Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:01:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs2_34983/04_2023/8hs2_34983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs2_34983/04_2023/8hs2_34983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs2_34983/04_2023/8hs2_34983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs2_34983/04_2023/8hs2_34983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs2_34983/04_2023/8hs2_34983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs2_34983/04_2023/8hs2_34983.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.012 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 34 5.16 5 C 3487 2.51 5 N 930 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 108": "OD1" <-> "OD2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 99": "OD1" <-> "OD2" Residue "R ASP 147": "OD1" <-> "OD2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ASP 269": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5456 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1617 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1623 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "R" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2216 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.49, per 1000 atoms: 0.64 Number of scatterers: 5456 At special positions: 0 Unit cell: (69.888, 92.352, 138.112, 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 34 16.00 O 1005 8.00 N 930 7.00 C 3487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 374 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 122 " 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: 2.15 Conformation dependent library (CDL) restraints added in 841.3 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 13 sheets defined 39.1% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.753A pdb=" N TYR B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.666A pdb=" N SER B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.688A pdb=" N LEU C 411 " --> pdb=" O THR C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.538A pdb=" N HIS C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 removed outlier: 4.059A pdb=" N ALA R 39 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 Processing helix chain 'R' and resid 86 through 116 Proline residue: R 107 - end of helix removed outlier: 4.233A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 122 No H-bonds generated for 'chain 'R' and resid 120 through 122' Processing helix chain 'R' and resid 123 through 151 removed outlier: 3.708A pdb=" N VAL R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER R 137 " --> pdb=" O ASN R 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE R 138 " --> pdb=" O MET R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 187 removed outlier: 3.815A pdb=" N ALA R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 205 removed outlier: 3.913A pdb=" N VAL R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 203 " --> pdb=" O ALA R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 225 Processing helix chain 'R' and resid 229 through 254 Processing helix chain 'R' and resid 254 through 267 removed outlier: 3.527A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 293 removed outlier: 4.380A pdb=" N SER R 290 " --> pdb=" O SER R 286 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS R 291 " --> pdb=" O SER R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 301 removed outlier: 3.967A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 317 removed outlier: 4.099A pdb=" N ALA R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.674A pdb=" N ILE B 53 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B 69 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.161A pdb=" N TYR B 131 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA B 119 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE B 129 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 153 removed outlier: 4.015A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 165 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 169 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 204 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 153 removed outlier: 4.015A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 165 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 169 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 204 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 198 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 292 through 293 removed outlier: 6.678A pdb=" N THR C 355 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AA9, first strand: chain 'C' and resid 319 through 321 Processing sheet with id=AB1, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AB2, first strand: chain 'C' and resid 371 through 372 Processing sheet with id=AB3, first strand: chain 'C' and resid 402 through 404 removed outlier: 3.742A pdb=" N VAL C 419 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR C 459 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 431 through 435 removed outlier: 4.009A pdb=" N LYS C 493 " --> pdb=" O CYS C 480 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 482 " --> pdb=" O VAL C 491 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 879 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: 1.69 Time building geometry restraints manager: 2.33 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: 1723 1.34 - 1.46: 1339 