Starting phenix.real_space_refine on Sun Mar 10 20:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzo_16344/03_2024/8bzo_16344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzo_16344/03_2024/8bzo_16344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzo_16344/03_2024/8bzo_16344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzo_16344/03_2024/8bzo_16344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzo_16344/03_2024/8bzo_16344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzo_16344/03_2024/8bzo_16344_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 17 5.16 5 C 3134 2.51 5 N 821 2.21 5 O 861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4834 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2212 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 19, 'TRANS': 264} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'TPO:plan-1': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2029 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 243} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 593 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 64} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.32, per 1000 atoms: 0.69 Number of scatterers: 4834 At special positions: 0 Unit cell: (81.32, 93.09, 80.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 1 15.00 O 861 8.00 N 821 7.00 C 3134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 844.0 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 2 sheets defined 41.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.913A pdb=" N GLU A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.701A pdb=" N LEU A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.710A pdb=" N LEU A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 175' Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.557A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.716A pdb=" N ARG A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 258 through 266 removed outlier: 3.601A pdb=" N SER A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 262 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 263 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 266 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'B' and resid 179 through 191 removed outlier: 4.279A pdb=" N VAL B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.730A pdb=" N ILE B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 3.827A pdb=" N HIS B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 removed outlier: 4.275A pdb=" N GLN B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 265 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 266 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 295 through 301 removed outlier: 4.178A pdb=" N LYS B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.900A pdb=" N LEU B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N HIS B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 removed outlier: 3.674A pdb=" N SER B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.599A pdb=" N GLY B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR B 365 " --> pdb=" O HIS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 403 removed outlier: 3.808A pdb=" N GLN B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Proline residue: B 402 - end of helix Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'C' and resid 38 through 51 removed outlier: 3.540A pdb=" N HIS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing sheet with id= A, first strand: chain 'A' and resid 30 through 36 removed outlier: 7.022A pdb=" N GLU A 81 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 66 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 133 through 135 132 hydrogen bonds defined for protein. 354 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: 1.04 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 982 1.33 - 1.45: 1144 1.45 - 1.57: 2811 1.57 - 1.69: 1 1.69 - 1.82: 27 Bond restraints: 4965 Sorted by residual: bond pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.717 1.627 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" N VAL B 311 " pdb=" CA VAL B 311 " ideal model delta sigma weight residual 1.462 1.513 -0.051 1.17e-02 7.31e+03 1.89e+01 bond pdb=" N ARG A 122 " pdb=" CA ARG A 122 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.15e-02 7.56e+03 1.39e+01 bond pdb=" CA SER B 386 " pdb=" CB SER B 386 " ideal model delta sigma weight residual 1.531 1.470 0.060 1.69e-02 3.50e+03 1.28e+01 bond pdb=" CB TPO A 160 " pdb=" OG1 TPO A 160 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 4960 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.01: 148 106.01 - 113.03: 2694 113.03 - 120.05: 1778 120.05 - 127.07: 2070 127.07 - 134.09: 75 Bond angle restraints: 6765 Sorted by residual: angle pdb=" N HIS C 23 " pdb=" CA HIS C 23 " pdb=" C HIS C 23 " ideal model delta sigma weight residual 109.64 101.51 8.13 1.27e+00 6.20e-01 4.09e+01 angle pdb=" N ILE B 377 " pdb=" CA ILE B 377 " pdb=" C ILE B 377 " ideal model delta sigma weight residual 112.90 107.27 5.63 9.60e-01 1.09e+00 3.44e+01 angle pdb=" N LEU B 384 " pdb=" CA LEU B 384 " pdb=" C LEU B 384 " ideal model delta sigma weight residual 113.18 107.93 5.25 1.21e+00 6.83e-01 1.88e+01 angle pdb=" C GLU A 195 " pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " ideal model delta sigma weight residual 109.67 101.08 8.59 2.01e+00 2.48e-01 1.83e+01 angle pdb=" C LEU A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 122.43 127.45 -5.02 1.26e+00 6.30e-01 1.59e+01 ... (remaining 6760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 2520 16.13 - 32.26: 319 32.26 - 48.38: 111 48.38 - 64.51: 15 64.51 - 80.64: 7 Dihedral angle restraints: 2972 sinusoidal: 1156 harmonic: 1816 Sorted by residual: