Starting phenix.real_space_refine on Tue Feb 11 16:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4k_25678/02_2025/7t4k_25678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4k_25678/02_2025/7t4k_25678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4k_25678/02_2025/7t4k_25678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4k_25678/02_2025/7t4k_25678.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4k_25678/02_2025/7t4k_25678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4k_25678/02_2025/7t4k_25678.cif" } resolution = 3.25 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= 0.009 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 41 5.16 5 C 3941 2.51 5 N 1048 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3039 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3141 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 5.42, per 1000 atoms: 0.88 Number of scatterers: 6180 At special positions: 0 Unit cell: (115.44, 78, 73.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 2 15.00 O 1148 8.00 N 1048 7.00 C 3941 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=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 961.7 milliseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 43.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.567A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.660A pdb=" N TRP A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.545A pdb=" N LEU A 443 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.566A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.531A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.925A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.703A pdb=" N ARG A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 574 Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.511A pdb=" N CYS B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.728A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.895A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.747A pdb=" N LEU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 542 through 555 removed outlier: 3.835A pdb=" N ARG B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.554A pdb=" N LYS A 177 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 167 removed outlier: 3.558A pdb=" N LYS B 177 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER B 175 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 173 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 286 " --> pdb=" O MET B 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 372 264 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1988 1.34 - 1.46: 1125 1.46 - 1.58: 3112 1.58 - 1.69: 8 1.69 - 1.81: 65 Bond restraints: 6298 Sorted by residual: bond pdb=" C VAL B 216 " pdb=" N PRO B 217 " ideal model delta sigma weight residual 1.334 1.374 -0.041 2.34e-02 1.83e+03 3.00e+00 bond pdb=" C LEU A 543 " pdb=" N PRO A 544 " ideal model delta sigma weight residual 1.334 1.359 -0.024 1.51e-02 4.39e+03 2.60e+00 bond pdb=" CB ASP B 442 " pdb=" CG ASP B 442 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.50e+00 bond pdb=" CG LEU A 571 " pdb=" CD1 LEU A 571 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" C LEU B 543 " pdb=" N PRO B 544 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.35e+00 ... (remaining 6293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 8301 2.34 - 4.68: 189 4.68 - 7.02: 30 7.02 - 9.36: 7 9.36 - 11.70: 5 Bond angle restraints: 8532 Sorted by residual: angle pdb=" CA GLU A 214 " pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA MET B 249 " pdb=" CB MET B 249 " pdb=" CG MET B 249 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 angle pdb=" N GLU B 441 " pdb=" CA GLU B 441 " pdb=" C GLU B 441 " ideal model delta sigma weight residual 111.36 115.39 -4.03 1.09e+00 8.42e-01 1.37e+01 angle pdb=" CB MET B 195 " pdb=" CG MET B 195 " pdb=" SD MET B 195 " ideal model delta sigma weight residual 112.70 101.71 10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB GLN A 569 " pdb=" CG GLN A 569 " pdb=" CD GLN A 569 " ideal model delta sigma weight residual 112.60 118.81 -6.21 1.70e+00 3.46e-01 1.33e+01 ... (remaining 8527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 3498 16.79 - 33.58: 296 33.58 - 50.37: 46 50.37 - 67.16: 7 67.16 - 83.95: 6 Dihedral angle restraints: 3853 sinusoidal: 1537 harmonic: 2316 Sorted by residual: dihedral pdb=" CA SER B 280 " pdb=" C SER B 280 " pdb=" N GLY B 281 " pdb=" CA GLY B 281 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASN A 326 " pdb=" CB ASN A 326 " pdb=" CG ASN A 326 " pdb=" OD1 ASN A 326 " ideal model delta