Starting phenix.real_space_refine on Tue Jan 14 12:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl9_38897/01_2025/8zl9_38897.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl9_38897/01_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_38897/01_2025/8zl9_38897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl9_38897/01_2025/8zl9_38897.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl9_38897/01_2025/8zl9_38897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl9_38897/01_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-5571/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: 4.28, per 1000 atoms: 0.64 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: 1.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.66 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: 1.79 Time building geometry restraints manager: 1.80 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: 1.200 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.280 Find NCS groups from input model: 0.080 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6834 Z= 0.315 Angle : 1.006 12.964 9299 Z= 0.549 Chirality : 0.058 0.271 972 Planarity : 0.009 0.097 1223 Dihedral : 14.246 89.668 2492 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.61 % Favored : 92.02 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.31 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.27), residues: 802 helix: -4.35 (0.70), residues: 12 sheet: -0.61 (0.38), residues: 171 loop : -1.94 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 100 HIS 0.004 0.001 HIS E 503 PHE 0.031 0.003 PHE A 29 TYR 0.032 0.002 TYR D 155 ARG 0.015 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.687 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: 0.1871 time to fit residues: 29.4285 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 : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 82 GLN B 35 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.217413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.201927 restraints weight = 14984.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.203391 restraints weight = 12389.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.204537 restraints weight = 10728.671| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6834 Z= 0.365 Angle : 0.841 12.398 9299 Z= 0.441 Chirality : 0.050 0.180 972 Planarity : 0.009 0.085 1223 Dihedral : 7.000 34.885 913 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.22 % Favored : 89.40 % Rotamer: Outliers : 0.27 % Allowed : 6.86 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.27), residues: 802 helix: -4.49 (0.49), residues: 12 sheet: -1.07 (0.34), residues: 205 loop : -2.08 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 112 HIS 0.006 0.001 HIS E 502 PHE 0.023 0.004 PHE E 375 TYR 0.040 0.003 TYR A 103 ARG 0.006 0.001 ARG E 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7504 (mp) cc_final: 0.7172 (mp) REVERT: B 25 SER cc_start: 0.6525 (p) cc_final: 0.6138 (m) REVERT: D 509 GLN cc_start: -0.0912 (OUTLIER) cc_final: -0.2143 (mm-40) REVERT: E 230 GLN cc_start: 0.7146 (pm20) cc_final: 0.6563 (pp30) REVERT: E 482 HIS cc_start: 0.6138 (m-70) cc_final: 0.5665 (m-70) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.1727 time to fit residues: 25.3859 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 : 0.763 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 127 GLN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.221508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.204158 restraints weight = 15022.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.206619 restraints weight = 11326.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.208002 restraints weight = 9047.090| |-----------------------------------------------------------------------------| r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6834 Z= 0.223 Angle : 0.698 8.723 9299 Z= 0.360 Chirality : 0.047 0.178 972 Planarity : 0.008 0.084 1223 Dihedral : 6.376 36.091 913 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.35 % Favored : 91.27 % Rotamer: Outliers : 0.27 % Allowed : 3.84 % Favored : 95.88 % 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: -2.51 (0.27), residues: 802 helix: -4.19 (0.68), residues: 12 sheet: -1.06 (0.31), residues: 226 loop : -1.99 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 HIS 0.006 0.001 HIS C 503 PHE 0.015 0.002 PHE E 371 TYR 0.020 0.002 TYR A 103 ARG 0.007 0.001 ARG C 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.5316 (t60) cc_final: 0.4936 (t60) REVERT: B 21 ILE cc_start: 0.7545 (mp) cc_final: 0.7229 (mp) REVERT: B 25 SER cc_start: 0.6358 (p) cc_final: 0.6048 (m) REVERT: E 230 GLN cc_start: 0.7447 (pm20) cc_final: 0.6989 (pp30) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.1896 time to fit residues: 30.2268 Evaluate side-chains 90 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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: 7.9990 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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** B 57 ASN C 503 HIS D 123 GLN D 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.222346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.207444 restraints weight = 15470.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.208935 restraints weight = 12607.