dihedral pdb=" C GLU A 195 " pdb=" N GLU A 195 " pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" CA HIS C 23 " pdb=" C HIS C 23 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LEU A 83 " pdb=" C LEU A 83 " pdb=" N HIS A 84 " pdb=" CA HIS A 84 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 2969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 559 0.046 - 0.093: 165 0.093 - 0.139: 30 0.139 - 0.185: 4 0.185 - 0.231: 3 Chirality restraints: 761 Sorted by residual: chirality pdb=" CA GLU A 195 " pdb=" N GLU A 195 " pdb=" C GLU A 195 " pdb=" CB GLU A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS C 47 " pdb=" N LYS C 47 " pdb=" C LYS C 47 " pdb=" CB LYS C 47 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG B 378 " pdb=" N ARG B 378 " pdb=" C ARG B 378 " pdb=" CB ARG B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 758 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 199 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C TYR B 199 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR B 199 " 0.018 2.00e-02 2.50e+03 pdb=" N MET B 200 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 353 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C SER B 353 " 0.043 2.00e-02 2.50e+03 pdb=" O SER B 353 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL B 354 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 60 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 61 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.027 5.00e-02 4.00e+02 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 946 2.77 - 3.30: 4584 3.30 - 3.83: 7583 3.83 - 4.37: 8941 4.37 - 4.90: 15198 Nonbonded interactions: 37252 Sorted by model distance: nonbonded pdb=" OD2 ASP A 68 " pdb=" NE1 TRP C 60 " model vdw 2.231 2.520 nonbonded pdb=" OG1 THR A 137 " pdb=" OE2 GLU A 138 " model vdw 2.232 2.440 nonbonded pdb=" O GLU A 42 " pdb=" NZ LYS B 266 " model vdw 2.251 2.520 nonbonded pdb=" OG SER B 331 " pdb=" O TYR B 418 " model vdw 2.258 2.440 nonbonded pdb=" NZ LYS A 278 " pdb=" O ASP B 177 " model vdw 2.267 2.520 ... (remaining 37247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 5.800 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.930 Find NCS groups from input model: 0.130 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.005 0.090 4965 Z= 0.340 Angle : 0.733 8.588 6765 Z= 0.428 Chirality : 0.046 0.231 761 Planarity : 0.005 0.048 860 Dihedral : 16.406 80.641 1796 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 0.99 % Allowed : 24.21 % Favored : 74.80 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.50 % 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: -1.51 (0.34), residues: 605 helix: -0.73 (0.33), residues: 270 sheet: -0.06 (1.14), residues: 25 loop : -1.27 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 167 HIS 0.010 0.001 HIS B 361 PHE 0.012 0.002 PHE A 80 TYR 0.015 0.001 TYR B 199 ARG 0.007 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.555 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 0.2096 time to fit residues: 25.3604 Evaluate side-chains 87 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain C residue 66 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.0060 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 GLN B 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4965 Z= 0.194 Angle : 0.575 7.310 6765 Z= 0.289 Chirality : 0.041 0.132 761 Planarity : 0.005 0.047 860 Dihedral : 4.959 41.736 672 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 2.38 % Allowed : 23.21 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.25 (0.34), residues: 605 helix: -0.37 (0.33), residues: 268 sheet: 0.06 (1.16), residues: 25 loop : -1.27 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.006 0.001 HIS B 296 PHE 0.009 0.001 PHE A 80 TYR 0.010 0.001 TYR C 88 ARG 0.005 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7543 (p0) outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.1822 time to fit residues: 24.1402 Evaluate side-chains 99 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4965 Z= 0.176 Angle : 0.546 7.521 6765 Z= 0.272 Chirality : 0.040 0.144 761 Planarity : 0.005 0.044 860 Dihedral : 4.424 31.905 670 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 3.37 % Allowed : 23.41 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.11 (0.35), residues: 605 helix: -0.31 (0.33), residues: 269 sheet: 0.19 (1.17), residues: 25 loop : -1.16 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.005 0.001 HIS B 296 PHE 0.008 0.001 PHE A 80 TYR 0.012 0.001 TYR C 88 ARG 0.006 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.593 Fit side-chains REVERT: A 86 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7391 (p0) outliers start: 17 outliers final: 8 residues processed: 106 average time/residue: 0.1649 time to fit residues: 22.5693 Evaluate side-chains 97 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4965 Z= 0.460 Angle : 0.710 7.815 6765 Z= 0.356 Chirality : 0.046 0.136 761 Planarity : 0.005 0.045 860 Dihedral : 5.060 28.305 668 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 5.16 % Allowed : 24.01 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.64 (0.33), residues: 605 helix: -0.76 (0.31), residues: 269 sheet: -0.23 (1.12), residues: 25 loop : -1.42 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 167 HIS 0.007 0.002 HIS A 125 PHE 0.017 0.002 PHE C 62 TYR 0.017 0.002 TYR B 199 ARG 0.005 0.001 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7563 (p0) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.1731 time to fit residues: 25.8165 Evaluate side-chains 108 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain C residue 66 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4965 Z= 0.190 Angle : 0.567 6.620 6765 Z= 0.283 