Starting phenix.real_space_refine on Sun Apr 27 22:35:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl9_60223/04_2025/8zl9_60223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl9_60223/04_2025/8zl9_60223.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/cci-nas-00/data/ceres_data/8zl9_60223/04_2025/8zl9_60223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl9_60223/04_2025/8zl9_60223.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl9_60223/04_2025/8zl9_60223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl9_60223/04_2025/8zl9_60223.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-5669/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: 4.57, per 1000 atoms: 0.69 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: 1.38 Conformation dependent library (CDL) restraints added in 904.2 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: 0.79 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: 1.74 Time building geometry restraints manager: 1.70 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: 0.010 Normalize map: mean=0, sd=1: 1.510 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.670 Find NCS groups from input model: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- 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 6838 Z= 0.222 Angle : 1.007 12.964 9307 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 Details of bonding type rmsd hydrogen bonds : bond 0.28950 ( 82) hydrogen bonds : angle 11.16141 ( 195) SS BOND : bond 0.00509 ( 4) SS BOND : angle 2.23700 ( 8) covalent geometry : bond 0.00450 ( 6834) covalent geometry : angle 1.00551 ( 9299) *********************** 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 : 0.762 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: 0.1857 time to fit residues: 29.0045 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 : 0.780 ------------------------------------------------------------------------------- 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: 0.0070 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: 2.1204 ------------------------------------------------------------------------------- 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 315 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.217259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.201940 restraints weight = 15064.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.203240 restraints weight = 12436.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.204384 restraints weight = 10932.537| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 6838 Z= 0.248 Angle : 0.844 12.426 9307 Z= 0.441 Chirality : 0.050 0.177 972 Planarity : 0.009 0.086 1223 Dihedral : 6.998 35.122 913 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.22 % Favored : 89.40 % Rotamer: Outliers : 0.41 % Allowed : 7.00 % Favored : 92.59 % 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: -2.63 (0.27), residues: 802 helix: -4.53 (0.46), residues: 12 sheet: -1.09 (0.34), residues: 205 loop : -2.08 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 112 HIS 0.006 0.001 HIS E 502 PHE 0.023 0.004 PHE E 375 TYR 0.041 0.003 TYR A 103 ARG 0.006 0.001 ARG D 380 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 82) hydrogen bonds : angle 8.35619 ( 195) SS BOND : bond 0.00943 ( 4) SS BOND : angle 2.87874 ( 8) covalent geometry : bond 0.00561 ( 6834) covalent geometry : angle 0.84040 ( 9299) *********************** 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 107 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7501 (mp) cc_final: 0.7173 (mp) REVERT: B 25 SER cc_start: 0.6546 (p) cc_final: 0.6184 (m) REVERT: D 509 GLN cc_start: -0.0840 (OUTLIER) cc_final: -0.2113 (mm-40) REVERT: E 230 GLN cc_start: 0.7141 (pm20) cc_final: 0.6561 (pp30) REVERT: E 482 HIS cc_start: 0.6142 (m-70) cc_final: 0.5664 (m-70) outliers start: 3 outliers final: 0 residues processed: 107 average time/residue: 0.1715 time to fit residues: 25.4822 Evaluate side-chains 85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.222306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.205453 restraints weight = 14904.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.207859 restraints weight = 11206.