Starting phenix.real_space_refine on Thu Nov 14 15:12:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zl9_38897/11_2024/8zl9_38897.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zl9_38897/11_2024/8zl9_38897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zl9_38897/11_2024/8zl9_38897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zl9_38897/11_2024/8zl9_38897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zl9_38897/11_2024/8zl9_38897.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zl9_38897/11_2024/8zl9_38897.cif" } resolution = 4.36 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4208 2.51 5 N 1171 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6644 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 926 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "B" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1276 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 143} Chain breaks: 4 Chain: "D" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1608 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 181} Chain breaks: 5 Chain: "E" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1959 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 220} Chain breaks: 4 Time building chain proxies: 4.34, per 1000 atoms: 0.65 Number of scatterers: 6644 At special positions: 0 Unit cell: (105.93, 90.95, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1235 8.00 N 1171 7.00 C 4208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 50 " distance=2.03 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 107 " distance=2.02 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 92 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.56 Conformation dependent library (CDL) restraints added in 946.0 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 17 sheets defined 3.2% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.553A pdb=" N ASP B 86 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 87 " --> pdb=" O ALA B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 87' Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'D' and resid 129 through 133 removed outlier: 4.022A pdb=" N GLY D 132 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN D 133 " --> pdb=" O ALA D 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 133' Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 482 through 487 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.659A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.964A pdb=" N TYR A 94 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 116 " --> pdb=" O TYR A 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.801A pdb=" N ALA B 19 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 79 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 75 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.916A pdb=" N GLY B 88 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP B 39 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 51 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 57 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 126 through 128 Processing sheet with id=AA8, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA9, first strand: chain 'C' and resid 241 through 244 removed outlier: 3.640A pdb=" N ASP C 305 " --> pdb=" O CYS C 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'D' and resid 154 through 158 removed outlier: 4.137A pdb=" N VAL D 154 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE D 375 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 394 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 154 through 158 removed outlier: 4.137A pdb=" N VAL D 154 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE D 375 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG D 389 " --> pdb=" O SER D 521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 241 through 242 removed outlier: 3.514A pdb=" N VAL D 310 " --> pdb=" O TYR E 312 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR E 312 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 496 through 498 Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 128 removed outlier: 3.536A pdb=" N THR E 125 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 375 through 377 Processing sheet with id=AB8, first strand: chain 'E' and resid 492 through 498 86 hydrogen bonds defined for protein. 195 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: 1.56 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1413 1.33 - 1.45: 1743 1.45 - 1.58: 3639 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 6834 Sorted by residual: bond pdb=" C PHE D 137 " pdb=" N PRO D 138 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.33e-02 5.65e+03 5.79e+00 bond pdb=" N PRO D 138 " pdb=" CA PRO D 138 " ideal model delta sigma weight residual 1.466 1.495 -0.029 1.23e-02 6.61e+03 5.48e+00 bond pdb=" C PRO D 138 " pdb=" O PRO D 138 " ideal model delta sigma weight residual 1.233 1.204 0.028 1.23e-02 6.61e+03 5.32e+00 bond pdb=" C LEU E 515 " pdb=" N PRO E 516 " ideal model delta sigma weight residual 1.334 1.385 -0.052 2.34e-02 1.83e+03 4.85e+00 bond pdb=" C PRO E 531 " pdb=" O PRO E 531 " ideal model delta sigma