Starting phenix.real_space_refine on Sun Mar 10 20:51:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lms_23441/03_2024/7lms_23441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lms_23441/03_2024/7lms_23441.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/7lms_23441/03_2024/7lms_23441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lms_23441/03_2024/7lms_23441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lms_23441/03_2024/7lms_23441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lms_23441/03_2024/7lms_23441_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= 0.079 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 Zn 1 6.06 5 S 24 5.16 5 C 3149 2.51 5 N 842 2.21 5 O 931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "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: 4947 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1066 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3854 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 455} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 391 SG CYS B 53 49.263 47.066 47.519 1.00 55.77 S ATOM 406 SG CYS B 55 47.370 44.708 48.994 1.00 70.90 S ATOM 857 SG CYS B 113 46.713 48.398 49.288 1.00 47.00 S Time building chain proxies: 3.44, per 1000 atoms: 0.70 Number of scatterers: 4947 At special positions: 0 Unit cell: (75.985, 80.995, 93.52, 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) Zn 1 29.99 S 24 16.00 O 931 8.00 N 842 7.00 C 3149 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: 1.85 Conformation dependent library (CDL) restraints added in 941.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 115 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 55 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 53 " Number of angles added : 3 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 42.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'A' and resid 23 through 36 Processing helix chain 'A' and resid 43 through 63 removed outlier: 5.467A pdb=" N TRP A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 54 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 Proline residue: A 80 - end of helix removed outlier: 3.583A pdb=" N MET A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 86 " --> pdb=" O MET A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 131 through 136 removed outlier: 4.101A pdb=" N ASN A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.306A pdb=" N THR A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 191 through 197 removed outlier: 4.092A pdb=" N TYR A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 226 removed outlier: 3.536A pdb=" N PHE A 207 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 318 through 324 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 420 through 440 removed outlier: 3.680A pdb=" N THR A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 459 through 493 Processing sheet with id= A, first strand: chain 'B' and resid 7 through 9 removed outlier: 6.381A pdb=" N THR B 41 " --> pdb=" O CYS B 28 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS B 28 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 57 through 62 Processing sheet with id= C, first strand: chain 'B' and resid 79 through 81 Processing sheet with id= D, first strand: chain 'B' and resid 95 through 99 removed outlier: 5.876A pdb=" N ALA B 132 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 121 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 111 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 96 through 101 Processing sheet with id= F, first strand: chain 'A' and resid 256 through 259 Processing sheet with id= G, first strand: chain 'A' and resid 286 through 289 Processing sheet with id= H, first strand: chain 'A' and resid 336 through 342 206 hydrogen bonds defined for protein. 441 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: 1.31 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1085 1.32 - 1.45: 1478 1.45 - 1.58: 2463 1.58 - 1.70: 1 1.70 - 1.83: 36 Bond restraints: 5063 Sorted by residual: bond pdb=" CD ARG A 75 " pdb=" NE ARG A 75 " ideal model delta sigma weight residual 1.458 1.398 0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" CD ARG B 13 " pdb=" NE ARG B 13 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" CB PHE A 106 " pdb=" CG PHE A 106 " ideal model delta sigma weight residual 1.502 1.410 0.092 2.30e-02 1.89e+03 1.59e+01 bond pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " ideal model delta sigma weight residual 1.516 1.417 0.099 2.50e-02 1.60e+03 1.56e+01 bond pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 1.502 1.411 0.091 2.30e-02 1.89e+03 1.55e+01 ... (remaining 5058 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.44: 164 106.44 - 113.90: 2688 113.90 - 121.36: 2832 121.36 - 128.82: 1133 128.82 - 136.27: 40 Bond angle