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.173235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131420 restraints weight = 4394.962| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.56 r_work: 0.3181 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4391 Z= 0.139 Angle : 0.477 5.117 5989 Z= 0.245 Chirality : 0.040 0.138 692 Planarity : 0.003 0.037 740 Dihedral : 6.846 64.409 679 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.86 % Allowed : 20.93 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.38), residues: 544 helix: 1.37 (0.32), residues: 279 sheet: -0.57 (0.54), residues: 97 loop : -1.31 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.001 HIS A 56 PHE 0.010 0.001 PHE B 56 TYR 0.020 0.001 TYR D 53 ARG 0.002 0.000 ARG B 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.32 seconds wall clock time: 32 minutes 19.20 seconds (1939.20 seconds total)