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.209628 restraints weight = 8944.545| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5483 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6838 Z= 0.139 Angle : 0.689 8.671 9307 Z= 0.355 Chirality : 0.047 0.179 972 Planarity : 0.007 0.084 1223 Dihedral : 6.254 36.445 913 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.86 % Favored : 91.77 % Rotamer: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % 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 (0.27), residues: 802 helix: -4.13 (0.71), residues: 12 sheet: -1.05 (0.31), residues: 233 loop : -1.99 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 100 HIS 0.005 0.001 HIS C 503 PHE 0.014 0.002 PHE E 393 TYR 0.019 0.001 TYR A 103 ARG 0.006 0.001 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 82) hydrogen bonds : angle 7.49611 ( 195) SS BOND : bond 0.00496 ( 4) SS BOND : angle 1.77210 ( 8) covalent geometry : bond 0.00319 ( 6834) covalent geometry : angle 0.68765 ( 9299) *********************** 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: 1 poor density : 117 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.5196 (t60) cc_final: 0.4849 (t60) REVERT: B 21 ILE cc_start: 0.7485 (mp) cc_final: 0.7178 (mp) REVERT: B 25 SER cc_start: 0.6279 (p) cc_final: 0.5974 (m) REVERT: E 230 GLN cc_start: 0.7402 (pm20) cc_final: 0.6956 (pp30) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1884 time to fit residues: 29.7092 Evaluate side-chains 95 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 123 GLN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.221191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.205850 restraints weight = 15395.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.207486 restraints weight = 12571.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.208508 restraints weight = 10707.181| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6838 Z= 0.140 Angle : 0.680 9.360 9307 Z= 0.348 Chirality : 0.047 0.187 972 Planarity : 0.007 0.083 1223 Dihedral : 6.032 37.357 913 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.98 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % 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: -2.42 (0.28), residues: 802 helix: -3.93 (0.77), residues: 12 sheet: -1.17 (0.33), residues: 223 loop : -1.85 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 112 HIS 0.007 0.001 HIS C 503 PHE 0.013 0.002 PHE E 371 TYR 0.021 0.002 TYR A 103 ARG 0.005 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 82) hydrogen bonds : angle 7.05471 ( 195) SS BOND : bond 0.00580 ( 4) SS BOND : angle 1.81925 ( 8) covalent geometry : bond 0.00329 ( 6834) covalent geometry : angle 0.67797 ( 9299) *********************** 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 114 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8027 (ptp90) cc_final: 0.7815 (ptp90) REVERT: B 21 ILE cc_start: 0.7464 (mp) cc_final: 0.7163 (mp) REVERT: B 25 SER cc_start: 0.6044 (p) cc_final: 0.5774 (m) REVERT: E 230 GLN cc_start: 0.7585 (pm20) cc_final: 0.7160 (pp30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1760 time to fit residues: 27.3641 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 : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** C 503 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.221790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.207234 restraints weight = 15358.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.208816 restraints weight = 12306.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.209670 restraints weight = 10400.876| |-----------------------------------------------------------------------------| r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5502 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6838 Z= 0.128 Angle : 0.662 7.828 9307 Z= 0.336 Chirality : 0.046 0.227 972 Planarity : 0.007 0.078 1223 Dihedral : 5.875 37.101 913 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -2.28 (0.28), residues: 802 helix: -3.80 (0.81), residues: 12 sheet: -1.00 (0.33), residues: 224 loop : -1.79 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 36 HIS 0.008 0.001 HIS C 503 PHE 0.013 0.002 PHE B 66 TYR 0.014 0.001 TYR A 103 ARG 0.004 0.001 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 82) hydrogen bonds : angle 6.75757 ( 195) SS BOND : bond 0.00578 ( 4) SS BOND : angle 1.62940 ( 8) covalent geometry : bond 0.00298 ( 6834) covalent geometry : angle 0.66079 ( 9299) *********************** 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 116 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.3765 (ttm) cc_final: 0.3276 (ttm) REVERT: B 21 ILE cc_start: 0.7389 (mp) cc_final: 0.7088 (mp) REVERT: B 25 SER cc_start: 0.5963 (p) cc_final: 0.5712 (m) REVERT: E 230 GLN cc_start: 0.7691 (pm20) cc_final: 0.7244 (pp30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1714 time to fit residues: 27.0914 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 : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 29 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 480 ASN E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.222975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.207198 restraints weight = 14986.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.209102 restraints weight = 11770.