Starting phenix.real_space_refine on Sat May 10 17:15:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl9_38897/05_2025/8zl9_38897.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl9_38897/05_2025/8zl9_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/cci-nas-00/data/ceres_data/8zl9_38897/05_2025/8zl9_38897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl9_38897/05_2025/8zl9_38897.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl9_38897/05_2025/8zl9_38897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl9_38897/05_2025/8zl9_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-5687/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: 4.08, per 1000 atoms: 0.61 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: 1.41 Conformation dependent library (CDL) restraints added in 807.8 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: 0.65 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: 1.48 Time building geometry restraints manager: 1.67 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.080 ------------------------------------------------------------------------------- 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 : 0.764 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: 0.1926 time to fit residues: 30.0120 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 : 0.756 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.201927 restraints weight = 15064.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.203380 restraints weight = 12451.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.204228 restraints weight = 10809.556| |-----------------------------------------------------------------------------| r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 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 : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7520 (mp) cc_final: 0.7189 (mp) REVERT: B 25 SER cc_start: 0.6549 (p) cc_final: 0.6189 (m) REVERT: C 319 THR cc_start: 0.8129 (m) cc_final: 0.7928 (p) REVERT: D 509 GLN cc_start: -0.0843 (OUTLIER) cc_final: -0.2117 (mm-40) REVERT: E 230 GLN cc_start: 0.7135 (pm20) cc_final: 0.6554 (pp30) REVERT: E 482 HIS cc_start: 0.6141 (m-70) cc_final: 0.5663 (m-70) outliers start: 3 outliers final: 0 residues processed: 107 average time/residue: 0.1643 time to fit residues: 24.3367 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 : 0.751 ------------------------------------------------------------------------------- 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: 0.0670 chunk 69 optimal weight: 5.9990 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: 5.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.220835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.203715 restraints weight = 15014.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.206082 restraints weight = 11388.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.207881 restraints weight = 9094.322| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.2575 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= 0.150 Angle : 0.707 9.087 9307 Z= 0.364 Chirality : 0.047 0.179 972 Planarity : 0.008 0.085 1223 Dihedral : 6.376 36.880 913 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.48 % Favored : 91.15 % 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: -2.54 (0.28), residues: 802 helix: -4.21 (0.69), residues: 12 sheet: -1.12 (0.31), residues: 227 loop : -2.00 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 100 HIS 0.006 0.001 HIS C 503 PHE 0.016 0.002 PHE E 393 TYR 0.023 0.002 TYR A 103 ARG 0.007 0.001 ARG C 511 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 82) hydrogen bonds : angle 7.62093 ( 195) SS BOND : bond 0.00532 ( 4) SS BOND : angle 1.92816 ( 8) covalent geometry : bond 0.00347 ( 6834) covalent geometry : angle 0.70513 ( 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 114 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.5294 (t60) cc_final: 0.4910 (t60) REVERT: B 21 ILE cc_start: 0.7527 (mp) cc_final: 0.7210 (mp) REVERT: B 25 SER cc_start: 0.6342 (p) cc_final: 0.6032 (m) REVERT: C 319 THR cc_start: 0.8412 (m) cc_final: 0.8183 (p) REVERT: E 230 GLN cc_start: 0.7497 (pm20) cc_final: 0.7052 (pp30) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1782 time to fit residues: 27.4811 Evaluate side-chains 89 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN 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 = 0.4706 r_free = 0.4706 target = 0.218391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.203098 restraints weight = 15228.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.204649 restraints weight = 12421.