Starting phenix.real_space_refine on Tue Mar 11 20:18:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl9_60223/03_2025/8zl9_60223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl9_60223/03_2025/8zl9_60223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zl9_60223/03_2025/8zl9_60223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl9_60223/03_2025/8zl9_60223.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl9_60223/03_2025/8zl9_60223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl9_60223/03_2025/8zl9_60223.cif" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4208 2.51 5 N 1171 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.46, per 1000 atoms: 0.67 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: 1.68 Conformation dependent library (CDL) restraints added in 963.8 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: 0.83 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: 1.61 Time building geometry restraints manager: 2.01 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.100 ------------------------------------------------------------------------------- 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 : 0.693 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: 0.1828 time to fit residues: 28.4112 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 : 0.753 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.201987 restraints weight = 14984.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.203522 restraints weight = 12323.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.204735 restraints weight = 10564.094| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 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 : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7514 (mp) cc_final: 0.7183 (mp) REVERT: B 25 SER cc_start: 0.6521 (p) cc_final: 0.6135 (m) REVERT: D 509 GLN cc_start: -0.0911 (OUTLIER) cc_final: -0.2147 (mm-40) REVERT: E 230 GLN cc_start: 0.7150 (pm20) cc_final: 0.6566 (pp30) REVERT: E 482 HIS cc_start: 0.6148 (m-70) cc_final: 0.5672 (m-70) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.1722 time to fit residues: 25.2270 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 : 0.747 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 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 = 0.4705 r_free = 0.4705 target = 0.217490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.200239 restraints weight = 14952.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.202479 restraints weight = 11485.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.203569 restraints weight = 9369.381| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6834 Z= 0.290 Angle : 0.761 10.146 9299 Z= 0.396 Chirality : 0.048 0.184 972 Planarity : 0.008 0.086 1223 Dihedral : 6.674 37.881 913 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.73 % Favored : 89.90 % Rotamer: Outliers : 0.27 % Allowed : 4.53 % Favored : 95.20 % 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 (0.28), residues: 802 helix: -4.28 (0.66), residues: 12 sheet: -1.32 (0.33), residues: 215 loop : -1.98 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 112 HIS 0.006 0.001 HIS C 503 PHE 0.018 0.002 PHE E 371 TYR 0.027 0.002 TYR A 103 ARG 0.008 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 116 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7496 (mp) cc_final: 0.7123 (mp) REVERT: B 25 SER cc_start: 0.6452 (p) cc_final: 0.6158 (m) REVERT: E 230 GLN cc_start: 0.7462 (pm20) cc_final: 0.6995 (pp30) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.1940 time to fit residues: 30.8577 Evaluate side-chains 87 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 42 optimal weight: 0.0670 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN D 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN ** E 369 ASN ** 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 = 0.4758 r_free = 0.4758 target = 0.223634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.207433 restraints weight = 15194.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.209652 restraints weight = 11330.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.211421 restraints weight = 9115.046| |-----------------------------------------------------------------------------| r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.2939 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 : 0.663 8.122 9299 Z= 0.338 Chirality : 0.046 0.171 972 Planarity : 0.007 0.083 1223 Dihedral : 6.022 37.729 913 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.73 % Favored : 91.02 % Rotamer: Outliers : 0.14 % Allowed : 2.06 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.28), residues: 802 helix: -3.89 (0.78), residues: 12 sheet: -1.08 (0.33), residues: 218 loop : -1.93 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 HIS 0.004 0.000 HIS E 484 PHE 0.011 0.002 PHE E 161 TYR 0.012 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 111 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7525 (mp) cc_final: 0.7161 (mp) REVERT: B 25 SER cc_start: 0.5997 (p) cc_final: 0.5721 (m) REVERT: E 230 GLN cc_start: 0.7588 (pm20) cc_final: 0.7165 (pp30) REVERT: E 530 TYR cc_start: 0.5259 (m-80) cc_final: 0.5001 (m-10) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1650 time to fit residues: 25.3937 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 : 0.694 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4698 r_free = 0.4698 target = 0.217488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.199973 restraints weight = 15021.