Starting phenix.real_space_refine on Sun Mar 10 18:29:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymh_33928/03_2024/7ymh_33928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymh_33928/03_2024/7ymh_33928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymh_33928/03_2024/7ymh_33928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymh_33928/03_2024/7ymh_33928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymh_33928/03_2024/7ymh_33928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymh_33928/03_2024/7ymh_33928_updated.pdb" } resolution = 3.52 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= 0.051 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 24 5.16 5 C 2577 2.51 5 N 657 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "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: 3948 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2038 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1389 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 197, 1384 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 183 Conformer: "B" Number of residues, atoms: 197, 1384 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 183 bond proxies already assigned to first conformer: 1403 Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 509 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA B 158 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 158 " occ=0.50 Time building chain proxies: 3.42, per 1000 atoms: 0.87 Number of scatterers: 3948 At special positions: 0 Unit cell: (58.1887, 61.4824, 139.433, 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 24 16.00 O 690 8.00 N 657 7.00 C 2577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " 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: 1.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 48.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 27 through 49 Processing helix chain 'A' and resid 60 through 89 removed outlier: 3.636A pdb=" N LEU A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 128 removed outlier: 3.719A pdb=" N ALA A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 184 through 210 removed outlier: 6.057A 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 264 through 273 removed outlier: 3.915A pdb=" N LYS A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 297 removed outlier: 4.635A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.946A pdb=" N GLY A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 3.576A pdb=" N TYR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 332 through 340 removed outlier: 4.241A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.941A pdb=" N ILE B 79 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 111 Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.605A pdb=" N GLU B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 206 through 224 Processing sheet with id= A, first strand: chain 'B' and resid 15 through 20 removed outlier: 7.543A pdb=" N ASN B 62 " --> pdb=" O HIS B 16 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU B 18 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS B 64 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 20 " --> pdb=" O HIS B 64 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 66 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 88 through 93 Processing sheet with id= C, first strand: chain 'D' and resid 91 through 97 removed outlier: 4.053A pdb=" N VAL D 91 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 66 through 69 196 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1232 1.34 - 1.46: 961 1.46 - 1.58: 1813 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4037 Sorted by residual: bond pdb=" CAJ E5E A 401 " pdb=" OAC E5E A 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" CAI E5E A 401 " pdb=" OAB E5E A 401 " ideal model delta sigma weight residual 1.354 1.400 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 1.469 1.482 -0.013 7.40e-03 1.83e+04 3.25e+00 bond pdb=" CAH E5E A 401 " pdb=" NAA E5E A 401 " ideal model delta sigma weight residual 1.486 1.451 0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C LEU A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.47e+00 ... (remaining 4032 