restraints: 6857 Sorted by residual: angle pdb=" C TYR B 87 " pdb=" N PRO B 88 " pdb=" CA PRO B 88 " ideal model delta sigma weight residual 120.21 126.84 -6.63 9.60e-01 1.09e+00 4.77e+01 angle pdb=" C SER A 38 " pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta sigma weight residual 120.03 126.73 -6.70 9.90e-01 1.02e+00 4.59e+01 angle pdb=" C GLY A 140 " pdb=" N PRO A 141 " pdb=" CA PRO A 141 " ideal model delta sigma weight residual 119.56 126.11 -6.55 1.02e+00 9.61e-01 4.13e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 120.04 126.84 -6.80 1.08e+00 8.57e-01 3.96e+01 angle pdb=" C GLY A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 119.28 126.18 -6.90 1.10e+00 8.26e-01 3.94e+01 ... (remaining 6852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 2849 14.10 - 28.20: 120 28.20 - 42.30: 17 42.30 - 56.39: 10 56.39 - 70.49: 11 Dihedral angle restraints: 3007 sinusoidal: 1217 harmonic: 1790 Sorted by residual: dihedral pdb=" CA ARG B 112 " pdb=" C ARG B 112 " pdb=" N CYS B 113 " pdb=" CA CYS B 113 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" C PHE A 409 " pdb=" N PHE A 409 " pdb=" CA PHE A 409 " pdb=" CB PHE A 409 " ideal model delta harmonic sigma weight residual -122.60 -131.16 8.56 0 2.50e+00 1.60e-01 1.17e+01 dihedral pdb=" CA VAL B 15 " pdb=" C VAL B 15 " pdb=" N ASN B 16 " pdb=" CA ASN B 16 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 381 0.062 - 0.123: 272 0.123 - 0.185: 61 0.185 - 0.247: 24 0.247 - 0.309: 6 Chirality restraints: 744 Sorted by residual: chirality pdb=" CA PHE A 79 " pdb=" N PHE A 79 " pdb=" C PHE A 79 " pdb=" CB PHE A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA PHE A 220 " pdb=" N PHE A 220 " pdb=" C PHE A 220 " pdb=" CB PHE A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA LYS A 126 " pdb=" N LYS A 126 " pdb=" C LYS A 126 " pdb=" CB LYS A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 741 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' SAH A 601 " -0.309 2.00e-02 2.50e+03 1.26e-01 4.34e+02 pdb=" C2 SAH A 601 " 0.057 2.00e-02 2.50e+03 pdb=" C4 SAH A 601 " 0.075 2.00e-02 2.50e+03 pdb=" C5 SAH A 601 " 0.027 2.00e-02 2.50e+03 pdb=" C6 SAH A 601 " -0.040 2.00e-02 2.50e+03 pdb=" C8 SAH A 601 " 0.123 2.00e-02 2.50e+03 pdb=" N1 SAH A 601 " -0.020 2.00e-02 2.50e+03 pdb=" N3 SAH A 601 " 0.092 2.00e-02 2.50e+03 pdb=" N6 SAH A 601 " -0.170 2.00e-02 2.50e+03 pdb=" N7 SAH A 601 " 0.072 2.00e-02 2.50e+03 pdb=" N9 SAH A 601 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 85 " -0.075 2.00e-02 2.50e+03 3.58e-02 3.21e+01 pdb=" CG TRP A 85 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 85 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 85 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP A 85 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 85 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 85 " 0.044 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 85 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 85 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 85 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 344 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C SER A 344 " 0.050 2.00e-02 2.50e+03 pdb=" O SER A 344 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS A 345 " -0.017 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 2283 2.93 - 3.42: 4754 3.42 - 3.91: 8336 3.91 - 4.41: 9674 4.41 - 4.90: 15291 Nonbonded interactions: 40338 Sorted by model distance: nonbonded pdb=" OH TYR A 288 " pdb=" OD1 ASP A 293 " model vdw 2.432 2.440 nonbonded pdb=" N ASP A 72 " pdb=" OD1 ASP A 72 " model vdw 2.466 2.520 nonbonded pdb=" OD1 ASP A 347 " pdb=" N ARG A 348 " model vdw 2.489 2.520 nonbonded pdb=" N ASN A 154 " pdb=" OD1 ASN A 154 " model vdw 2.506 2.520 nonbonded pdb=" NZ LYS A 84 " pdb=" OE2 GLU A 88 " model vdw 2.508 2.520 ... (remaining 40333 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: 0.830 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: 3.710 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.019 0.107 5063 Z= 1.258 Angle : 1.521 9.540 6857 Z= 1.037 Chirality : 0.085 0.309 744 Planarity : 0.009 0.126 880 Dihedral : 10.075 70.493 1855 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.31), residues: 608 helix: 0.26 (0.29), residues: 259 sheet: -0.63 (0.55), residues: 85 loop : 1.18 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.008 TRP A 85 HIS 0.006 0.001 HIS B 68 PHE 0.029 0.005 PHE A 368 TYR 0.036 0.004 TYR B 60 ARG 0.007 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7545 (ttm-80) REVERT: B 80 GLU cc_start: 0.8326 (tt0) cc_final: 0.7965 (tt0) REVERT: A 276 MET cc_start: 0.8548 (mmm) cc_final: 0.7855 (mmt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2062 time to fit residues: 40.6832 Evaluate side-chains 82 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5063 Z= 0.197 Angle : 0.547 6.111 