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.202086 restraints weight = 11658.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.203726 restraints weight = 9577.572| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6834 Z= 0.267 Angle : 0.735 8.827 9299 Z= 0.376 Chirality : 0.048 0.238 972 Planarity : 0.007 0.081 1223 Dihedral : 6.259 37.438 913 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.10 % Favored : 89.65 % Rotamer: Outliers : 0.14 % Allowed : 4.25 % 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: -2.53 (0.28), residues: 802 helix: -3.95 (0.82), residues: 12 sheet: -1.33 (0.33), residues: 220 loop : -1.89 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 36 HIS 0.005 0.001 HIS E 484 PHE 0.016 0.003 PHE D 393 TYR 0.018 0.002 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 106 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7988 (ptp90) REVERT: B 21 ILE cc_start: 0.7478 (mp) cc_final: 0.7162 (mp) REVERT: B 51 LEU cc_start: 0.6125 (tt) cc_final: 0.5255 (tt) REVERT: E 230 GLN cc_start: 0.7681 (pm20) cc_final: 0.7139 (pp30) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1683 time to fit residues: 24.5796 Evaluate side-chains 94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 480 ASN ** E 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.221201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.205997 restraints weight = 15118.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.207761 restraints weight = 11945.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.209203 restraints weight = 9965.512| |-----------------------------------------------------------------------------| r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6834 Z= 0.208 Angle : 0.668 7.691 9299 Z= 0.340 Chirality : 0.046 0.201 972 Planarity : 0.007 0.077 1223 Dihedral : 5.963 37.259 913 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.10 % Favored : 90.65 % 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: -2.43 (0.28), residues: 802 helix: -3.89 (0.91), residues: 12 sheet: -1.13 (0.33), residues: 215 loop : -1.87 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 36 HIS 0.002 0.000 HIS D 311 PHE 0.010 0.002 PHE E 393 TYR 0.015 0.001 TYR D 155 ARG 0.004 0.001 ARG E 186 *********************** 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 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7429 (mp) cc_final: 0.7136 (mp) REVERT: B 25 SER cc_start: 0.5879 (p) cc_final: 0.5641 (m) REVERT: B 51 LEU cc_start: 0.5820 (tt) cc_final: 0.4938 (tt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1805 time to fit residues: 26.7287 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 : 0.811 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.0060 chunk 30 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.0000 overall best weight: 0.4400 ------------------------------------------------------------------------------- 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 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.223828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.207787 restraints weight = 15078.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.209763 restraints weight = 11879.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.211047 restraints weight = 9833.280| |-----------------------------------------------------------------------------| r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6834 Z= 0.189 Angle : 0.648 7.227 9299 Z= 0.327 Chirality : 0.046 0.218 972 Planarity : 0.006 0.071 1223 Dihedral : 5.703 34.433 913 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 802 helix: -3.69 (1.02), residues: 12 sheet: -0.89 (0.33), residues: 227 loop : -1.78 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.003 0.000 HIS E 484 PHE 0.009 0.001 PHE D 508 TYR 0.010 0.001 TYR D 155 ARG 0.013 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7438 (mp) cc_final: 0.7181 (mp) REVERT: B 25 SER cc_start: 0.5985 (p) cc_final: 0.5753 (m) REVERT: B 51 LEU cc_start: 0.5775 (tt) cc_final: 0.4952 (tt) REVERT: D 235 GLU cc_start: 0.7956 (tp30) cc_final: 0.7732 (tp30) REVERT: E 178 TYR cc_start: 0.7140 (p90) cc_final: 0.6535 (p90) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1686 time to fit residues: 24.8924 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 : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.221352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.205842 restraints weight = 15053.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.207171 restraints weight = 13500.