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.210314 restraints weight = 9839.852| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6838 Z= 0.121 Angle : 0.648 7.631 9307 Z= 0.329 Chirality : 0.046 0.206 972 Planarity : 0.007 0.076 1223 Dihedral : 5.703 33.716 913 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.73 % Favored : 90.02 % Rotamer: Outliers : 0.14 % Allowed : 2.06 % Favored : 97.81 % 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: -2.23 (0.28), residues: 802 helix: -3.75 (0.82), residues: 12 sheet: -0.99 (0.33), residues: 214 loop : -1.73 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 36 HIS 0.003 0.000 HIS E 131 PHE 0.010 0.002 PHE E 393 TYR 0.014 0.001 TYR D 155 ARG 0.005 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 82) hydrogen bonds : angle 6.47015 ( 195) SS BOND : bond 0.00478 ( 4) SS BOND : angle 1.58070 ( 8) covalent geometry : bond 0.00286 ( 6834) covalent geometry : angle 0.64665 ( 9299) *********************** 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 112 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8185 (ptp90) cc_final: 0.7947 (ptp90) REVERT: A 109 MET cc_start: 0.4554 (ttm) cc_final: 0.4242 (ttm) REVERT: B 21 ILE cc_start: 0.7496 (mp) cc_final: 0.7200 (mp) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1765 time to fit residues: 26.8660 Evaluate side-chains 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.224158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.208391 restraints weight = 15495.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.210218 restraints weight = 12374.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.210982 restraints weight = 10365.109| |-----------------------------------------------------------------------------| r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6838 Z= 0.116 Angle : 0.641 7.541 9307 Z= 0.324 Chirality : 0.046 0.161 972 Planarity : 0.007 0.071 1223 Dihedral : 5.628 36.140 913 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.85 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.18 (0.28), residues: 802 helix: -3.59 (0.87), residues: 12 sheet: -0.88 (0.32), residues: 227 loop : -1.74 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 47 HIS 0.002 0.000 HIS D 311 PHE 0.024 0.002 PHE D 393 TYR 0.017 0.001 TYR D 155 ARG 0.004 0.000 ARG C 392 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 82) hydrogen bonds : angle 6.32693 ( 195) SS BOND : bond 0.00452 ( 4) SS BOND : angle 1.92363 ( 8) covalent geometry : bond 0.00274 ( 6834) covalent geometry : angle 0.63877 ( 9299) *********************** 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 107 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8045 (ptp90) cc_final: 0.7706 (ptp90) REVERT: A 48 LEU cc_start: 0.6599 (mt) cc_final: 0.5999 (mt) REVERT: B 21 ILE cc_start: 0.7390 (mp) cc_final: 0.7062 (mp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1941 time to fit residues: 29.7597 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 0.0000 chunk 46 optimal weight: 0.0070 chunk 55 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 HIS ** 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 = 0.4770 r_free = 0.4770 target = 0.225819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.209914 restraints weight = 15396.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.211803 restraints weight = 12233.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.212775 restraints weight = 10222.289| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5379 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6838 Z= 0.109 Angle : 0.628 7.191 9307 Z= 0.315 Chirality : 0.046 0.181 972 Planarity : 0.006 0.070 1223 Dihedral : 5.423 34.846 913 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -2.04 (0.29), residues: 802 helix: -3.35 (0.99), residues: 12 sheet: -0.74 (0.34), residues: 216 loop : -1.66 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.003 0.000 HIS A 59 PHE 0.015 0.001 PHE D 393 TYR 0.015 0.001 TYR D 155 ARG 0.006 0.000 ARG E 186 Details of bonding type rmsd hydrogen bonds : bond 0.02647 ( 82) hydrogen bonds : angle 6.12929 ( 195) SS BOND : bond 0.00449 ( 4) SS BOND : angle 1.80834 ( 8) covalent geometry : bond 0.00261 ( 6834) covalent geometry : angle 0.62567 ( 9299) *********************** 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 109 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7332 (mp) cc_final: 0.7006 (mp) REVERT: E 135 GLN cc_start: 0.7156 (mm110) cc_final: 0.6936 (mm110) REVERT: E 505 GLU cc_start: 0.7864 (mp0) cc_final: 0.7614 (mp0) REVERT: E 530 TYR cc_start: 0.5369 (m-80) cc_final: 0.5154 (m-10) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2074 time to fit residues: 31.1817 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 : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 46 optimal weight: 0.0060 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 1.