sinusoidal sigma weight residual 120.00 -173.25 -66.75 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP B 121 " pdb=" CB ASP B 121 " pdb=" CG ASP B 121 " pdb=" OD1 ASP B 121 " ideal model delta sinusoidal sigma weight residual -30.00 -84.01 54.01 1 2.00e+01 2.50e-03 9.90e+00 ... (remaining 3850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 693 0.048 - 0.095: 201 0.095 - 0.143: 61 0.143 - 0.191: 14 0.191 - 0.239: 2 Chirality restraints: 971 Sorted by residual: chirality pdb=" CA GLU A 158 " pdb=" N GLU A 158 " pdb=" C GLU A 158 " pdb=" CB GLU A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE B 257 " pdb=" N ILE B 257 " pdb=" C ILE B 257 " pdb=" CB ILE B 257 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 968 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 439 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C LYS B 439 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 439 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 440 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 125 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C GLU B 125 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 125 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY B 126 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 129 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C TRP B 129 " -0.034 2.00e-02 2.50e+03 pdb=" O TRP B 129 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 130 " 0.011 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1569 2.81 - 3.33: 5732 3.33 - 3.85: 9613 3.85 - 4.38: 11703 4.38 - 4.90: 20259 Nonbonded interactions: 48876 Sorted by model distance: nonbonded pdb=" OE2 GLU B 346 " pdb=" OG1 THR B 352 " model vdw 2.287 3.040 nonbonded pdb=" ND2 ASN B 197 " pdb=" O MET B 284 " model vdw 2.361 3.120 nonbonded pdb=" OE2 GLU A 320 " pdb=" NH2 ARG A 555 " model vdw 2.379 3.120 nonbonded pdb=" OE2 GLU B 320 " pdb=" NH2 ARG B 555 " model vdw 2.388 3.120 nonbonded pdb=" O TYR B 212 " pdb=" NH1 ARG B 239 " model vdw 2.397 3.120 ... (remaining 48871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 200 or (resid 201 and (name N or name CA or name C or n \ ame O or name CB )) or resid 202 through 223 or (resid 237 and (name N or name C \ A or name C or name O or name CB )) or resid 238 through 493 or (resid 494 and ( \ name N or name CA or name C or name O or name CB )) or resid 495 through 574)) selection = (chain 'B' and (resid 120 through 136 or resid 148 through 256 or (resid 282 and \ (name N or name CA or name C or name O or name CB )) or resid 283 through 511 o \ r resid 541 through 574)) } 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: 6.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.250 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6298 Z= 0.301 Angle : 0.881 11.701 8532 Z= 0.468 Chirality : 0.051 0.239 971 Planarity : 0.006 0.046 1080 Dihedral : 12.764 83.950 2339 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.15 % Allowed : 1.20 % Favored : 98.65 % 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: 0.51 (0.30), residues: 754 helix: 1.27 (0.28), residues: 298 sheet: -0.64 (0.49), residues: 114 loop : -0.02 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 567 HIS 0.005 0.001 HIS B 559 PHE 0.032 0.002 PHE B 222 TYR 0.030 0.002 TYR A 373 ARG 0.010 0.001 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.700 Fit side-chains REVERT: A 214 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7845 (mm-30) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1645 time to fit residues: 22.5616 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105234 restraints weight = 8604.757| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.96 r_work: 0.3097 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6298 Z= 0.212 Angle : 0.518 6.519 8532 Z= 0.268 Chirality : 0.040 0.148 971 Planarity : 0.004 0.039 1080 Dihedral : 5.862 78.963 847 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.05 % Allowed : 5.25 % Favored : 93.70 % 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: 1.31 (0.30), residues: 754 helix: 2.30 (0.28), residues: 301 sheet: -0.41 (0.47), residues: 114 loop : 0.11 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 129 HIS 0.003 0.001 HIS A 559 PHE 0.010 0.001 PHE A 253 TYR 0.014 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.715 Fit side-chains REVERT: A 152 GLN cc_start: 0.7671 (mt0) cc_final: 0.7443 (mt0) REVERT: A 167 LYS cc_start: 0.7999 (mptt) cc_final: 0.7741 (mttp) REVERT: A 570 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7867 (mt-10) REVERT: B 189 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7589 (mm110) REVERT: B 203 ASN cc_start: 0.8387 (t0) cc_final: 0.8148 (t0) REVERT: B 284 MET cc_start: 0.8360 (mmm) cc_final: 0.7795 (mmm) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 0.1690 time to fit residues: 20.2098 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 573 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.0030 chunk 33 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.0060 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN B 504 GLN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104675 restraints weight = 8723.080| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.93 r_work: 0.3100 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6298 Z= 0.174 Angle : 0.467 5.834 8532 Z= 0.241 Chirality : 0.039 0.143 971 Planarity : 0.004 0.035 1080 Dihedral : 5.776 78.510 847 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.05 % Allowed : 7.50 % Favored : 91.45 % 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: 1.70 (0.31), residues: 754 helix: 2.58 (0.29), residues: 303 sheet: -0.04 (0.49), residues: 108 loop : 0.29 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 401 HIS 0.003 0.001 HIS B 559 PHE 0.010 0.001 PHE A 452 TYR 0.012 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.709 Fit side-chains REVERT: A 152 GLN cc_start: 0.7743 (mt0) cc_final: 0.7521 (mt0) REVERT: A 167 LYS cc_start: 0.7937 (mptt) cc_final: 0.7592 (mttp) REVERT: A 491 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7345 (mtmm) REVERT: A 570 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7919 (mt-10) REVERT: B 189 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7572 (mm110) REVERT: B 203 ASN cc_start: 0.8350 (t0) cc_final: 0.8097 (t0) REVERT: B 284 MET cc_start: 0.8341 (mmm) cc_final: 0.7695 (mmm) outliers start: 7 outliers final: 4 residues processed: 81 average time/residue: 0.1650 time to fit residues: 18.5897 Evaluate side-chains 81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.0030 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104851 restraints weight = 8800.195| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.95 r_work: 0.3088 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6298 Z= 0.177 Angle : 0.456 5.297 8532 Z= 0.236 Chirality : 0.038 0.141 971 Planarity : 0.004 0.033 1080 Dihedral : 5.723 77.580 847 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.65 % Allowed : 7.95 % Favored : 90.40 % 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: 1.81 (0.31), residues: 754 helix: 2.65 (0.29), residues: 304 sheet: 0.02 (0.49), residues: 108 loop : 0.35 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 401 HIS 0.003 0.001 HIS B 559 PHE 0.010 0.001 PHE A 452 TYR 0.012 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.747 Fit side-chains REVERT: A 152 GLN cc_start: 0.7754 (mt0) cc_final: 0.7526 (mt0) REVERT: A 167 LYS cc_start: 0.7949 (mptt) cc_final: 0.7561 (mttp) REVERT: A 491 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7346 (mtmm) REVERT: A 494 TYR cc_start: 0.6998 (p90) cc_final: 0.6775 (p90) REVERT: A 570 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7937 (mt-10) REVERT: B 189 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7567 (mm110) REVERT: B 203 ASN cc_start: 0.8389 (t0) cc_final: 0.7978 (t0) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.1656 time to fit residues: 19.1633 Evaluate side-chains 80 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 0.0000 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN B 366 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103391 restraints weight = 8720.056| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.95 r_work: 0.3069 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6298 Z= 0.216 Angle : 0.472 6.255 8532 Z= 0.240 Chirality : 0.039 0.142 971 Planarity : 0.004 0.034 1080 Dihedral : 5.696 76.121 847 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.65 % Allowed : 8.25 % Favored : 90.10 % 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: 1.72 (0.31), residues: 754 helix: 2.65 (0.29), residues: 304 sheet: -0.21 (0.48), residues: 114 loop : 0.31 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 505 HIS 0.003 0.001 HIS B 332 PHE 0.010 0.001 PHE A 452 TYR 0.013 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.759 Fit side-chains REVERT: A 152 GLN cc_start: 0.7751 (mt0) cc_final: 0.7517 (mt0) REVERT: A 167 LYS cc_start: 0.7951 (mptt) cc_final: 0.7564 (mttp) REVERT: A 491 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7401 (mtmm) REVERT: A 494 TYR cc_start: 0.7153 (p90) cc_final: 0.6860 (p90) REVERT: A 570 