Starting phenix.real_space_refine on Wed Mar 5 20:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qta_18647/03_2025/8qta_18647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qta_18647/03_2025/8qta_18647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qta_18647/03_2025/8qta_18647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qta_18647/03_2025/8qta_18647.map" model { file = "/net/cci-nas-00/data/ceres_data/8qta_18647/03_2025/8qta_18647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qta_18647/03_2025/8qta_18647.cif" } resolution = 2.64 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= 0.000 sd= 0.099 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 5 5.49 5 S 11 5.16 5 C 2276 2.51 5 N 555 2.21 5 O 623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3258 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 214 Unusual residues: {'FAD': 1, 'HEM': 2, 'NDP': 1} Classifications: {'undetermined': 4, 'water': 27} Link IDs: {None: 30} Time building chain proxies: 2.85, per 1000 atoms: 0.82 Number of scatterers: 3472 At special positions: 0 Unit cell: (57.9384, 65.7378, 94.707, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 11 16.00 P 5 15.00 O 623 8.00 N 555 7.00 C 2276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 347.4 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 53.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.587A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.690A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 147 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.611A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.780A pdb=" N TYR A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.728A pdb=" N ALA A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.673A pdb=" N GLN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.792A pdb=" N LYS A 268 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR A 186 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY A 188 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER A 208 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLN A 243 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.879A pdb=" N ASN A 286 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR A 368 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 288 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS A 370 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 290 " --> pdb=" O CYS A 370 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 549 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: 0.92 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1304 1.38 - 1.56: 2222 1.56 - 1.74: 8 1.74 - 1.93: 22 1.93 - 2.11: 7 Bond restraints: 3563 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.624 0.209 3.80e-02 6.93e+02 3.02e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.600 0.157 3.50e-02 8.16e+02 2.02e+01 bond pdb=" C3C HEM A 503 " pdb=" CAC HEM A 503 " ideal model delta sigma weight residual 1.544 1.467 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " ideal model delta sigma weight residual 1.544 1.467 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O5B FAD A 502 " pdb=" PA FAD A 502 " ideal model delta sigma weight residual 1.634 1.560 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 3558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 4831 4.67 - 9.33: 37 9.33 - 14.00: 1 14.00 - 18.67: 2 18.67 - 23.34: 1 Bond angle restraints: 4872 Sorted by residual: angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 131.08 -23.34 1.95e+00 2.62e-01 1.43e+02 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 118.26 -14.42 1.91e+00 2.73e-01 5.67e+01 angle pdb=" C5D NDP A 501 " pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 104.93 121.79 -16.86 2.66e+00 1.41e-01 4.02e+01 angle pdb=" N ASP A 254 " pdb=" CA ASP A 254 " pdb=" CB ASP A 254 " ideal model delta sigma weight residual 110.33 102.70 7.63 1.50e+00 4.44e-01 2.59e+01 angle pdb=" O2N NDP A 501 " pdb=" PN NDP A 501 " pdb=" O5D NDP A 501 " ideal model delta sigma weight residual 100.52 109.84 -9.32 1.91e+00 2.74e-01 2.38e+01 ... (remaining 4867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.91: 1709 19.91 - 39.83: 211 39.83 - 59.74: 69 59.74 - 79.65: 14 79.65 - 99.56: 7 Dihedral angle restraints: 2010 sinusoidal: 848 harmonic: 1162 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 75.48 99.56 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" C2D HEM A 503 " pdb=" C3D HEM A 503 " pdb=" CAD HEM A 503 " pdb=" CBD HEM A 503 " ideal model delta sinusoidal sigma weight residual -180.00 -99.38 -80.62 2 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" C1A HEM A 504 " pdb=" C2A HEM A 504 " pdb=" CAA HEM A 504 " pdb=" CBA HEM A 504 " ideal model delta sinusoidal sigma weight residual 180.00 101.87 78.13 2 2.00e+01 2.50e-03 1.15e+01 ... (remaining 2007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 390 0.045 - 0.090: 83 0.090 - 0.134: 29 0.134 - 0.179: 4 0.179 - 0.224: 3 Chirality restraints: 509 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 506 not shown) Planarity restraints: 580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.106 2.00e-02 2.50e+03 6.76e-02 5.71e+01 pdb=" C3N NDP A 501 " -0.025 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.013 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.061 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM A 503 " 0.003 2.00e-02 2.50e+03 1.58e-02 5.61e+00 pdb=" C2C HEM A 503 " -0.005 2.00e-02 2.50e+03 pdb=" C3C HEM A 503 " -0.002 2.00e-02 2.50e+03 pdb=" C4C HEM A 503 " -0.010 2.00e-02 2.50e+03 pdb=" CAC HEM