Chirality : 0.040 0.136 761 Planarity : 0.005 0.049 860 Dihedral : 4.577 27.697 668 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.37 % Allowed : 24.80 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.23 (0.35), residues: 605 helix: -0.39 (0.33), residues: 268 sheet: -0.07 (1.14), residues: 25 loop : -1.22 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 217 HIS 0.005 0.001 HIS B 361 PHE 0.011 0.001 PHE A 240 TYR 0.010 0.001 TYR B 199 ARG 0.005 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 243 TRP cc_start: 0.7196 (OUTLIER) cc_final: 0.6209 (m-90) REVERT: A 265 GLN cc_start: 0.8260 (mp10) cc_final: 0.7959 (mp10) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 0.1730 time to fit residues: 23.3338 Evaluate side-chains 100 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 66 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 0.036 4965 Z= 0.202 Angle : 0.555 6.551 6765 Z= 0.277 Chirality : 0.041 0.142 761 Planarity : 0.005 0.048 860 Dihedral : 4.403 25.624 668 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.56 % Allowed : 25.00 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.14 (0.35), residues: 605 helix: -0.32 (0.33), residues: 271 sheet: 0.01 (1.14), residues: 25 loop : -1.17 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 372 HIS 0.005 0.001 HIS B 296 PHE 0.011 0.001 PHE A 240 TYR 0.013 0.001 TYR B 199 ARG 0.006 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8259 (tpt90) cc_final: 0.7853 (tpt170) REVERT: A 265 GLN cc_start: 0.8324 (mp10) cc_final: 0.7960 (mp10) outliers start: 23 outliers final: 16 residues processed: 105 average time/residue: 0.1722 time to fit residues: 23.1058 Evaluate side-chains 101 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS C 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4965 Z= 0.256 Angle : 0.583 7.066 6765 Z= 0.291 Chirality : 0.042 0.152 761 Planarity : 0.005 0.048 860 Dihedral : 4.537 24.132 668 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.56 % Allowed : 24.60 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.35), residues: 605 helix: -0.33 (0.33), residues: 269 sheet: -0.06 (1.13), residues: 25 loop : -1.20 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.004 0.001 HIS B 361 PHE 0.012 0.002 PHE C 62 TYR 0.017 0.001 TYR B 199 ARG 0.006 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 110 average time/residue: 0.1749 time to fit residues: 24.5562 Evaluate side-chains 109 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.199 Angle : 0.555 6.638 6765 Z= 0.278 Chirality : 0.041 0.146 761 Planarity : 0.005 0.048 860 Dihedral : 4.400 23.493 668 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.76 % Allowed : 25.40 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.08 (0.35), residues: 605 helix: -0.30 (0.33), residues: 272 sheet: 0.04 (1.15), residues: 25 loop : -1.12 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.004 0.001 HIS B 361 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR B 199 ARG 0.007 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 104 average time/residue: 0.1720 time to fit residues: 22.8126 Evaluate side-chains 104 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.198 Angle : 0.555 6.577 6765 Z= 0.278 Chirality : 0.041 0.142 761 Planarity : 0.005 0.047 860 Dihedral : 4.326 22.368 668 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.37 % Allowed : 25.40 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.35), residues: 605 helix: -0.24 (0.33), residues: 272 sheet: 1.29 (1.40), residues: 15 loop : -1.09 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.004 0.001 HIS B 361 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR B 199 ARG 0.007 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.583 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 21 residues processed: 101 average time/residue: 0.1651 time to fit residues: 21.5198 Evaluate side-chains 103 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.0060 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.181 Angle : 0.551 6.573 6765 Z= 0.277 Chirality : 0.041 0.141 761 Planarity : 0.005 0.047 860 Dihedral : 4.237 21.512 668 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.57 % Allowed : 26.19 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.92 (0.35), residues: 605 helix: -0.18 (0.33), residues: 272 sheet: -0.09 (1.26), residues: 21 loop : -0.98 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.004 0.001 HIS B 361 PHE 0.009 0.001 PHE A 240 TYR 0.010 0.001 TYR B 199 ARG 0.007 0.000 ARG A 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.8228 (mp10) cc_final: 0.7992 (mp10) outliers start: 18 outliers final: 17 residues processed: 99 average time/residue: 0.1700 time to fit residues: 21.6154 Evaluate side-chains 100 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.186502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161237 restraints weight = 6522.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165459 restraints weight = 4247.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168406 restraints weight = 3129.393| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.176 Angle : 0.557 6.536 6765 Z= 0.282 Chirality : 0.040 0.139 761 Planarity : 0.005 0.046 860 Dihedral : 4.149 20.547 668 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.77 % Allowed : 26.19 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.86 (0.35), residues: 605 helix: -0.11 (0.33), residues: 270 sheet: -0.03 (1.27), residues: 21 loop : -0.96 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.004 0.001 HIS B 361 PHE 0.009 0.001 PHE B 304 TYR 0.010 0.001 TYR B 199 ARG 0.007 0.000 ARG A 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.66 seconds wall clock time: 25 minutes 57.64 seconds (1557.64 seconds total)