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 107 106.88 - 113.67: 2235 113.67 - 120.46: 1634 120.46 - 127.25: 1504 127.25 - 134.04: 44 Bond angle restraints: 5524 Sorted by residual: angle pdb=" N ILE A 159 " pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 111.91 106.40 5.51 8.90e-01 1.26e+00 3.83e+01 angle pdb=" N ASP A 300 " pdb=" CA ASP A 300 " pdb=" C ASP A 300 " ideal model delta sigma weight residual 114.31 108.59 5.72 1.29e+00 6.01e-01 1.97e+01 angle pdb=" N ILE A 178 " pdb=" CA ILE A 178 " pdb=" C ILE A 178 " ideal model delta sigma weight residual 110.05 106.05 4.00 1.09e+00 8.42e-01 1.35e+01 angle pdb=" C ILE A 321 " pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta sigma weight residual 120.06 124.17 -4.11 1.19e+00 7.06e-01 1.19e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 116.27 -6.46 2.21e+00 2.05e-01 8.54e+00 ... (remaining 5519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 2063 15.48 - 30.95: 209 30.95 - 46.43: 49 46.43 - 61.90: 4 61.90 - 77.38: 4 Dihedral angle restraints: 2329 sinusoidal: 744 harmonic: 1585 Sorted by residual: dihedral pdb=" CA PRO A 161 " pdb=" C PRO A 161 " pdb=" N LEU A 162 " pdb=" CA LEU A 162 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+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 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE A 193 " pdb=" C PHE A 193 " pdb=" N TYR A 194 " pdb=" CA TYR A 194 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 393 0.038 - 0.075: 190 0.075 - 0.113: 56 0.113 - 0.151: 21 0.151 - 0.189: 6 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CAL E5E A 401 " pdb=" CAH E5E A 401 " pdb=" CAK E5E A 401 " pdb=" OAD E5E A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.49 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA TYR A 326 " pdb=" N TYR A 326 " pdb=" C TYR A 326 " pdb=" CB TYR A 326 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 663 not shown) Planarity restraints: 688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 322 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO A 323 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO A 327 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 286 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 287 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.034 5.00e-02 4.00e+02 ... (remaining 685 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1346 2.84 - 3.35: 3542 3.35 - 3.87: 6351 3.87 - 4.38: 6892 4.38 - 4.90: 12231 Nonbonded interactions: 30362 Sorted by model distance: nonbonded pdb=" OH TYR B 194 " pdb=" OD2 ASP B 215 " model vdw 2.324 2.440 nonbonded pdb=" OD1 ASP A 172 " pdb=" OH TYR D 37 " model vdw 2.331 2.440 nonbonded pdb=" OG SER D 69 " pdb=" O TYR D 78 " model vdw 2.383 2.440 nonbonded pdb=" O THR A 139 " pdb=" N GLY A 143 " model vdw 2.383 2.520 nonbonded pdb=" O ASP A 72 " pdb=" OG1 THR A 76 " model vdw 2.417 2.440 ... (remaining 30357 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=0.50 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: 0.460 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: 2.570 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.600 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 4037 Z= 0.286 Angle : 0.780 8.018 5524 Z= 0.448 Chirality : 0.050 0.189 666 Planarity : 0.007 0.075 688 Dihedral : 13.786 77.379 1300 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % 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: -4.54 (0.28), residues: 527 helix: -2.63 (0.23), residues: 283 sheet: -3.00 (0.49), residues: 67 loop : -3.32 (0.39), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 111 HIS 0.006 0.001 HIS B 191 PHE 0.012 0.002 PHE A 308 TYR 0.018 0.001 TYR A 134 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8592 (mp) cc_final: 0.8371 (mp) REVERT: A 165 TRP cc_start: 0.4361 (m100) cc_final: 0.4151 (m100) REVERT: A 272 LYS cc_start: 0.8785 (tppp) cc_final: 0.8292 (tptt) REVERT: B 215 ASP cc_start: 0.8499 (t70) cc_final: 0.7595 (t0) REVERT: D 100 TYR cc_start: 0.8228 (p90) cc_final: 0.7856 (p90) REVERT: D 102 ASP cc_start: 0.8443 (t70) cc_final: 0.7816 (t70) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2034 time to fit residues: 28.2773 Evaluate side-chains 87 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 48 optimal weight: 10.