A 503 " -0.002 2.00e-02 2.50e+03 pdb=" CHC HEM A 503 " 0.019 2.00e-02 2.50e+03 pdb=" CHD HEM A 503 " 0.027 2.00e-02 2.50e+03 pdb=" CMC HEM A 503 " 0.003 2.00e-02 2.50e+03 pdb=" NC HEM A 503 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM A 503 " 0.006 2.00e-02 2.50e+03 1.44e-02 4.64e+00 pdb=" C2A HEM A 503 " 0.004 2.00e-02 2.50e+03 pdb=" C3A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" C4A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" CAA HEM A 503 " 0.000 2.00e-02 2.50e+03 pdb=" CHA HEM A 503 " -0.023 2.00e-02 2.50e+03 pdb=" CHB HEM A 503 " -0.019 2.00e-02 2.50e+03 pdb=" CMA HEM A 503 " -0.000 2.00e-02 2.50e+03 pdb=" NA HEM A 503 " 0.030 2.00e-02 2.50e+03 ... (remaining 577 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 110 2.70 - 3.25: 3175 3.25 - 3.80: 5818 3.80 - 4.35: 8071 4.35 - 4.90: 12933 Nonbonded interactions: 30107 Sorted by model distance: nonbonded pdb=" NE2 HIS A 142 " pdb="FE HEM A 503 " model vdw 2.155 3.080 nonbonded pdb=" NE2 HIS A 129 " pdb="FE HEM A 504 " model vdw 2.212 3.080 nonbonded pdb=" O SER A 238 " pdb=" OG SER A 238 " model vdw 2.220 3.040 nonbonded pdb=" O HOH A 613 " pdb=" O HOH A 617 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP A 254 " pdb=" O HOH A 601 " model vdw 2.242 3.040 ... (remaining 30102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic 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: 0.580 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.009 0.209 3563 Z= 0.618 Angle : 0.967 23.336 4872 Z= 0.430 Chirality : 0.045 0.224 509 Planarity : 0.004 0.068 580 Dihedral : 20.123 99.565 1270 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.16 % Allowed : 26.88 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.55 (0.39), residues: 397 helix: -0.29 (0.34), residues: 200 sheet: 0.66 (0.54), residues: 87 loop : -1.06 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.004 0.001 HIS A 69 PHE 0.009 0.001 PHE A 218 TYR 0.013 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 394 TYR cc_start: 0.6008 (p90) cc_final: 0.5495 (p90) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 1.2626 time to fit residues: 69.0482 Evaluate side-chains 52 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 370 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117968 restraints weight = 3375.632| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.59 r_work: 0.3225 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3563 Z= 0.263 Angle : 0.672 14.243 4872 Z= 0.296 Chirality : 0.043 0.161 509 Planarity : 0.004 0.031 580 Dihedral : 11.633 85.403 516 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 26.30 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.45 (0.41), residues: 397 helix: 1.04 (0.35), residues: 201 sheet: 0.19 (0.53), residues: 93 loop : -0.90 (0.57), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.002 TYR A 275 ARG 0.002 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7625 (p0) REVERT: A 320 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7177 (tpp-160) REVERT: A 385 LYS cc_start: 0.5765 (mmtt) cc_final: 0.5006 (mmmm) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 1.3432 time to fit residues: 71.9124 Evaluate side-chains 49 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118869 restraints weight = 3380.930| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.59 r_work: 0.3239 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3563 Z= 0.225 Angle : 0.637 13.414 4872 Z= 0.277 Chirality : 0.041 0.151 509 Planarity : 0.003 0.028 580 Dihedral : 11.046 77.441 515 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.47 % Allowed : 25.72 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.73 (0.41), residues: 397 helix: 1.47 (0.36), residues: 201 sheet: 0.08 (0.54), residues: 93 loop : -0.96 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.002 TYR A 275 ARG 0.002 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7585 (p0) REVERT: A 320 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6366 (mpt-90) outliers start: 12 outliers final: 5 residues processed: 58 average time/residue: 1.3134 time to fit residues: 78.6273 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120615 restraints weight = 3435.795| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.60 r_work: 0.3258 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3563 Z= 0.182 Angle : 0.604 12.797 4872 Z= 0.262 Chirality : 0.040 0.145 509 Planarity : 0.003 0.024 580 Dihedral : 10.769 76.032 513 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.89 % Allowed : 26.59 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.95 (0.42), residues: 397 helix: 1.74 (0.36), residues: 201 sheet: 0.02 (0.54), residues: 93 loop : -0.92 (0.55), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7459 (p0) REVERT: A 318 SER cc_start: 0.7122 (t) cc_final: 0.6837 (p) REVERT: A 320 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6272 (mpt-90) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 1.2703 time to fit residues: 72.1035 Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116210 restraints weight = 3472.882| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.60 r_work: 0.3202 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3563 Z= 0.336 Angle : 0.707 14.217 4872 Z= 0.309 Chirality : 0.044 0.163 509 Planarity : 0.003 0.024 580 Dihedral : 11.418 81.580 513 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.05 % Allowed : 26.01 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.56 (0.41), residues: 397 helix: 1.32 (0.36), residues: 201 sheet: 0.02 (0.53), residues: 93 loop : -1.07 