weight residual 1.235 1.208 0.027 1.30e-02 5.92e+03 4.21e+00 ... (remaining 6829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 9025 2.59 - 5.19: 227 5.19 - 7.78: 36 7.78 - 10.37: 8 10.37 - 12.96: 3 Bond angle restraints: 9299 Sorted by residual: angle pdb=" N PRO D 138 " pdb=" CA PRO D 138 " pdb=" C PRO D 138 " ideal model delta sigma weight residual 111.11 124.07 -12.96 1.59e+00 3.96e-01 6.65e+01 angle pdb=" C THR D 136 " pdb=" N PHE D 137 " pdb=" CA PHE D 137 " ideal model delta sigma weight residual 122.85 115.30 7.55 1.10e+00 8.26e-01 4.71e+01 angle pdb=" C PRO D 138 " pdb=" CA PRO D 138 " pdb=" CB PRO D 138 " ideal model delta sigma weight residual 111.39 102.76 8.63 1.28e+00 6.10e-01 4.54e+01 angle pdb=" C PHE D 137 " pdb=" CA PHE D 137 " pdb=" CB PHE D 137 " ideal model delta sigma weight residual 111.27 120.71 -9.44 1.47e+00 4.63e-01 4.13e+01 angle pdb=" C ARG E 511 " pdb=" N ASP E 512 " pdb=" CA ASP E 512 " ideal model delta sigma weight residual 121.54 133.32 -11.78 1.91e+00 2.74e-01 3.80e+01 ... (remaining 9294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3616 17.93 - 35.87: 356 35.87 - 53.80: 57 53.80 - 71.73: 6 71.73 - 89.67: 9 Dihedral angle restraints: 4044 sinusoidal: 1642 harmonic: 2402 Sorted by residual: dihedral pdb=" CA MET A 109 " pdb=" C MET A 109 " pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta harmonic sigma weight residual -180.00 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 dihedral pdb=" CB CYS A 102 " pdb=" SG CYS A 102 " pdb=" SG CYS A 107 " pdb=" CB CYS A 107 " ideal model delta sinusoidal sigma weight residual -86.00 -163.06 77.06 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 50 " pdb=" CB CYS A 50 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 727 0.054 - 0.108: 170 0.108 - 0.162: 62 0.162 - 0.217: 7 0.217 - 0.271: 6 Chirality restraints: 972 Sorted by residual: chirality pdb=" CB THR A 91 " pdb=" CA THR A 91 " pdb=" OG1 THR A 91 " pdb=" CG2 THR A 91 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR E 513 " pdb=" CA THR E 513 " pdb=" OG1 THR E 513 " pdb=" CG2 THR E 513 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA PRO D 138 " pdb=" N PRO D 138 " pdb=" C PRO D 138 " pdb=" CB PRO D 138 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 969 not shown) Planarity restraints: 1223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 515 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO E 516 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 516 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 516 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 159 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO C 160 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 511 " -0.215 9.50e-02 1.11e+02 9.67e-02 6.04e+00 pdb=" NE ARG C 511 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 511 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 511 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 511 " -0.011 2.00e-02 2.50e+03 ... (remaining 1220 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1116 2.77 - 3.31: 5859 3.31 - 3.84: 11071 3.84 - 4.37: 11863 4.37 - 4.90: 20066 Nonbonded interactions: 49975 Sorted by model distance: nonbonded pdb=" NH1 ARG A 100 " pdb=" OG SER E 387 " model vdw 2.243 3.120 nonbonded pdb=" OD1 ASN D 390 " pdb=" OG SER D 521 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR B 56 " pdb=" OD1 ASN B 57 " model vdw 2.281 3.040 nonbonded pdb=" O PRO B 8 " pdb=" OG1 THR B 106 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR B 5 " pdb=" O ARG B 24 " model vdw 2.286 3.040 ... (remaining 49970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.850 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.190 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5197 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 0.067 6834 Z= 0.315 Angle : 1.006 12.964 9299 Z= 0.549 Chirality : 0.058 0.271 972 Planarity : 0.009 0.097 1223 Dihedral : 14.246 89.668 2492 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.61 % Favored : 92.02 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.31 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.27), residues: 802 helix: -4.35 (0.70), residues: 12 sheet: -0.61 (0.38), residues: 171 loop : -1.94 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 100 HIS 0.004 0.001 HIS E 503 PHE 0.031 0.003 PHE A 29 TYR 0.032 0.002 TYR D 155 ARG 0.015 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 THR cc_start: 0.8307 (m) cc_final: 0.8024 (p) REVERT: C 509 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5994 (mm-40) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1869 time to fit residues: 29.2006 Evaluate side-chains 86 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 82 GLN B 35 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6834 Z= 0.365 Angle : 0.841 12.398 9299 Z= 0.441 Chirality : 0.050 0.180 972 Planarity : 0.009 0.085 1223 Dihedral : 7.000 34.885 913 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.22 % Favored : 89.40 % Rotamer: Outliers : 0.27 % Allowed : 6.86 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.27), residues: 802 helix: -4.49 (0.49), residues: 12 sheet: -1.07 (0.34), residues: 205 loop : -2.08 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 112 HIS 0.006 0.001 HIS E 502 PHE 0.023 0.004 PHE E 375 TYR 0.040 0.003 TYR A 103 ARG 0.006 0.001 ARG E 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7180 (mp) cc_final: 0.6866 (mp) REVERT: B 25 SER cc_start: 0.6465 (p) cc_final: 0.6040 (m) REVERT: D 509 GLN cc_start: -0.0924 (OUTLIER) cc_final: -0.1995 (mm-40) REVERT: E 230 GLN cc_start: 0.7197 (pm20) cc_final: 0.6691 (pp30) REVERT: E 482 HIS cc_start: 0.5049 (m-70) cc_final: 0.4728 (m-70) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.1694 time to fit residues: 24.7652 Evaluate side-chains 86 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 25 optimal weight: 0.0040 chunk 60 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 57 ASN C 503 HIS D 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 127 GLN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6834 Z= 0.210 Angle : 0.680 8.136 9299 Z= 0.350 Chirality : 0.047 0.176 972 Planarity : 0.008 0.083 1223 Dihedral : 6.247 35.960 913 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.61 % Favored : 92.02 % Rotamer: Outliers : 0.27 % Allowed : 4.12 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.28), residues: 802 helix: -4.08 (0.72), residues: 12 sheet: -1.03 (0.31), residues: 234 loop : -2.00 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 HIS 0.006 0.001 HIS C 503 PHE 0.012 0.002 PHE E 371 TYR 0.018 0.001 TYR A 103 ARG 0.006 0.001 ARG C 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.5129 (t60) cc_final: 0.4822 (t60) REVERT: A 109 MET cc_start: 0.4690 (ttm) cc_final: 0.4040 (ttm) REVERT: B 21 ILE cc_start: 0.7064 (mp) cc_final: 0.6806 (mp) REVERT: B 25 SER cc_start: 0.6204 (p) cc_final: 0.5874 (m) REVERT: E 230 GLN cc_start: 0.7381 (pm20) cc_final: 0.7000 (pp30) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.1870 time to fit residues: 29.5637 Evaluate side-chains 93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN D 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5308 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6834 Z= 0.183 Angle : 0.643 7.699 9299 Z= 0.327 Chirality : 0.045 0.172 972 Planarity : 0.007 0.082 1223 Dihedral : 5.783 36.055 913 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.73 % Favored : 91.02 % Rotamer: Outliers : 0.14 % Allowed : 2.33 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.28), residues: 802 helix: -3.71 (0.86), residues: 12 sheet: -0.98 (0.32), residues: 235 loop : -1.80 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 36 HIS 0.005 0.000 HIS E 484 PHE 0.010 0.001 PHE E 371 TYR 0.014 0.001 TYR A 103 ARG 0.005 0.001 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4584 (ttm) cc_final: 0.4134 (ttm) REVERT: B 21 ILE cc_start: 0.7023 (mp) cc_final: 0.6766 (mp) REVERT: B 25 SER cc_start: 0.5940 (p) cc_final: 0.5651 (m) REVERT: E 230 GLN cc_start: 0.7475 (pm20) cc_final: 0.7137 (pp30) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1773 time to fit residues: 28.3306 Evaluate side-chains 93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 HIS D 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6834 Z= 0.226 Angle : 0.679 7.670 9299 Z= 0.346 Chirality : 0.047 0.260 972 Planarity : 0.007 0.079 1223 Dihedral : 5.880 35.954 913 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.48 % Favored : 90.27 % Rotamer: Outliers : 0.14 % Allowed : 2.61 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.28), residues: 802 helix: -3.72 (0.83), residues: 12 sheet: -1.07 (0.32), residues: 232 loop : -1.78 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 36 HIS 0.007 0.001 HIS C 503 PHE 0.012 0.002 PHE E 371 TYR 0.017 0.001 TYR A 103 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.3718 (ttm) cc_final: 0.3097 (ttm) REVERT: B 21 ILE cc_start: 0.6967 (mp) cc_final: 0.6690 (mp) REVERT: B 25 SER cc_start: 0.5970 (p) cc_final: 0.5679 (m) REVERT: E 230 GLN cc_start: 0.7631 (pm20) cc_final: 0.7263 (pp30) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2104 time to fit residues: 33.6432 Evaluate side-chains 93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN D 480 ASN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6834 Z= 0.262 Angle : 0.720 8.583 9299 Z= 0.369 Chirality : 0.048 0.201 972 Planarity : 0.007 0.077 1223 Dihedral : 6.079 37.039 913 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.10 % Favored : 89.65 % Rotamer: Outliers : 0.27 % Allowed : 2.33 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.28), residues: 802 helix: -3.79 (0.87), residues: 12 sheet: -1.30 (0.32), residues: 220 loop : -1.83 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 36 HIS 0.004 0.001 HIS E 502 PHE 0.016 0.002 PHE D 393 TYR 0.020 0.002 TYR D 155 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.6979 (mt) cc_final: 0.6704 (mt) REVERT: A 109 MET cc_start: 0.4047 (ttm) cc_final: 0.3554 (ttm) REVERT: B 21 ILE cc_start: 0.7081 (mp) cc_final: 0.6780 (mp) REVERT: C 313 SER cc_start: 0.5479 (t) cc_final: 0.5278 (m) outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.1831 time to fit residues: 27.5988 Evaluate side-chains 97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 58 optimal