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.205648 restraints weight = 10559.206| |-----------------------------------------------------------------------------| r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6838 Z= 0.162 Angle : 0.719 10.404 9307 Z= 0.368 Chirality : 0.048 0.174 972 Planarity : 0.007 0.083 1223 Dihedral : 6.255 38.691 913 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.22 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: -2.53 (0.28), residues: 802 helix: -4.07 (0.77), residues: 12 sheet: -1.30 (0.32), residues: 220 loop : -1.90 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 112 HIS 0.006 0.001 HIS C 503 PHE 0.014 0.002 PHE E 393 TYR 0.022 0.002 TYR A 103 ARG 0.004 0.001 ARG E 392 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 82) hydrogen bonds : angle 7.31484 ( 195) SS BOND : bond 0.00683 ( 4) SS BOND : angle 2.13472 ( 8) covalent geometry : bond 0.00379 ( 6834) covalent geometry : angle 0.71658 ( 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 117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8156 (ptp90) cc_final: 0.7939 (ptp90) REVERT: B 21 ILE cc_start: 0.7455 (mp) cc_final: 0.7101 (mp) REVERT: B 25 SER cc_start: 0.6033 (p) cc_final: 0.5814 (m) REVERT: C 319 THR cc_start: 0.8386 (m) cc_final: 0.8132 (p) REVERT: E 230 GLN cc_start: 0.7511 (pm20) cc_final: 0.7081 (pp30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1873 time to fit residues: 29.4031 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 : 0.769 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.216186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.200981 restraints weight = 15137.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.202483 restraints weight = 12190.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.203494 restraints weight = 10447.527| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5687 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6838 Z= 0.184 Angle : 0.748 9.560 9307 Z= 0.385 Chirality : 0.049 0.231 972 Planarity : 0.007 0.078 1223 Dihedral : 6.424 38.513 913 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.60 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: -2.61 (0.28), residues: 802 helix: -4.11 (0.76), residues: 12 sheet: -1.37 (0.32), residues: 221 loop : -1.95 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 36 HIS 0.008 0.001 HIS C 503 PHE 0.016 0.003 PHE D 393 TYR 0.020 0.002 TYR A 103 ARG 0.004 0.001 ARG C 392 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 82) hydrogen bonds : angle 7.32748 ( 195) SS BOND : bond 0.00691 ( 4) SS BOND : angle 2.05817 ( 8) covalent geometry : bond 0.00426 ( 6834) covalent geometry : angle 0.74624 ( 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 107 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7398 (mp) cc_final: 0.7075 (mp) REVERT: C 319 THR cc_start: 0.8388 (m) cc_final: 0.8129 (p) REVERT: E 230 GLN cc_start: 0.7649 (pm20) cc_final: 0.7108 (pp30) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1780 time to fit residues: 25.5589 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 : 0.674 ------------------------------------------------------------------------------- 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: 0.0970 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** D 390 ASN D 480 ASN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.218237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.200884 restraints weight = 14987.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.202895 restraints weight = 11835.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.204052 restraints weight = 9823.074| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6838 Z= 0.156 Angle : 0.717 9.003 9307 Z= 0.367 Chirality : 0.048 0.202 972 Planarity : 0.007 0.074 1223 Dihedral : 6.230 37.953 913 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.35 % Favored : 89.40 % 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: -2.52 (0.28), residues: 802 helix: -3.84 (0.95), residues: 12 sheet: -1.22 (0.33), residues: 213 loop : -1.93 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 112 HIS 0.003 0.001 HIS E 502 PHE 0.015 0.002 PHE D 393 TYR 0.013 0.002 TYR D 155 ARG 0.008 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 82) hydrogen bonds : angle 7.11569 ( 195) SS BOND : bond 0.00618 ( 4) SS BOND : angle 2.49641 ( 8) covalent geometry : bond 0.00364 ( 6834) covalent geometry : angle 0.71332 ( 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 : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4507 (ttm) cc_final: 0.4186 (ttm) REVERT: B 21 ILE cc_start: 0.7519 (mp) cc_final: 0.7186 (mp) REVERT: B 25 SER cc_start: 0.6169 (p) cc_final: 0.5887 (m) REVERT: C 313 SER cc_start: 0.5805 (t) cc_final: 0.5561 (m) REVERT: C 319 THR cc_start: 0.8324 (m) cc_final: 0.8060 (p) REVERT: E 230 GLN cc_start: 0.7658 (pm20) cc_final: 0.7010 (pp30) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1781 time to fit residues: 26.9598 Evaluate side-chains 98 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.210668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.192265 restraints weight = 15057.