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 125 HIS 0.008 0.001 HIS A 69 PHE 0.013 0.002 PHE A 218 TYR 0.012 0.002 TYR A 164 ARG 0.003 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7596 (p0) REVERT: A 270 THR cc_start: 0.8473 (p) cc_final: 0.8248 (p) REVERT: A 394 TYR cc_start: 0.6687 (p90) cc_final: 0.6141 (p90) outliers start: 14 outliers final: 6 residues processed: 57 average time/residue: 1.2862 time to fit residues: 75.5490 Evaluate side-chains 54 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118269 restraints weight = 3510.444| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.61 r_work: 0.3232 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3563 Z= 0.223 Angle : 0.651 13.243 4872 Z= 0.279 Chirality : 0.041 0.147 509 Planarity : 0.003 0.023 580 Dihedral : 10.917 76.228 513 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.89 % Allowed : 27.17 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.71 (0.41), residues: 397 helix: 1.51 (0.36), residues: 201 sheet: -0.03 (0.53), residues: 93 loop : -1.03 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.012 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7511 (p0) REVERT: A 394 TYR cc_start: 0.6722 (p90) cc_final: 0.6204 (p90) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 1.1318 time to fit residues: 64.3561 Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119150 restraints weight = 3431.002| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.59 r_work: 0.3243 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3563 Z= 0.210 Angle : 0.644 13.071 4872 Z= 0.275 Chirality : 0.041 0.153 509 Planarity : 0.003 0.023 580 Dihedral : 10.806 75.940 513 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.89 % Allowed : 27.17 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.74 (0.42), residues: 397 helix: 1.57 (0.36), residues: 201 sheet: -0.06 (0.53), residues: 93 loop : -1.03 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7351 (p0) REVERT: A 394 TYR cc_start: 0.6764 (p90) cc_final: 0.6223 (p90) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 1.2007 time to fit residues: 66.9805 Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119020 restraints weight = 3450.333| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.59 r_work: 0.3245 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3563 Z= 0.204 Angle : 0.647 13.025 4872 Z= 0.275 Chirality : 0.041 0.164 509 Planarity : 0.003 0.023 580 Dihedral : 10.729 75.777 513 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.60 % Allowed : 27.46 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.73 (0.42), residues: 397 helix: 1.57 (0.36), residues: 202 sheet: -0.12 (0.53), residues: 93 loop : -1.03 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7322 (p0) REVERT: A 394 TYR cc_start: 0.6676 (p90) cc_final: 0.6075 (p90) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 1.2174 time to fit residues: 69.0664 Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.150552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121343 restraints weight = 3356.103| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.58 r_work: 0.3271 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3563 Z= 0.173 Angle : 0.623 12.692 4872 Z= 0.265 Chirality : 0.040 0.165 509 Planarity : 0.003 0.023 580 Dihedral : 10.263 75.556 513 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.60 % Allowed : 27.46 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.88 (0.42), residues: 397 helix: 1.73 (0.36), residues: 202 sheet: -0.13 (0.53), residues: 93 loop : -0.96 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7234 (p0) REVERT: A 269 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7828 (m) REVERT: A 394 TYR cc_start: 0.6614 (p90) cc_final: 0.6034 (p90) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 1.0786 time to fit residues: 61.4426 Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119166 restraints weight = 3471.824| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.60 r_work: 0.3244 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3563 Z= 0.214 Angle : 0.670 13.195 4872 Z= 0.283 Chirality : 0.041 0.164 509 Planarity : 0.003 0.022 580 Dihedral : 10.520 76.273 513 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.31 % Allowed : 27.46 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.76 (0.41), residues: 397 helix: 1.61 (0.36), residues: 202 sheet: -0.17 (0.52), residues: 93 loop : -0.98 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7371 (p0) REVERT: A 269 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7883 (m) REVERT: A 394 TYR cc_start: 0.6756 (p90) cc_final: 0.6107 (p90) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 1.1656 time to fit residues: 63.8481 Evaluate side-chains 52 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121673 restraints weight = 3451.278| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.60 r_work: 0.3278 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3563 Z= 0.163 Angle : 0.634 13.124 4872 Z= 0.267 Chirality : 0.040 0.168 509 Planarity : 0.003 0.023 580 Dihedral : 9.929 75.907 513 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 28.03 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.92 (0.42), residues: 397 helix: 1.79 (0.36), residues: 202 sheet: -0.20 (0.52), residues: 93 loop : -0.90 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.004 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.011 0.001 TYR A 275 ARG 0.001 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2936.48 seconds wall clock time: 50 minutes 54.15 seconds (3054.15 seconds total)