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.208587 restraints weight = 10437.125| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6834 Z= 0.210 Angle : 0.674 7.562 9299 Z= 0.339 Chirality : 0.047 0.189 972 Planarity : 0.007 0.070 1223 Dihedral : 5.708 33.451 913 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.35 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % 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: -2.15 (0.29), residues: 802 helix: -3.63 (1.05), residues: 12 sheet: -0.83 (0.34), residues: 216 loop : -1.72 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 36 HIS 0.003 0.000 HIS D 311 PHE 0.010 0.002 PHE E 393 TYR 0.018 0.001 TYR E 155 ARG 0.008 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 103 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7449 (mp) cc_final: 0.7134 (mp) REVERT: B 51 LEU cc_start: 0.5884 (tt) cc_final: 0.4621 (tt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1804 time to fit residues: 25.2254 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 : 0.748 ------------------------------------------------------------------------------- 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: 4.9990 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 46 optimal weight: 0.0040 chunk 1 optimal weight: 0.0170 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5830 ------------------------------------------------------------------------------- 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 108 HIS ** E 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.223251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.205187 restraints weight = 15580.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.207612 restraints weight = 11804.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.208890 restraints weight = 9517.957| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.3964 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= 0.193 Angle : 0.660 7.191 9299 Z= 0.328 Chirality : 0.047 0.292 972 Planarity : 0.006 0.071 1223 Dihedral : 5.555 36.781 913 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.85 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.03 (0.29), residues: 802 helix: -3.57 (1.07), residues: 12 sheet: -0.75 (0.35), residues: 213 loop : -1.64 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 HIS 0.003 0.000 HIS A 59 PHE 0.009 0.001 PHE E 393 TYR 0.017 0.001 TYR D 155 ARG 0.006 0.000 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 104 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7468 (mp) cc_final: 0.7198 (mp) REVERT: E 178 TYR cc_start: 0.7074 (p90) cc_final: 0.6456 (p90) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1816 time to fit residues: 25.6793 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 : 0.796 ------------------------------------------------------------------------------- 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: 0.0010 chunk 41 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 overall best weight: 0.2206 ------------------------------------------------------------------------------- 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 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.226824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.208198 restraints weight = 15589.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.210927 restraints weight = 11165.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.213117 restraints weight = 8727.073| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5361 moved from start: 0.4070 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= 0.171 Angle : 0.636 7.494 9299 Z= 0.312 Chirality : 0.046 0.256 972 Planarity : 0.006 0.070 1223 Dihedral : 5.225 36.205 913 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.35 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.29), residues: 802 helix: -3.54 (1.08), residues: 12 sheet: -0.65 (0.35), residues: 216 loop : -1.56 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 47 HIS 0.003 0.000 HIS A 59 PHE 0.010 0.001 PHE D 375 TYR 0.015 0.001 TYR A 94 ARG 0.008 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.7462 (mp) cc_final: 0.7097 (mp) REVERT: E 135 GLN cc_start: 0.7193 (mm110) cc_final: 0.6985 (mm110) REVERT: E 174 ARG cc_start: 0.6855 (mtt180) cc_final: 0.6310 (mtp180) REVERT: E 532 ILE cc_start: 0.7557 (mt) cc_final: 0.7349 (mt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1822 time to fit residues: 27.4666 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 : 0.740 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 0.0570 chunk 57 optimal weight: 0.0070 chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.228534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.218332 restraints weight = 15899.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.218699 restraints weight = 14543.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.219272 restraints weight = 12983.028| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6834 Z= 0.182 Angle : 0.648 8.426 9299 Z= 0.319 Chirality : 0.046 0.248 972 Planarity : 0.006 0.068 1223 Dihedral : 5.214 36.407 913 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.35 % Favored : 91.40 % 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: -1.81 (0.29), residues: 802 helix: -3.55 (1.02), residues: 12 sheet: -0.55 (0.35), residues: 214 loop : -1.49 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 47 HIS 0.002 0.000 HIS D 502 PHE 0.019 0.001 PHE D 393 TYR 0.037 0.001 TYR E 155 ARG 0.008 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.80 seconds wall clock time: 38 minutes 12.32 seconds (2292.32 seconds total)