6857 Z= 0.295 Chirality : 0.043 0.181 744 Planarity : 0.005 0.034 880 Dihedral : 4.518 18.047 674 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.82 % Allowed : 8.46 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.77 (0.33), residues: 608 helix: 0.68 (0.33), residues: 260 sheet: -1.04 (0.53), residues: 85 loop : 1.21 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 30 HIS 0.003 0.001 HIS B 68 PHE 0.021 0.002 PHE A 159 TYR 0.016 0.002 TYR B 86 ARG 0.004 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 HIS cc_start: 0.8028 (p-80) cc_final: 0.7710 (p-80) REVERT: B 86 TYR cc_start: 0.8211 (m-80) cc_final: 0.7883 (m-10) REVERT: A 293 ASP cc_start: 0.8440 (t0) cc_final: 0.7723 (t0) REVERT: A 400 LEU cc_start: 0.8277 (mm) cc_final: 0.7788 (pp) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 0.1631 time to fit residues: 21.3294 Evaluate side-chains 87 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.0000 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN A 209 GLN A 380 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5063 Z= 0.175 Angle : 0.522 7.301 6857 Z= 0.271 Chirality : 0.041 0.193 744 Planarity : 0.004 0.033 880 Dihedral : 4.265 20.139 674 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.82 % Allowed : 9.02 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.45 (0.33), residues: 608 helix: 0.46 (0.33), residues: 265 sheet: -0.98 (0.52), residues: 79 loop : 0.84 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 85 HIS 0.003 0.001 HIS B 68 PHE 0.014 0.002 PHE A 159 TYR 0.014 0.001 TYR A 489 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8071 (mpt180) REVERT: B 89 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7861 (ttt180) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.1637 time to fit residues: 20.5250 Evaluate side-chains 86 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8160 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5063 Z= 0.150 Angle : 0.490 5.946 6857 Z= 0.257 Chirality : 0.040 0.191 744 Planarity : 0.004 0.032 880 Dihedral : 4.030 17.693 674 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.01 % Allowed : 9.21 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.44 (0.33), residues: 608 helix: 0.50 (0.33), residues: 265 sheet: -1.04 (0.52), residues: 81 loop : 0.81 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 30 HIS 0.002 0.000 HIS B 18 PHE 0.010 0.001 PHE A 303 TYR 0.023 0.001 TYR A 489 ARG 0.004 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 TYR cc_start: 0.8428 (m-80) cc_final: 0.8175 (m-80) REVERT: B 89 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7870 (ttt180) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.1644 time to fit residues: 19.5445 Evaluate side-chains 88 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 52 optimal weight: 0.0040 chunk 14 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 overall best weight: 0.1630 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5063 Z= 0.116 Angle : 0.472 6.339 6857 Z= 0.246 Chirality : 0.039 0.177 744 Planarity : 0.004 0.031 880 Dihedral : 3.843 17.961 674 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.07 % Allowed : 10.90 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.33), residues: 608 helix: 0.62 (0.34), residues: 261 sheet: -1.27 (0.51), residues: 83 loop : 0.93 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 25 HIS 0.001 0.000 HIS B 45 PHE 0.028 0.001 PHE A 207 TYR 0.017 0.001 TYR A 489 ARG 0.004 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 TYR cc_start: 0.8402 (m-80) cc_final: 0.8111 (m-80) REVERT: B 89 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7793 (ttt90) REVERT: A 155 ILE cc_start: 0.9428 (mm) cc_final: 0.9217 (mm) REVERT: A 276 MET cc_start: 0.8010 (mmt) cc_final: 0.7541 (mmt) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.1778 time to fit residues: 21.9144 Evaluate side-chains 85 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5063 Z= 0.250 Angle : 0.530 5.548 6857 Z= 0.277 Chirality : 0.042 0.220 744 Planarity : 0.004 0.032 880 Dihedral : 4.058 22.489 674 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.01 % Allowed : 12.03 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.39 (0.33), residues: 608 helix: 0.55 (0.33), residues: 261 sheet: -1.22 (0.53), residues: 81 loop : 0.71 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.003 0.001 HIS B 68 PHE 0.031 0.002 PHE A 207 TYR 0.019 0.002 TYR A 489 ARG 0.005 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8211 (mpt180) cc_final: 0.7988 (mmp80) REVERT: B 85 GLU cc_start: 0.8452 (pm20) cc_final: 0.8092 (pm20) REVERT: B 86 TYR cc_start: 0.8446 (m-80) cc_final: 0.7763 (m-10) REVERT: B 89 ARG cc_start: 0.8084 (ttm170) cc_final: 0.7765 (ttt180) outliers start: 16 outliers final: 13 residues processed: 85 average time/residue: 0.1700 time to fit residues: 19.0009 Evaluate side-chains 83 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8217 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5063 Z= 0.191 Angle : 0.497 5.824 6857 Z= 0.259 Chirality : 0.041 0.186 744 Planarity : 0.004 0.032 880 Dihedral : 3.990 20.246 674 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.63 % Allowed : 13.