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.194237 restraints weight = 11962.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.195738 restraints weight = 10033.348| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 6838 Z= 0.255 Angle : 0.863 11.382 9307 Z= 0.447 Chirality : 0.052 0.203 972 Planarity : 0.008 0.075 1223 Dihedral : 6.892 37.994 913 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.09 % Favored : 86.66 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -2.75 (0.28), residues: 802 helix: -3.74 (1.07), residues: 12 sheet: -1.46 (0.34), residues: 210 loop : -2.07 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 112 HIS 0.005 0.001 HIS A 59 PHE 0.021 0.003 PHE D 393 TYR 0.025 0.002 TYR B 90 ARG 0.007 0.001 ARG E 186 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 82) hydrogen bonds : angle 7.81508 ( 195) SS BOND : bond 0.00985 ( 4) SS BOND : angle 3.16707 ( 8) covalent geometry : bond 0.00590 ( 6834) covalent geometry : angle 0.85788 ( 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 104 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7528 (mp) cc_final: 0.7147 (mp) REVERT: B 51 LEU cc_start: 0.6463 (tt) cc_final: 0.6152 (tt) REVERT: C 319 THR cc_start: 0.8408 (m) cc_final: 0.8185 (p) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1760 time to fit residues: 25.0224 Evaluate side-chains 86 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 0.5980 chunk 49 optimal weight: 0.0470 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 overall best weight: 0.4680 ------------------------------------------------------------------------------- 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 324 GLN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.219656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.201709 restraints weight = 14951.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.204062 restraints weight = 11466.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.205560 restraints weight = 9339.828| |-----------------------------------------------------------------------------| r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.4252 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= 0.129 Angle : 0.699 7.672 9307 Z= 0.352 Chirality : 0.048 0.194 972 Planarity : 0.007 0.068 1223 Dihedral : 6.196 38.478 913 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.48 % Favored : 90.27 % 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: -2.41 (0.28), residues: 802 helix: -3.49 (1.20), residues: 12 sheet: -1.08 (0.34), residues: 214 loop : -1.89 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 144 HIS 0.011 0.001 HIS C 503 PHE 0.032 0.002 PHE D 393 TYR 0.018 0.002 TYR D 173 ARG 0.007 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 82) hydrogen bonds : angle 6.99803 ( 195) SS BOND : bond 0.01763 ( 4) SS BOND : angle 2.17255 ( 8) covalent geometry : bond 0.00301 ( 6834) covalent geometry : angle 0.69633 ( 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 107 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7478 (mp) cc_final: 0.7116 (mp) REVERT: B 51 LEU cc_start: 0.5788 (tt) cc_final: 0.4713 (tt) REVERT: B 66 PHE cc_start: 0.5248 (m-10) cc_final: 0.4899 (m-10) REVERT: C 319 THR cc_start: 0.8407 (m) cc_final: 0.8144 (p) REVERT: E 178 TYR cc_start: 0.7223 (p90) cc_final: 0.6577 (p90) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1934 time to fit residues: 27.4952 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 : 0.729 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 51 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 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.215475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.199005 restraints weight = 15237.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.200805 restraints weight = 12105.