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.210256 restraints weight = 10763.055| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5494 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6834 Z= 0.210 Angle : 0.670 8.692 9299 Z= 0.343 Chirality : 0.046 0.171 972 Planarity : 0.007 0.083 1223 Dihedral : 6.003 37.346 913 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.98 % Favored : 89.78 % 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: -2.41 (0.28), residues: 802 helix: -3.94 (0.79), residues: 12 sheet: -1.14 (0.33), residues: 223 loop : -1.84 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 36 HIS 0.007 0.001 HIS C 503 PHE 0.013 0.002 PHE E 371 TYR 0.018 0.001 TYR A 103 ARG 0.003 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4561 (ttm) cc_final: 0.4062 (ttm) REVERT: B 21 ILE cc_start: 0.7551 (mp) cc_final: 0.7253 (mp) REVERT: B 25 SER cc_start: 0.6028 (p) cc_final: 0.5774 (m) REVERT: E 230 GLN cc_start: 0.7561 (pm20) cc_final: 0.7130 (pp30) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1717 time to fit residues: 26.9512 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 : 0.727 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 0.0030 chunk 76 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 HIS D 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.224098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.209137 restraints weight = 15266.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.210966 restraints weight = 12153.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.211950 restraints weight = 10083.435| |-----------------------------------------------------------------------------| r_work (final): 0.4623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6834 Z= 0.185 Angle : 0.638 7.555 9299 Z= 0.323 Chirality : 0.046 0.258 972 Planarity : 0.006 0.078 1223 Dihedral : 5.707 37.146 913 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 0.14 % Allowed : 2.47 % 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: -2.24 (0.28), residues: 802 helix: -3.59 (0.88), residues: 12 sheet: -0.87 (0.32), residues: 230 loop : -1.82 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 36 HIS 0.007 0.001 HIS C 503 PHE 0.008 0.001 PHE E 393 TYR 0.013 0.001 TYR A 103 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7859 (ptp90) REVERT: A 109 MET cc_start: 0.3491 (ttm) cc_final: 0.2936 (ttm) REVERT: B 21 ILE cc_start: 0.7531 (mp) cc_final: 0.7173 (mp) REVERT: B 25 SER cc_start: 0.5950 (p) cc_final: 0.5688 (m) REVERT: E 230 GLN cc_start: 0.7565 (pm20) cc_final: 0.7126 (pp30) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1932 time to fit residues: 30.4400 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 : 0.710 ------------------------------------------------------------------------------- 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: 0.8980 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 D 315 ASN D 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.222675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.207549 restraints weight = 14996.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.209047 restraints weight = 11797.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.210648 restraints weight = 9874.661| |-----------------------------------------------------------------------------| r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6834 Z= 0.201 Angle : 0.649 7.416 9299 Z= 0.330 Chirality : 0.046 0.195 972 Planarity : 0.006 0.075 1223 Dihedral : 5.648 33.913 913 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.98 % Favored : 90.77 % Rotamer: Outliers : 0.27 % Allowed : 1.78 % Favored : 97.94 % 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: -2.20 (0.28), residues: 802 helix: -3.47 (0.90), residues: 12 sheet: -1.10 (0.32), residues: 220 loop : -1.66 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 36 HIS 0.008 0.001 HIS C 503 PHE 0.009 0.002 PHE E 393 TYR 0.015 0.001 TYR D 155 ARG 0.004 0.000 ARG E 511 *********************** 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 116 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8152 (ptp90) cc_final: 0.7860 (ptp90) REVERT: A 48 LEU cc_start: 0.6777 (mt) cc_final: 0.6180 (mt) REVERT: A 109 MET cc_start: 0.3665 (ttm) cc_final: 0.3019 (ttm) REVERT: B 21 ILE cc_start: 0.7384 (mp) cc_final: 0.7101 (mp) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.1709 time to fit residues: 27.6334 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 : 0.775 ------------------------------------------------------------------------------- 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: 5.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.224909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.214197 restraints weight = 15655.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.215167 restraints weight = 13192.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.215936 restraints weight = 11490.894| |-----------------------------------------------------------------------------| r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5378 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6834 Z= 0.196 Angle : 0.649 7.355 9299 Z= 0.329 Chirality : 0.046 0.172 972 Planarity : 0.007 0.072 1223 Dihedral : 5.615 34.797 913 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.98 % Favored : 89.78 % Rotamer: Outliers : 0.14 % Allowed : 1.65 % Favored : 98.22 % 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: -2.11 (0.28), residues: 802 helix: -3.51 (0.94), residues: 12 sheet: -0.82 (0.34), residues: 203 loop : -1.68 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 36 HIS 0.003 0.000 HIS D 311 PHE 0.012 0.002 PHE D 393 TYR 0.017 0.001 TYR E 155 ARG 0.007 0.001 ARG E 186 *********************** 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: 1 poor density : 106 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 GLU cc_start: 0.2948 (tm-30) cc_final: 0.2351 (tm-30) REVERT: A 109 MET cc_start: 0.3543 (ttm) cc_final: 0.3093 (ttm) REVERT: B 21 ILE cc_start: 0.7349 (mp) cc_final: 0.7011 (mp) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1748 time to fit residues: 25.7548 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 : 0.766 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 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 = 0.4767 r_free = 0.4767 target = 0.224638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.209067 restraints weight = 15368.