1.46 - 1.58: 2481 1.58 - 1.70: 0 1.70 - 1.81: 44 Bond restraints: 5587 Sorted by residual: bond pdb=" CB GLN B 200 " pdb=" CG GLN B 200 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.77e+00 bond pdb=" CB LYS C 435 " pdb=" CG LYS C 435 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CA ASP R 269 " pdb=" CB ASP R 269 " ideal model delta sigma weight residual 1.529 1.555 -0.025 1.74e-02 3.30e+03 2.13e+00 bond pdb=" CB ASP B 108 " pdb=" CG ASP B 108 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CB ASP R 269 " pdb=" CG ASP R 269 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.95e+00 ... (remaining 5582 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.17: 166 106.17 - 113.12: 3060 113.12 - 120.06: 1824 120.06 - 127.01: 2483 127.01 - 133.96: 80 Bond angle restraints: 7613 Sorted by residual: angle pdb=" CA GLN B 200 " pdb=" CB GLN B 200 " pdb=" CG GLN B 200 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CA ARG C 442 " pdb=" CB ARG C 442 " pdb=" CG ARG C 442 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CA LYS C 433 " pdb=" CB LYS C 433 " pdb=" CG LYS C 433 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB LYS C 435 " pdb=" CG LYS C 435 " pdb=" CD LYS C 435 " ideal model delta sigma weight residual 111.30 119.88 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA ASP R 269 " pdb=" CB ASP R 269 " pdb=" CG ASP R 269 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 ... (remaining 7608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2921 17.85 - 35.70: 299 35.70 - 53.55: 71 53.55 - 71.40: 4 71.40 - 89.25: 7 Dihedral angle restraints: 3302 sinusoidal: 1237 harmonic: 2065 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 122 " pdb=" CB CYS R 122 " ideal model delta sinusoidal sigma weight residual -86.00 -175.25 89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CA LEU R 229 " pdb=" C LEU R 229 " pdb=" N HIS R 230 " pdb=" CA HIS R 230 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER C 402 " pdb=" C SER C 402 " pdb=" N ILE C 403 " pdb=" CA ILE C 403 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 3299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 665 0.044 - 0.088: 153 0.088 - 0.131: 61 0.131 - 0.175: 9 0.175 - 0.219: 4 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA TYR C 426 " pdb=" N TYR C 426 " pdb=" C TYR C 426 " pdb=" CB TYR C 426 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL R 32 " pdb=" CA VAL R 32 " pdb=" CG1 VAL R 32 " pdb=" CG2 VAL R 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO C 427 " pdb=" N PRO C 427 " pdb=" C PRO C 427 " pdb=" CB PRO C 427 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 889 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 269 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ASP R 269 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP R 269 " 0.015 2.00e-02 2.50e+03 pdb=" N MET R 270 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 344 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 345 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 108 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" CG ASP B 108 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP B 108 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 108 " -0.012 2.00e-02 2.50e+03 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 303 2.73 - 3.27: 5506 3.27 - 3.82: 9267 3.82 - 4.36: 10235 4.36 - 4.90: 18460 Nonbonded interactions: 43771 Sorted by model distance: nonbonded pdb=" O LEU C 392 " pdb=" OH TYR C 426 " model vdw 2.192 2.440 nonbonded pdb=" OG1 THR C 289 " pdb=" OE2 GLU C 379 " model vdw 2.249 2.440 nonbonded pdb=" OD2 ASP C 453 " pdb=" OG1 THR C 458 " model vdw 2.331 2.440 nonbonded pdb=" OG SER R 88 " pdb=" OD2 ASP R 147 " model vdw 2.333 2.440 nonbonded pdb=" N GLN R 305 " pdb=" OE1 GLN R 305 " model vdw 2.334 2.520 ... (remaining 43766 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.280 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.160 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 5587 Z= 0.267 Angle : 0.777 11.154 7613 Z= 0.410 Chirality : 0.046 0.219 892 Planarity : 0.005 0.054 954 Dihedral : 14.964 85.417 1963 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.10 (0.31), residues: 708 helix: 1.52 (0.32), residues: 244 sheet: 0.12 (0.38), residues: 186 loop : -1.28 (0.35), residues: 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.625 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.2528 time to fit residues: 27.3930 Evaluate side-chains 82 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5587 Z= 0.197 Angle : 0.558 7.194 7613 Z= 0.293 Chirality : 0.042 0.166 892 Planarity : 0.004 0.043 954 Dihedral : 4.116 19.591 774 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.54 (0.32), residues: 708 helix: 2.23 (0.33), residues: 238 sheet: -0.13 (0.36), residues: 211 loop : -0.96 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.676 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.2275 time to fit residues: 27.7839 Evaluate side-chains 87 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0543 time to fit residues: 1.6429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5587 Z= 0.249 Angle : 0.558 6.156 7613 Z= 0.292 Chirality : 0.042 0.153 892 Planarity : 0.004 0.040 954 Dihedral : 4.033 17.144 774 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.69 (0.32), residues: 708 helix: 2.50 (0.33), residues: 238 sheet: -0.11 (0.35), residues: 214 loop : -0.98 (0.38), residues: 