Starting phenix.real_space_refine on Tue Feb 11 01:18:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qta_18647/02_2025/8qta_18647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qta_18647/02_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_18647/02_2025/8qta_18647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qta_18647/02_2025/8qta_18647.map" model { file = "/net/cci-nas-00/data/ceres_data/8qta_18647/02_2025/8qta_18647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qta_18647/02_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-5592/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: 2.75, per 1000 atoms: 0.79 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: 1.05 Conformation dependent library (CDL) restraints added in 402.9 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: 0.27 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: 0.96 Time building geometry restraints manager: 1.20 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: 0.480 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.610 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- 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 : 0.406 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: 1.2568 time to fit residues: 68.6681 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 : 0.386 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.149360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120058 restraints weight = 3367.536| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.58 r_work: 0.3251 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3563 Z= 0.203 Angle : 0.633 13.461 4872 Z= 0.278 Chirality : 0.041 0.156 509 Planarity : 0.003 0.030 580 Dihedral : 11.554 84.317 516 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 26.88 % 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: 0.65 (0.41), residues: 397 helix: 1.27 (0.35), residues: 201 sheet: 0.20 (0.54), residues: 93 loop : -0.85 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.005 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 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 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7556 (p0) REVERT: A 320 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6592 (mpt-90) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 1.3407 time to fit residues: 73.1421 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 0.0770 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7544 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.148749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119593 restraints weight = 3378.943| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.58 r_work: 0.3246 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1352 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= 0.213 Angle : 0.627 13.288 4872 Z= 0.273 Chirality : 0.041 0.151 509 Planarity : 0.003 0.027 580 Dihedral : 10.950 77.222 515 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.89 % Allowed : 26.30 % 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: 0.86 (0.41), residues: 397 helix: 1.57 (0.36), residues: 201 sheet: 0.12 (0.54), residues: 93 loop : -0.87 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 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 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7455 (p0) REVERT: A 320 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6385 (mpt-90) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 1.2795 time to fit residues: 71.3626 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.149109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119884 restraints weight = 3443.873| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.60 r_work: 0.3252 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1439 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= 0.194 Angle : 0.612 12.907 4872 Z= 0.265 Chirality : 0.040 0.147 509 Planarity : 0.003 0.025 580 Dihedral : 10.815 76.678 513 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.76 % Allowed : 25.43 % 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: 0.97 (0.42), residues: 397 helix: 1.75 (0.36), residues: 201 sheet: 0.01 (0.54), residues: 93 loop : -0.88 (0.55), residues: 103 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 0.010 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 60 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7441 (p0) REVERT: A 320 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6312 (mpt-90) outliers start: 13 outliers final: 5 residues processed: 56 average time/residue: 1.2793 time to fit residues: 73.8480 Evaluate side-chains 52 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.149654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120419 restraints weight = 3452.343| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.60 r_work: 0.3259 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1532 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= 0.184 Angle : 0.606 12.782 4872 Z= 0.261 Chirality : 0.040 0.145 509 Planarity : 0.003 0.022 580 Dihedral : 10.638 76.807 513 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 26.88 % 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: 1.04 (0.42), residues: 397 helix: 1.80 (0.36), residues: 201 sheet: 0.03 (0.54), residues: 93 loop : -0.82 (0.56), residues: 103 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 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 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 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7316 (p0) REVERT: A 318 SER cc_start: 0.7149 (t) cc_final: 0.6918 (p) REVERT: A 320 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6263 (mpt-90) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 1.2663 time to fit residues: 67.9350 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 320 ARG Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.148113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118672 restraints weight = 3514.880| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.61 r_work: 0.3239 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1456 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= 0.225 Angle : 0.647 13.210 4872 Z= 0.277 Chirality : 0.041 0.150 509 Planarity : 0.003 0.021 580 Dihedral : 10.845 76.949 513 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.47 % Allowed : 26.30 % 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: 0.89 (0.42), residues: 397 helix: 1.66 (0.36), residues: 201 