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 331 GLN B 16 HIS B 62 ASN B 219 GLN B 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4037 Z= 0.178 Angle : 0.521 5.811 5524 Z= 0.281 Chirality : 0.039 0.124 666 Planarity : 0.004 0.043 688 Dihedral : 4.400 17.879 583 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.91 % Allowed : 15.26 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.33), residues: 527 helix: -0.87 (0.29), residues: 279 sheet: -2.60 (0.53), residues: 67 loop : -2.99 (0.40), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS B 191 PHE 0.008 0.001 PHE B 197 TYR 0.013 0.001 TYR A 326 ARG 0.007 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8655 (mp) cc_final: 0.8395 (mp) REVERT: A 115 MET cc_start: 0.8075 (mtp) cc_final: 0.7672 (mtt) REVERT: A 165 TRP cc_start: 0.4025 (m100) cc_final: 0.3778 (m100) REVERT: A 272 LYS cc_start: 0.8741 (tppp) cc_final: 0.8249 (tptt) REVERT: A 292 MET cc_start: 0.7903 (ttm) cc_final: 0.7589 (tpt) REVERT: B 215 ASP cc_start: 0.8402 (t70) cc_final: 0.8078 (t0) REVERT: D 100 TYR cc_start: 0.8239 (p90) cc_final: 0.7916 (p90) outliers start: 7 outliers final: 4 residues processed: 101 average time/residue: 0.1725 time to fit residues: 21.2219 Evaluate side-chains 93 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 61 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4037 Z= 0.250 Angle : 0.539 5.669 5524 Z= 0.286 Chirality : 0.041 0.132 666 Planarity : 0.004 0.037 688 Dihedral : 4.300 16.929 583 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.36 % Allowed : 16.35 % Favored : 79.29 % 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: -2.08 (0.35), residues: 527 helix: -0.18 (0.31), residues: 281 sheet: -2.41 (0.56), residues: 69 loop : -2.83 (0.42), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 102 HIS 0.005 0.001 HIS B 191 PHE 0.014 0.001 PHE A 187 TYR 0.014 0.001 TYR A 326 ARG 0.007 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.443 Fit side-chains REVERT: A 115 MET cc_start: 0.8050 (mtp) cc_final: 0.7613 (mtt) REVERT: A 165 TRP cc_start: 0.4013 (m100) cc_final: 0.3554 (m100) REVERT: A 272 LYS cc_start: 0.8795 (tppp) cc_final: 0.8299 (tptt) REVERT: B 215 ASP cc_start: 0.8432 (t70) cc_final: 0.8066 (t0) REVERT: D 100 TYR cc_start: 0.8245 (p90) cc_final: 0.7962 (p90) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.1785 time to fit residues: 20.4224 Evaluate side-chains 96 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.0010 chunk 42 optimal weight: 0.4980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4037 Z= 0.157 Angle : 0.481 5.673 5524 Z= 0.253 Chirality : 0.039 0.126 666 Planarity : 0.004 0.032 688 Dihedral : 3.954 16.334 583 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.09 % Allowed : 18.26 % Favored : 77.66 % 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: -1.50 (0.36), residues: 527 helix: 0.27 (0.31), residues: 285 sheet: -2.21 (0.55), residues: 69 loop : -2.54 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 102 HIS 0.003 0.001 HIS B 191 PHE 0.013 0.001 PHE A 187 TYR 0.013 0.001 TYR A 91 ARG 0.005 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.473 Fit side-chains REVERT: A 165 TRP cc_start: 0.4026 (m100) cc_final: 0.3615 (m100) REVERT: A 179 ASN cc_start: 0.7997 (t0) cc_final: 0.7483 (t0) REVERT: A 180 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7545 (mp0) REVERT: A 272 LYS cc_start: 0.8778 (tppp) cc_final: 0.8277 (tptt) REVERT: B 35 MET cc_start: 0.7872 (pmm) cc_final: 0.7613 (pmm) REVERT: B 215 ASP cc_start: 0.8387 (t70) cc_final: 0.7842 (t0) REVERT: D 100 TYR cc_start: 0.8204 (p90) cc_final: 0.7931 (p90) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.1845 time to fit residues: 22.1460 Evaluate side-chains 103 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4037 Z= 0.335 Angle : 0.574 5.685 5524 Z= 0.302 Chirality : 0.042 0.137 666 Planarity : 0.004 0.031 688 Dihedral : 4.246 17.885 583 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.90 % Allowed : 19.62 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.36), residues: 527 helix: 0.23 (0.31), residues: 287 sheet: -2.25 (0.57), residues: 69 loop : -2.35 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.005 0.001 HIS B 191 PHE 