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7929 (mt-10) REVERT: B 189 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7582 (mm110) REVERT: B 203 ASN cc_start: 0.8369 (t0) cc_final: 0.7913 (t0) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 0.1698 time to fit residues: 20.1539 Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 571 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.0010 chunk 58 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 71 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104342 restraints weight = 8667.583| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.93 r_work: 0.3092 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6298 Z= 0.173 Angle : 0.462 5.896 8532 Z= 0.236 Chirality : 0.038 0.141 971 Planarity : 0.003 0.034 1080 Dihedral : 5.672 75.399 847 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.20 % Allowed : 9.00 % Favored : 89.81 % 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: 1.82 (0.31), residues: 754 helix: 2.72 (0.29), residues: 304 sheet: -0.18 (0.48), residues: 115 loop : 0.38 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 401 HIS 0.002 0.001 HIS B 559 PHE 0.011 0.001 PHE A 253 TYR 0.011 0.001 TYR A 373 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.025 Fit side-chains REVERT: A 152 GLN cc_start: 0.7733 (mt0) cc_final: 0.7511 (mt0) REVERT: A 167 LYS cc_start: 0.7993 (mptt) cc_final: 0.7581 (mttp) REVERT: A 194 MET cc_start: 0.8285 (ppp) cc_final: 0.7965 (tmm) REVERT: A 214 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7740 (tp30) REVERT: A 491 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7458 (mtmm) REVERT: A 494 TYR cc_start: 0.7094 (p90) cc_final: 0.6806 (p90) REVERT: A 570 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7928 (mt-10) REVERT: B 189 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7616 (mm110) REVERT: B 203 ASN cc_start: 0.8426 (t0) cc_final: 0.7996 (t0) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.1776 time to fit residues: 20.3671 Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 571 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.0770 chunk 2 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.137866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105127 restraints weight = 8747.788| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.94 r_work: 0.3109 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6298 Z= 0.140 Angle : 0.444 6.241 8532 Z= 0.227 Chirality : 0.038 0.140 971 Planarity : 0.003 0.035 1080 Dihedral : 5.573 74.684 847 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.65 % Allowed : 8.85 % Favored : 89.51 % 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: 1.94 (0.31), residues: 754 helix: 2.82 (0.29), residues: 305 sheet: -0.12 (0.49), residues: 115 loop : 0.44 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.002 0.001 HIS B 559 PHE 0.011 0.001 PHE A 452 TYR 0.010 0.001 TYR B 482 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.742 Fit side-chains REVERT: A 152 GLN cc_start: 0.7754 (mt0) cc_final: 0.7518 (mt0) REVERT: A 167 LYS cc_start: 0.7879 (mptt) cc_final: 0.7632 (mttp) REVERT: A 194 MET cc_start: 0.8313 (ppp) cc_final: 0.7900 (tmm) REVERT: A 214 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7769 (tp30) REVERT: A 491 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (mtmm) REVERT: A 570 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7886 (mt-10) REVERT: B 189 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7549 (mm110) REVERT: B 203 ASN cc_start: 0.8455 (t0) cc_final: 0.8006 (t0) outliers start: 11 outliers final: 5 residues processed: 88 average time/residue: 0.1662 time to fit residues: 20.2847 Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 72 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103997 restraints weight = 8672.761| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.81 r_work: 0.3077 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6298 Z= 0.230 Angle : 0.494 8.748 8532 Z= 0.247 Chirality : 0.039 0.144 971 Planarity : 0.004 0.035 1080 Dihedral : 5.566 73.431 847 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.20 % Allowed : 9.75 % Favored : 89.06 % 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: 1.81 (0.31), residues: 754 helix: 2.70 (0.29), residues: 305 sheet: 0.11 (0.50), residues: 100 loop : 0.25 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 567 HIS 0.003 0.001 HIS B 332 PHE 0.020 0.001 PHE B 452 TYR 0.013 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.755 Fit side-chains REVERT: A 152 GLN cc_start: 0.7744 (mt0) cc_final: 0.7496 (mt0) REVERT: A 167 LYS cc_start: 