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.34), residues: 608 helix: 0.62 (0.34), residues: 259 sheet: -1.35 (0.53), residues: 81 loop : 0.72 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 25 HIS 0.002 0.001 HIS B 68 PHE 0.034 0.002 PHE A 207 TYR 0.011 0.001 TYR A 241 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8189 (mpt180) cc_final: 0.7925 (mmp80) REVERT: B 80 GLU cc_start: 0.8505 (tt0) cc_final: 0.8180 (tt0) REVERT: B 85 GLU cc_start: 0.8403 (pm20) cc_final: 0.8198 (pm20) REVERT: B 86 TYR cc_start: 0.8404 (m-80) cc_final: 0.8075 (m-80) REVERT: A 98 MET cc_start: 0.8180 (mmt) cc_final: 0.7779 (mmm) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.1719 time to fit residues: 18.9502 Evaluate side-chains 84 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 52 optimal weight: 0.0000 chunk 55 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 overall best weight: 0.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN A 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5063 Z= 0.127 Angle : 0.477 6.022 6857 Z= 0.248 Chirality : 0.040 0.175 744 Planarity : 0.004 0.031 880 Dihedral : 3.796 17.612 674 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.88 % Allowed : 13.16 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.34), residues: 608 helix: 0.85 (0.34), residues: 253 sheet: -1.59 (0.57), residues: 71 loop : 0.71 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 25 HIS 0.003 0.001 HIS A 455 PHE 0.032 0.001 PHE A 207 TYR 0.011 0.001 TYR A 489 ARG 0.008 0.001 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8098 (mpt180) cc_final: 0.7896 (mmp80) REVERT: B 86 TYR cc_start: 0.8313 (m-80) cc_final: 0.7960 (m-80) outliers start: 10 outliers final: 10 residues processed: 88 average time/residue: 0.1535 time to fit residues: 17.8711 Evaluate side-chains 86 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5063 Z= 0.183 Angle : 0.507 6.709 6857 Z= 0.262 Chirality : 0.042 0.226 744 Planarity : 0.004 0.031 880 Dihedral : 3.871 19.167 674 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.88 % Allowed : 14.66 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.34), residues: 608 helix: 0.95 (0.35), residues: 254 sheet: -1.44 (0.54), residues: 81 loop : 0.68 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.006 0.001 HIS A 455 PHE 0.032 0.001 PHE A 207 TYR 0.011 0.001 TYR B 86 ARG 0.007 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8141 (mpt180) cc_final: 0.7900 (mmp80) REVERT: B 85 GLU cc_start: 0.8464 (pm20) cc_final: 0.8215 (pm20) REVERT: B 86 TYR cc_start: 0.8263 (m-80) cc_final: 0.8009 (m-80) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.1604 time to fit residues: 17.3273 Evaluate side-chains 82 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5063 Z= 0.150 Angle : 0.502 7.000 6857 Z= 0.256 Chirality : 0.041 0.236 744 Planarity : 0.004 0.031 880 Dihedral : 3.758 17.820 674 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.88 % Allowed : 14.66 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.35), residues: 608 helix: 1.11 (0.35), residues: 247 sheet: -1.55 (0.53), residues: 85 loop : 0.87 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 25 HIS 0.006 0.001 HIS A 455 PHE 0.032 0.001 PHE A 207 TYR 0.010 0.001 TYR A 489 ARG 0.007 0.000 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 79 average time/residue: 0.1654 time to fit residues: 17.1769 Evaluate side-chains 82 residues out of total 532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 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: 5.9990 chunk 41 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083830 restraints weight = 8070.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087991 restraints weight = 3958.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.090830 restraints weight = 2457.140| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5063 Z= 0.158 Angle : 0.493 6.696 6857 Z= 0.254 Chirality : 0.041 0.222 744 Planarity : 0.004 0.031 880 Dihedral : 3.731 18.757 674 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.26 % Allowed : 14.66 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.75 (0.35), residues: 608 helix: 1.14 (0.35), residues: 249 sheet: -1.57 (0.53), residues: 85 loop : 0.82 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 25 HIS 0.006 0.001 HIS A 455 PHE 0.031 0.001 PHE A 207 TYR 0.010 0.001 TYR A 489 ARG 0.007 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.60 seconds wall clock time: 26 minutes 28.37 seconds (1588.37 seconds total)