sheet: -0.01 (0.53), residues: 93 loop : -0.87 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.007 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.003 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: 12 poor density : 46 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7355 (p0) REVERT: A 318 SER cc_start: 0.7201 (OUTLIER) cc_final: 0.6878 (p) REVERT: A 320 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6170 (mpt-90) REVERT: A 394 TYR cc_start: 0.6606 (p90) cc_final: 0.6109 (p90) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 1.3176 time to fit residues: 74.7245 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 : 0.366 ------------------------------------------------------------------------------- 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 318 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.147977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118635 restraints weight = 3424.775| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.59 r_work: 0.3234 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1469 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= 0.238 Angle : 0.661 13.367 4872 Z= 0.284 Chirality : 0.042 0.154 509 Planarity : 0.003 0.022 580 Dihedral : 10.871 76.779 513 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.05 % Allowed : 25.43 % 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: 0.78 (0.41), residues: 397 helix: 1.58 (0.36), residues: 201 sheet: -0.06 (0.53), residues: 93 loop : -0.95 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 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 0.003 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 60 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7372 (p0) REVERT: A 320 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6206 (mpt-90) REVERT: A 394 TYR cc_start: 0.6756 (p90) cc_final: 0.6221 (p90) outliers start: 14 outliers final: 5 residues processed: 58 average time/residue: 1.2577 time to fit residues: 75.1618 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 320 ARG 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: 0.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.148200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118884 restraints weight = 3446.431| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.59 r_work: 0.3240 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1467 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= 0.226 Angle : 0.657 13.325 4872 Z= 0.282 Chirality : 0.041 0.155 509 Planarity : 0.003 0.022 580 Dihedral : 10.833 76.480 513 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.60 % Allowed : 26.59 % 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: 0.77 (0.41), residues: 397 helix: 1.58 (0.36), residues: 201 sheet: -0.09 (0.53), residues: 93 loop : -0.93 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.007 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.003 0.000 ARG A 320 *********************** 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 57 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7330 (p0) REVERT: A 320 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6353 (mpt-90) REVERT: A 394 TYR cc_start: 0.6722 (p90) cc_final: 0.6120 (p90) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 1.2726 time to fit residues: 72.0581 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL 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: 0.8980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.150102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121038 restraints weight = 3366.215| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.57 r_work: 0.3272 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1624 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= 0.171 Angle : 0.639 13.015 4872 Z= 0.271 Chirality : 0.040 0.160 509 Planarity : 0.003 0.022 580 Dihedral : 10.421 75.826 513 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 26.88 % 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: 0.91 (0.42), residues: 397 helix: 1.75 (0.36), residues: 202 sheet: -0.15 (0.52), residues: 93 loop : -0.87 (0.57), 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 0.002 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 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7287 (p0) REVERT: A 394 TYR cc_start: 0.6717 (p90) cc_final: 0.6086 (p90) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 1.2454 time to fit residues: 68.1598 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.148419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118973 restraints weight = 3470.634| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.60 r_work: 0.3242 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3563 Z= 0.227 Angle : 0.680 13.317 4872 Z= 0.290 Chirality : 0.042 0.160 509 Planarity : 0.003 0.022 580 Dihedral : 10.705 76.496 513 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.45 % Allowed : 27.46 % Favored : 71.10 % 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: 1.62 (0.36), residues: 201 sheet: -0.19 (0.52), residues: 93 loop : -0.95 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.007 0.001 HIS A 69 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.004 0.000 ARG A 320 ********************** 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 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7363 (p0) REVERT: A 394 TYR cc_start: 0.6744 (p90) cc_final: 0.6112 (p90) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 1.1988 time to fit residues: 60.7030 Evaluate side-chains 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.0040 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.151350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123328 restraints weight = 3482.777| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.54 r_work: 0.3302 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3563 Z= 0.150 Angle : 0.620 13.329 4872 Z= 0.262 Chirality : 0.039 0.169 509 Planarity : 0.003 0.022 580 Dihedral : 9.811 76.071 513 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.45 % Allowed : 28.03 % 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: 1.04 (0.42), residues: 397 helix: 1.88 (0.36), residues: 202 sheet: -0.16 (0.53), residues: 92 loop : -0.82 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.004 0.000 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.010 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.43 seconds wall clock time: 52 minutes 13.87 seconds (3133.87 seconds total)