0.011 0.002 PHE A 297 TYR 0.014 0.001 TYR A 326 ARG 0.005 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.437 Fit side-chains REVERT: A 145 MET cc_start: 0.7917 (mmm) cc_final: 0.7455 (mtt) REVERT: A 165 TRP cc_start: 0.3968 (m100) cc_final: 0.3494 (m100) REVERT: A 179 ASN cc_start: 0.8016 (t0) cc_final: 0.7709 (t0) REVERT: A 269 LYS cc_start: 0.8603 (tptm) cc_final: 0.8187 (tppt) REVERT: A 272 LYS cc_start: 0.8808 (tppp) cc_final: 0.8293 (tptt) REVERT: B 215 ASP cc_start: 0.8465 (t70) cc_final: 0.8160 (t0) REVERT: D 100 TYR cc_start: 0.8229 (p90) cc_final: 0.7938 (p90) outliers start: 18 outliers final: 13 residues processed: 99 average time/residue: 0.1669 time to fit residues: 20.2447 Evaluate side-chains 101 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.0470 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 126 ASN B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4037 Z= 0.170 Angle : 0.500 7.904 5524 Z= 0.261 Chirality : 0.039 0.127 666 Planarity : 0.003 0.027 688 Dihedral : 3.975 16.667 583 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.63 % Allowed : 20.16 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.37), residues: 527 helix: 0.49 (0.31), residues: 287 sheet: -2.02 (0.57), residues: 69 loop : -2.16 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 102 HIS 0.004 0.001 HIS B 191 PHE 0.011 0.001 PHE A 187 TYR 0.013 0.001 TYR A 91 ARG 0.004 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.451 Fit side-chains REVERT: A 145 MET cc_start: 0.7690 (mmm) cc_final: 0.7277 (mtt) REVERT: A 165 TRP cc_start: 0.3850 (m100) cc_final: 0.3388 (m100) REVERT: A 269 LYS cc_start: 0.8572 (tptm) cc_final: 0.8138 (tppt) REVERT: A 272 LYS cc_start: 0.8765 (tppp) cc_final: 0.8252 (tptt) REVERT: B 35 MET cc_start: 0.7895 (pmm) cc_final: 0.7611 (pmm) REVERT: B 215 ASP cc_start: 0.8394 (t70) cc_final: 0.8108 (t0) REVERT: D 100 TYR cc_start: 0.8112 (p90) cc_final: 0.7899 (p90) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.1719 time to fit residues: 20.9983 Evaluate side-chains 102 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 51 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4037 Z= 0.168 Angle : 0.503 9.446 5524 Z= 0.261 Chirality : 0.039 0.127 666 Planarity : 0.003 0.027 688 Dihedral : 3.819 15.649 583 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.09 % Allowed : 20.98 % Favored : 74.93 % 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: -0.88 (0.38), residues: 527 helix: 0.67 (0.32), residues: 283 sheet: -1.81 (0.58), residues: 69 loop : -2.10 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.004 0.001 HIS B 191 PHE 0.019 0.001 PHE A 187 TYR 0.015 0.001 TYR A 91 ARG 0.005 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.389 Fit side-chains REVERT: A 63 TYR cc_start: 0.7355 (m-10) cc_final: 0.7097 (m-10) REVERT: A 145 MET cc_start: 0.7646 (mmm) cc_final: 0.7227 (mtt) REVERT: A 165 TRP cc_start: 0.3862 (m100) cc_final: 0.3516 (m100) REVERT: A 181 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 269 LYS cc_start: 0.8585 (tptm) cc_final: 0.8143 (tppt) REVERT: A 272 LYS cc_start: 0.8768 (tppp) cc_final: 0.8256 (tptt) REVERT: A 313 TRP cc_start: 0.8762 (m100) cc_final: 0.8537 (m100) REVERT: B 35 MET cc_start: 0.7890 (pmm) cc_final: 0.7639 (pmm) REVERT: B 215 ASP cc_start: 0.8388 (t70) cc_final: 0.8116 (t0) REVERT: D 100 TYR cc_start: 0.8123 (p90) cc_final: 0.7849 (p90) outliers start: 15 outliers final: 14 residues processed: 101 average time/residue: 0.1792 time to fit residues: 21.7831 Evaluate side-chains 107 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 46 optimal weight: 0.0050 chunk 48 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4037 Z= 0.154 Angle : 0.504 9.567 5524 Z= 0.260 Chirality : 0.039 0.127 666 Planarity : 0.003 0.029 688 Dihedral : 3.734 15.028 583 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.36 % Allowed : 20.98 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.38), residues: 527 helix: 0.78 (0.32), residues: 285 sheet: -1.68 (0.59), residues: 69 loop : -1.91 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.003 0.001 HIS B 191 PHE 0.017 0.001 PHE A 187 TYR 0.013 0.001 TYR A 91 ARG 0.004 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.480 Fit side-chains