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.711 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 92 average time/residue: 0.2270 time to fit residues: 26.0996 Evaluate side-chains 87 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1184 time to fit residues: 1.7005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 5587 Z= 0.308 Angle : 0.576 6.116 7613 Z= 0.300 Chirality : 0.043 0.155 892 Planarity : 0.004 0.038 954 Dihedral : 4.132 18.218 774 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.73 (0.33), residues: 708 helix: 2.51 (0.33), residues: 239 sheet: -0.17 (0.36), residues: 215 loop : -0.86 (0.39), residues: 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.686 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.2374 time to fit residues: 25.8136 Evaluate side-chains 83 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0552 time to fit residues: 1.2852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 272 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 5587 Z= 0.412 Angle : 0.636 7.905 7613 Z= 0.329 Chirality : 0.044 0.168 892 Planarity : 0.004 0.038 954 Dihedral : 4.296 17.808 774 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.57 (0.32), residues: 708 helix: 2.33 (0.33), residues: 244 sheet: -0.22 (0.36), residues: 215 loop : -1.02 (0.39), residues: 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.679 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.2342 time to fit residues: 24.4134 Evaluate side-chains 84 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1299 time to fit residues: 1.6469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5587 Z= 0.207 Angle : 0.565 7.710 7613 Z= 0.294 Chirality : 0.042 0.174 892 Planarity : 0.004 0.039 954 Dihedral : 4.105 19.259 774 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.73 (0.32), residues: 708 helix: 2.47 (0.33), residues: 244 sheet: -0.10 (0.36), residues: 215 loop : -0.97 (0.39), residues: 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.731 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 86 average time/residue: 0.2459 time to fit residues: 26.2396 Evaluate side-chains 78 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0604 time to fit residues: 1.1712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 0.0000 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.055 5587 Z= 0.557 Angle : 0.702 8.600 7613 Z= 0.363 Chirality : 0.047 0.185 892 Planarity : 0.004 0.039 954 Dihedral : 4.451 17.336 774 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.59 (0.33), residues: 708 helix: 2.15 (0.33), residues: 250 sheet: -0.12 (0.36), residues: 219 loop : -0.96 (0.41), residues: 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.698 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.2426 time to fit residues: 24.3732 Evaluate side-chains 78 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0550 time to fit residues: 1.4613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5587 Z= 0.204 Angle : 0.593 8.071 7613 Z= 0.310 Chirality : 0.042 0.185 892 Planarity : 0.004 0.039 954 Dihedral : 4.192 19.127 774 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.69 (0.32), residues: 708 helix: 2.42 (0.33), residues: 244 sheet: -0.10 (0.35), residues: 215 loop : -1.00 (0.39), residues: 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.689 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2240 time to fit residues: 23.0154 Evaluate side-chains 75 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 5587 Z= 0.280 Angle : 0.614 8.536 7613 Z= 0.321 Chirality : 0.043 0.196 892 Planarity : 0.004 0.038 954 Dihedral : 4.205 19.750 774 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.74 (0.33), residues: 708 helix: 2.44 (0.33), residues: 244 sheet: -0.08 (0.36), residues: 215 loop : -0.92 (0.40), residues: 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.668 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2282 time to fit residues: 22.2758 Evaluate side-chains 76 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.0060 chunk 8 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 272 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5587 Z= 0.201 Angle : 0.603 8.152 7613 Z= 0.313 Chirality : 0.043 0.209 892 Planarity : 0.004 0.047 954 Dihedral : 4.135 20.194 774 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.81 (0.33), residues: 708 helix: 2.45 (0.33), residues: 244 sheet: 0.03 (0.35), residues: 215 loop : -0.92 (0.40), residues: 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.721 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 76 average time/residue: 0.2339 time to fit residues: 22.3084 Evaluate side-chains 73 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0540 time to fit residues: 1.0915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065861 restraints weight = 11238.175| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.00 r_work: 0.2743 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 5587 Z= 0.273 Angle : 0.621 8.323 7613 Z= 0.323 Chirality : 0.043 0.200 892 Planarity : 0.004 0.038 954 Dihedral : 4.182 20.087 774 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.78 (0.33), residues: 708 helix: 2.43 (0.33), residues: 244 sheet: -0.00 (0.36), residues: 215 loop : -0.92 (0.40), residues: 249 =============================================================================== Job complete usr+sys time: 1440.40 seconds wall clock time: 26 minutes 45.40 seconds (1605.40 seconds total)