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.221041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.205037 restraints weight = 15511.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.206708 restraints weight = 12481.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.208121 restraints weight = 10514.929| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6838 Z= 0.152 Angle : 0.692 7.811 9307 Z= 0.349 Chirality : 0.048 0.293 972 Planarity : 0.007 0.072 1223 Dihedral : 5.677 34.950 913 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.10 % Favored : 89.65 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -2.12 (0.29), residues: 802 helix: -3.66 (0.96), residues: 12 sheet: -1.00 (0.35), residues: 209 loop : -1.61 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 47 HIS 0.003 0.001 HIS D 311 PHE 0.022 0.002 PHE B 66 TYR 0.019 0.002 TYR D 155 ARG 0.013 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 82) hydrogen bonds : angle 6.27881 ( 195) SS BOND : bond 0.00635 ( 4) SS BOND : angle 2.19020 ( 8) covalent geometry : bond 0.00362 ( 6834) covalent geometry : angle 0.68909 ( 9299) *********************** 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 104 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7372 (mp) cc_final: 0.7038 (mp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3052 time to fit residues: 42.3854 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 : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 27 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.0070 chunk 13 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.225956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.214753 restraints weight = 15999.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.214887 restraints weight = 16828.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.215758 restraints weight = 15216.603| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6838 Z= 0.118 Angle : 0.653 7.105 9307 Z= 0.327 Chirality : 0.047 0.266 972 Planarity : 0.007 0.071 1223 Dihedral : 5.475 35.916 913 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.73 % Favored : 91.15 % 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: -1.94 (0.29), residues: 802 helix: -3.49 (1.10), residues: 12 sheet: -0.77 (0.36), residues: 198 loop : -1.52 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 47 HIS 0.002 0.000 HIS A 59 PHE 0.014 0.002 PHE D 393 TYR 0.017 0.001 TYR D 155 ARG 0.007 0.001 ARG E 186 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 82) hydrogen bonds : angle 6.08157 ( 195) SS BOND : bond 0.00508 ( 4) SS BOND : angle 1.82396 ( 8) covalent geometry : bond 0.00284 ( 6834) covalent geometry : angle 0.65104 ( 9299) ********************** 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 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.5117 (m100) cc_final: 0.4867 (m100) REVERT: B 21 ILE cc_start: 0.7421 (mp) cc_final: 0.7060 (mp) REVERT: E 530 TYR cc_start: 0.5300 (m-80) cc_final: 0.5053 (m-10) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1972 time to fit residues: 30.2353 Evaluate side-chains 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 77 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 HIS E 108 HIS E 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.217158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.202352 restraints weight = 15651.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.202622 restraints weight = 14261.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.203185 restraints weight = 13114.347| |-----------------------------------------------------------------------------| r_work (final): 0.4520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6838 Z= 0.184 Angle : 0.767 9.401 9307 Z= 0.390 Chirality : 0.050 0.246 972 Planarity : 0.008 0.072 1223 Dihedral : 6.088 33.671 913 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.60 % Favored : 88.28 % 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 : 0.40 % 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: -2.19 (0.29), residues: 802 helix: -3.53 (1.07), residues: 12 sheet: -1.11 (0.35), residues: 208 loop : -1.64 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 112 HIS 0.004 0.001 HIS E 502 PHE 0.016 0.002 PHE E 393 TYR 0.020 0.002 TYR E 322 ARG 0.006 0.001 ARG E 186 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 82) hydrogen bonds : angle 6.66887 ( 195) SS BOND : bond 0.00749 ( 4) SS BOND : angle 2.64712 ( 8) covalent geometry : bond 0.00435 ( 6834) covalent geometry : angle 0.76362 ( 9299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.42 seconds wall clock time: 47 minutes 54.61 seconds (2874.61 seconds total)