0.7839 (mptt) cc_final: 0.7583 (mttp) REVERT: A 194 MET cc_start: 0.8235 (ppp) cc_final: 0.7830 (tmm) REVERT: A 214 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7764 (tp30) REVERT: A 360 CYS cc_start: 0.8386 (m) cc_final: 0.7734 (t) REVERT: A 491 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7571 (mtmm) REVERT: A 494 TYR cc_start: 0.7791 (p90) cc_final: 0.7427 (p90) REVERT: A 570 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7896 (mt-10) REVERT: B 203 ASN cc_start: 0.8472 (t0) cc_final: 0.8019 (t0) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.1749 time to fit residues: 20.0126 Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 25 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103680 restraints weight = 8841.697| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.92 r_work: 0.3071 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6298 Z= 0.219 Angle : 0.496 9.518 8532 Z= 0.248 Chirality : 0.039 0.142 971 Planarity : 0.003 0.035 1080 Dihedral : 5.521 73.782 847 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.20 % Allowed : 9.75 % Favored : 89.06 % 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: 1.81 (0.31), residues: 754 helix: 2.69 (0.29), residues: 304 sheet: 0.11 (0.50), residues: 100 loop : 0.26 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.002 0.001 HIS B 332 PHE 0.018 0.001 PHE B 452 TYR 0.012 0.001 TYR A 373 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.709 Fit side-chains REVERT: A 152 GLN cc_start: 0.7747 (mt0) cc_final: 0.7500 (mt0) REVERT: A 167 LYS cc_start: 0.7896 (mptt) cc_final: 0.7637 (mttp) REVERT: A 194 MET cc_start: 0.8258 (ppp) cc_final: 0.7863 (tmm) REVERT: A 214 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7799 (tp30) REVERT: A 360 CYS cc_start: 0.8444 (m) cc_final: 0.7778 (t) REVERT: A 491 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7636 (mtmm) REVERT: A 494 TYR cc_start: 0.7749 (p90) cc_final: 0.7414 (p90) REVERT: A 570 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7910 (mt-10) REVERT: B 203 ASN cc_start: 0.8482 (t0) cc_final: 0.8029 (t0) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.1604 time to fit residues: 18.5714 Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103047 restraints weight = 8843.347| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.97 r_work: 0.3065 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6298 Z= 0.209 Angle : 0.514 9.914 8532 Z= 0.255 Chirality : 0.039 0.170 971 Planarity : 0.003 0.034 1080 Dihedral : 5.479 73.846 847 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.35 % Allowed : 10.19 % Favored : 88.46 % 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: 1.79 (0.31), residues: 754 helix: 2.70 (0.29), residues: 304 sheet: 0.02 (0.50), residues: 101 loop : 0.24 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.002 0.001 HIS B 332 PHE 0.018 0.001 PHE B 452 TYR 0.012 0.001 TYR A 373 ARG 0.002 0.000 ARG B 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.703 Fit side-chains REVERT: A 152 GLN cc_start: 0.7805 (mt0) cc_final: 0.7572 (mt0) REVERT: A 167 LYS cc_start: 0.7985 (mptt) cc_final: 0.7716 (mttp) REVERT: A 194 MET cc_start: 0.8312 (ppp) cc_final: 0.7925 (tmm) REVERT: A 214 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7822 (tp30) REVERT: A 360 CYS cc_start: 0.8484 (m) cc_final: 0.7905 (t) REVERT: A 491 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7723 (mtmm) REVERT: A 494 TYR cc_start: 0.7702 (p90) cc_final: 0.7423 (p90) REVERT: B 203 ASN cc_start: 0.8476 (t0) cc_final: 0.8041 (t0) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.1665 time to fit residues: 19.1612 Evaluate side-chains 84 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 64 optimal weight: 0.0370 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103910 restraints weight = 8866.734| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.78 r_work: 0.3072 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6298 Z= 0.195 Angle : 0.518 9.969 8532 Z= 0.257 Chirality : 0.039 0.141 971 Planarity : 0.003 0.034 1080 Dihedral : 5.428 73.926 847 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.05 % Allowed : 10.49 % Favored : 88.46 % 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: 1.82 (0.31), residues: 754 helix: 2.72 (0.29), residues: 304 sheet: 0.07 (0.50), residues: 101 loop : 0.25 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.002 0.001 HIS B 559 PHE 0.018 0.001 PHE B 452 TYR 0.011 0.001 TYR A 373 ARG 0.002 0.000 ARG B 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.75 seconds wall clock time: 53 minutes 19.18 seconds (3199.18 seconds total)