REVERT: A 63 TYR cc_start: 0.7300 (m-10) cc_final: 0.7067 (m-10) REVERT: A 145 MET cc_start: 0.7582 (mmm) cc_final: 0.7197 (mtt) REVERT: A 269 LYS cc_start: 0.8591 (tptm) cc_final: 0.8162 (tppt) REVERT: A 272 LYS cc_start: 0.8746 (tppp) cc_final: 0.8258 (tptt) REVERT: A 313 TRP cc_start: 0.8691 (m100) cc_final: 0.8444 (m100) REVERT: B 35 MET cc_start: 0.7893 (pmm) cc_final: 0.7670 (pmm) REVERT: B 215 ASP cc_start: 0.8292 (t70) cc_final: 0.8031 (t0) REVERT: D 100 TYR cc_start: 0.8137 (p90) cc_final: 0.7896 (p90) outliers start: 16 outliers final: 15 residues processed: 103 average time/residue: 0.1775 time to fit residues: 22.1441 Evaluate side-chains 105 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4037 Z= 0.273 Angle : 0.565 9.306 5524 Z= 0.293 Chirality : 0.041 0.123 666 Planarity : 0.004 0.028 688 Dihedral : 4.026 22.940 583 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.09 % Allowed : 21.80 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.37), residues: 527 helix: 0.68 (0.32), residues: 286 sheet: -1.74 (0.58), residues: 69 loop : -1.91 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 313 HIS 0.007 0.001 HIS B 16 PHE 0.015 0.001 PHE A 187 TYR 0.014 0.001 TYR A 91 ARG 0.006 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.467 Fit side-chains REVERT: A 145 MET cc_start: 0.7797 (mmm) cc_final: 0.7438 (mtt) REVERT: A 165 TRP cc_start: 0.3742 (m100) cc_final: 0.3304 (m100) REVERT: A 269 LYS cc_start: 0.8611 (tptm) cc_final: 0.8350 (tppt) REVERT: A 272 LYS cc_start: 0.8786 (tppp) cc_final: 0.8242 (tptt) REVERT: B 35 MET cc_start: 0.7901 (pmm) cc_final: 0.7659 (pmm) REVERT: B 215 ASP cc_start: 0.8373 (t70) cc_final: 0.7459 (t0) REVERT: D 100 TYR cc_start: 0.8150 (p90) cc_final: 0.7906 (p90) outliers start: 15 outliers final: 14 residues processed: 96 average time/residue: 0.1706 time to fit residues: 20.0158 Evaluate side-chains 105 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4037 Z= 0.163 Angle : 0.518 10.311 5524 Z= 0.267 Chirality : 0.039 0.125 666 Planarity : 0.004 0.029 688 Dihedral : 3.822 19.327 583 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.27 % Allowed : 22.34 % Favored : 74.39 % 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: -0.50 (0.38), residues: 527 helix: 0.92 (0.32), residues: 283 sheet: -1.60 (0.59), residues: 69 loop : -1.82 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.003 0.001 HIS B 16 PHE 0.017 0.001 PHE A 187 TYR 0.015 0.001 TYR A 91 ARG 0.007 0.000 ARG B 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.520 Fit side-chains REVERT: A 63 TYR cc_start: 0.7321 (m-10) cc_final: 0.7095 (m-10) REVERT: A 145 MET cc_start: 0.7641 (mmm) cc_final: 0.7281 (mtt) REVERT: A 269 LYS cc_start: 0.8523 (tptm) cc_final: 0.8319 (tppt) REVERT: A 272 LYS cc_start: 0.8721 (tppp) cc_final: 0.8192 (tptt) REVERT: A 313 TRP cc_start: 0.8698 (m100) cc_final: 0.8437 (m100) REVERT: B 35 MET cc_start: 0.7884 (pmm) cc_final: 0.7652 (pmm) REVERT: B 215 ASP cc_start: 0.8323 (t70) cc_final: 0.7354 (t0) REVERT: D 100 TYR cc_start: 0.8118 (p90) cc_final: 0.7874 (p90) outliers start: 12 outliers final: 12 residues processed: 97 average time/residue: 0.2045 time to fit residues: 23.7202 Evaluate side-chains 101 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.0370 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108216 restraints weight = 5903.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108207 restraints weight = 3777.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109790 restraints weight = 3049.859| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4037 Z= 0.178 Angle : 0.520 10.168 5524 Z= 0.268 Chirality : 0.039 0.124 666 Planarity : 0.004 0.030 688 Dihedral : 3.762 18.020 583 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.09 % Allowed : 21.53 % Favored : 74.39 % 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: -0.41 (0.38), residues: 527 helix: 0.95 (0.32), residues: 287 sheet: -1.54 (0.60), residues: 69 loop : -1.76 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.004 0.001 HIS B 191 PHE 0.016 0.001 PHE A 187 TYR 0.015 0.001 TYR A 91 ARG 0.007 0.000 ARG B 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.74 seconds wall clock time: 23 minutes 36.21 seconds (1416.21 seconds total)