weight: 0.2980 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.0030 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.3308 ------------------------------------------------------------------------------- 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: 0.5306 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6834 Z= 0.179 Angle : 0.642 7.271 9299 Z= 0.326 Chirality : 0.046 0.170 972 Planarity : 0.007 0.071 1223 Dihedral : 5.683 35.497 913 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.98 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 802 helix: -3.53 (1.02), residues: 12 sheet: -0.95 (0.32), residues: 227 loop : -1.76 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 36 HIS 0.002 0.000 HIS D 311 PHE 0.024 0.002 PHE D 393 TYR 0.012 0.001 TYR D 155 ARG 0.009 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.6315 (mtm180) cc_final: 0.6007 (mtp180) REVERT: B 21 ILE cc_start: 0.6877 (mp) cc_final: 0.6231 (tp) REVERT: E 174 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6655 (mtp180) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2257 time to fit residues: 33.5113 Evaluate side-chains 91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 HIS E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6834 Z= 0.273 Angle : 0.737 8.687 9299 Z= 0.378 Chirality : 0.049 0.287 972 Planarity : 0.007 0.074 1223 Dihedral : 6.114 40.530 913 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.72 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.28), residues: 802 helix: -3.49 (1.13), residues: 12 sheet: -1.24 (0.34), residues: 217 loop : -1.76 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 112 HIS 0.005 0.001 HIS A 59 PHE 0.015 0.002 PHE E 393 TYR 0.019 0.002 TYR D 155 ARG 0.014 0.001 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7029 (mtm180) cc_final: 0.6519 (mpp80) REVERT: B 21 ILE cc_start: 0.6971 (mp) cc_final: 0.6707 (mp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1717 time to fit residues: 25.7464 Evaluate side-chains 99 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 78 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 HIS ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6834 Z= 0.223 Angle : 0.691 7.537 9299 Z= 0.351 Chirality : 0.048 0.252 972 Planarity : 0.007 0.074 1223 Dihedral : 5.930 36.659 913 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.35 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.28), residues: 802 helix: -3.46 (1.17), residues: 12 sheet: -0.99 (0.36), residues: 198 loop : -1.71 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 47 HIS 0.003 0.001 HIS E 502 PHE 0.019 0.002 PHE B 102 TYR 0.016 0.002 TYR D 155 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.6861 (mtm180) cc_final: 0.6163 (mpp80) REVERT: B 21 ILE cc_start: 0.6971 (mp) cc_final: 0.6671 (mp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1849 time to fit residues: 26.4532 Evaluate side-chains 93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 76 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 0.0010 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6834 Z= 0.184 Angle : 0.654 7.224 9299 Z= 0.330 Chirality : 0.047 0.238 972 Planarity : 0.007 0.071 1223 Dihedral : 5.582 38.158 913 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.10 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.29), residues: 802 helix: -3.43 (1.17), residues: 12 sheet: -0.89 (0.35), residues: 200 loop : -1.62 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.002 0.000 HIS D 311 PHE 0.015 0.002 PHE B 102 TYR 0.013 0.001 TYR D 155 ARG 0.008 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.5690 (mt) cc_final: 0.5457 (mt) REVERT: B 21 ILE cc_start: 0.6860 (mp) cc_final: 0.6593 (mp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1845 time to fit residues: 27.1390 Evaluate side-chains 91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 0.0040 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 0.0010 chunk 75 optimal weight: 3.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 509 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.227775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.217486 restraints weight = 15669.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.217805 restraints weight = 15202.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.218451 restraints weight = 13577.832| |-----------------------------------------------------------------------------| r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5308 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6834 Z= 0.176 Angle : 0.638 7.503 9299 Z= 0.321 Chirality : 0.046 0.234 972 Planarity : 0.007 0.071 1223 Dihedral : 5.334 36.728 913 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.23 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.95 (0.29), residues: 802 helix: -3.49 (1.11), residues: 12 sheet: -0.69 (0.35), residues: 215 loop : -1.58 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 36 HIS 0.001 0.000 HIS D 311 PHE 0.012 0.001 PHE B 102 TYR 0.013 0.001 TYR D 155 ARG 0.013 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.52 seconds wall clock time: 35 minutes 44.30 seconds (2144.30 seconds total)