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.201784 restraints weight = 10178.471| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6838 Z= 0.181 Angle : 0.775 9.306 9307 Z= 0.398 Chirality : 0.050 0.282 972 Planarity : 0.007 0.073 1223 Dihedral : 6.321 38.691 913 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.35 % Favored : 88.40 % 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 : 0.27 % 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: -2.50 (0.28), residues: 802 helix: -3.50 (1.19), residues: 12 sheet: -1.26 (0.35), residues: 205 loop : -1.90 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 112 HIS 0.004 0.001 HIS E 502 PHE 0.020 0.002 PHE D 393 TYR 0.017 0.002 TYR C 155 ARG 0.009 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 82) hydrogen bonds : angle 7.32969 ( 195) SS BOND : bond 0.00667 ( 4) SS BOND : angle 2.33216 ( 8) covalent geometry : bond 0.00424 ( 6834) covalent geometry : angle 0.77258 ( 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 100 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.5845 (mt) cc_final: 0.5627 (mt) REVERT: B 21 ILE cc_start: 0.7385 (mp) cc_final: 0.6951 (mp) REVERT: B 51 LEU cc_start: 0.5926 (tt) cc_final: 0.4758 (tt) REVERT: B 66 PHE cc_start: 0.5250 (m-10) cc_final: 0.4992 (m-10) REVERT: C 319 THR cc_start: 0.8440 (m) cc_final: 0.8182 (p) REVERT: E 178 TYR cc_start: 0.7246 (p90) cc_final: 0.6611 (p90) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1764 time to fit residues: 24.0262 Evaluate side-chains 85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- 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 324 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 = 0.4701 r_free = 0.4701 target = 0.218347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.202744 restraints weight = 15474.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.204406 restraints weight = 12347.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.205829 restraints weight = 10423.710| |-----------------------------------------------------------------------------| r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6838 Z= 0.140 Angle : 0.717 7.924 9307 Z= 0.365 Chirality : 0.049 0.260 972 Planarity : 0.007 0.071 1223 Dihedral : 6.076 34.766 913 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.35 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.38 (0.29), residues: 802 helix: -3.48 (1.19), residues: 12 sheet: -1.21 (0.34), residues: 216 loop : -1.79 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 112 HIS 0.009 0.001 HIS E 114 PHE 0.017 0.002 PHE D 393 TYR 0.014 0.002 TYR E 155 ARG 0.009 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 82) hydrogen bonds : angle 7.03369 ( 195) SS BOND : bond 0.00665 ( 4) SS BOND : angle 2.48698 ( 8) covalent geometry : bond 0.00329 ( 6834) covalent geometry : angle 0.71318 ( 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 103 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.4701 (t60) cc_final: 0.4494 (t60) REVERT: B 21 ILE cc_start: 0.7240 (mp) cc_final: 0.6826 (mp) REVERT: B 51 LEU cc_start: 0.5831 (tt) cc_final: 0.4816 (tt) REVERT: B 66 PHE cc_start: 0.5116 (m-10) cc_final: 0.4765 (m-10) REVERT: C 319 THR cc_start: 0.8440 (m) cc_final: 0.8152 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1824 time to fit residues: 25.6780 Evaluate side-chains 89 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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: 5.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.0470 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 114 HIS E 483 GLN ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.219700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.203941 restraints weight = 15032.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.205796 restraints weight = 11888.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.207299 restraints weight = 9886.585| |-----------------------------------------------------------------------------| r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6838 Z= 0.128 Angle : 0.694 7.312 9307 Z= 0.349 Chirality : 0.048 0.250 972 Planarity : 0.007 0.070 1223 Dihedral : 5.828 35.624 913 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.85 % Favored : 89.90 % 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: -2.22 (0.29), residues: 802 helix: -3.53 (1.16), residues: 12 sheet: -1.05 (0.35), residues: 213 loop : -1.70 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 112 HIS 0.003 0.000 HIS E 484 PHE 0.014 0.002 PHE D 393 TYR 0.012 0.001 TYR D 155 ARG 0.005 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02854 ( 82) hydrogen bonds : angle 6.78564 ( 195) SS BOND : bond 0.00608 ( 4) SS BOND : angle 2.06583 ( 8) covalent geometry : bond 0.00307 ( 6834) covalent geometry : angle 0.69156 ( 9299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.43 seconds wall clock time: 38 minutes 10.00 seconds (2290.00 seconds total)