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.210921 restraints weight = 12331.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.212294 restraints weight = 10280.472| |-----------------------------------------------------------------------------| r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6834 Z= 0.187 Angle : 0.648 9.127 9299 Z= 0.325 Chirality : 0.047 0.275 972 Planarity : 0.007 0.073 1223 Dihedral : 5.550 35.809 913 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 0.14 % Allowed : 1.23 % 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: -2.01 (0.28), residues: 802 helix: -3.42 (1.05), residues: 12 sheet: -0.72 (0.34), residues: 210 loop : -1.63 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 47 HIS 0.002 0.000 HIS D 311 PHE 0.018 0.002 PHE B 102 TYR 0.015 0.001 TYR D 155 ARG 0.009 0.001 ARG A 38 *********************** 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 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 GLU cc_start: 0.2805 (tm-30) cc_final: 0.2276 (tm-30) REVERT: A 109 MET cc_start: 0.3909 (ttm) cc_final: 0.3500 (ttm) REVERT: B 21 ILE cc_start: 0.7332 (mp) cc_final: 0.6568 (tp) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1750 time to fit residues: 25.9949 Evaluate side-chains 93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 HIS D 315 ASN E 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.219211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.203958 restraints weight = 15589.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.205329 restraints weight = 12850.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.206576 restraints weight = 11062.601| |-----------------------------------------------------------------------------| r_work (final): 0.4559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6834 Z= 0.267 Angle : 0.731 8.541 9299 Z= 0.371 Chirality : 0.049 0.253 972 Planarity : 0.007 0.075 1223 Dihedral : 5.932 33.884 913 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.85 % Favored : 89.03 % Rotamer: Outliers : 0.14 % Allowed : 0.69 % Favored : 99.18 % 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: -3.56 (1.06), residues: 12 sheet: -0.92 (0.35), residues: 201 loop : -1.70 (0.25), residues: 589 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 0.018 0.002 PHE D 393 TYR 0.020 0.002 TYR D 155 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.5416 (m100) cc_final: 0.4978 (m100) REVERT: A 38 ARG cc_start: 0.7955 (ptp90) cc_final: 0.7610 (ptp90) REVERT: A 109 MET cc_start: 0.4315 (ttm) cc_final: 0.3956 (ttm) REVERT: B 21 ILE cc_start: 0.7410 (mp) cc_final: 0.7076 (mp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1687 time to fit residues: 25.5713 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 : 0.791 ------------------------------------------------------------------------------- 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: 0.0770 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 309 ASN D 315 ASN E 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.222271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.206362 restraints weight = 15409.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.208270 restraints weight = 12245.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.208827 restraints weight = 10116.676| |-----------------------------------------------------------------------------| r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6834 Z= 0.203 Angle : 0.685 11.397 9299 Z= 0.340 Chirality : 0.048 0.246 972 Planarity : 0.007 0.072 1223 Dihedral : 5.722 35.321 913 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.35 % Favored : 90.52 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % 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: -2.08 (0.29), residues: 802 helix: -3.54 (1.10), residues: 12 sheet: -0.84 (0.36), residues: 200 loop : -1.64 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 47 HIS 0.002 0.000 HIS D 311 PHE 0.023 0.002 PHE B 102 TYR 0.016 0.001 TYR D 155 ARG 0.012 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7939 (ptp90) cc_final: 0.7659 (ptp90) REVERT: A 109 MET cc_start: 0.3991 (ttm) cc_final: 0.3579 (ttm) REVERT: B 21 ILE cc_start: 0.7427 (mp) cc_final: 0.7103 (mp) REVERT: E 522 ILE cc_start: 0.5402 (mp) cc_final: 0.4814 (mm) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1768 time to fit residues: 26.5895 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 : 0.674 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 309 ASN D 315 ASN E 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.221563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.205221 restraints weight = 15363.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.206965 restraints weight = 12368.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.208361 restraints weight = 10436.228| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6834 Z= 0.217 Angle : 0.689 10.318 9299 Z= 0.344 Chirality : 0.047 0.233 972 Planarity : 0.007 0.072 1223 Dihedral : 5.640 33.915 913 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.35 % Favored : 89.53 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % 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: -2.10 (0.29), residues: 802 helix: -3.46 (1.14), residues: 12 sheet: -0.91 (0.35), residues: 201 loop : -1.63 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 47 HIS 0.003 0.001 HIS D 311 PHE 0.023 0.002 PHE B 102 TYR 0.017 0.001 TYR D 155 ARG 0.007 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2060.67 seconds wall clock time: 38 minutes 35.45 seconds (2315.45 seconds total)