Starting phenix.real_space_refine on Tue Jan 14 11:09:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdb_61387/01_2025/9jdb_61387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdb_61387/01_2025/9jdb_61387.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/9jdb_61387/01_2025/9jdb_61387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdb_61387/01_2025/9jdb_61387.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdb_61387/01_2025/9jdb_61387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdb_61387/01_2025/9jdb_61387.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= 0.056 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 Fe 2 7.16 5 S 32 5.16 5 C 4214 2.51 5 N 1122 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6592 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3253 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3253 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 374} Chain breaks: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.43, per 1000 atoms: 0.67 Number of scatterers: 6592 At special positions: 0 Unit cell: (101.15, 107.95, 66.3, 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) Fe 2 26.01 S 32 16.00 O 1222 8.00 N 1122 7.00 C 4214 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: 1.61 Conformation dependent library (CDL) restraints added in 872.0 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 44.6% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 removed outlier: 3.632A pdb=" N ARG A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 156 through 167 removed outlier: 4.086A pdb=" N TRP A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 179 through 184 removed outlier: 4.082A pdb=" N MET A 184 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.645A pdb=" N PHE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.571A pdb=" N HIS A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.818A pdb=" N SER A 400 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 Proline residue: A 410 - end of helix Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 422 through 438 removed outlier: 3.806A pdb=" N GLN A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'B' and resid 33 through 44 removed outlier: 3.627A pdb=" N ARG B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 156 through 167 removed outlier: 4.003A pdb=" N TRP B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 179 through 184 removed outlier: 4.106A pdb=" N MET B 184 " --> pdb=" O PHE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 333 through 351 removed outlier: 3.644A pdb=" N PHE B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix removed outlier: 3.569A pdb=" N HIS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.869A pdb=" N SER B 400 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 421 removed outlier: 4.054A pdb=" N TYR B 407 " --> pdb=" O ASN B 403 " (cutoff:3.500A) Proline residue: B 410 - end of helix Proline residue: B 418 - end of helix Processing helix chain 'B' and resid 422 through 438 removed outlier: 3.757A pdb=" N GLN B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 456 through 468 Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330 removed outlier: 3.831A pdb=" N GLY A 299 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 259 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N CYS A 297 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR A 60 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 61 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.823A pdb=" N GLY B 299 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 259 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N CYS B 297 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR B 60 " --> pdb=" O LYS B 304 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 792 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: 1.88 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.22: 1 1.22 - 1.43: 2999 1.43 - 1.65: 3732 1.65 - 1.87: 52 1.87 - 2.08: 8 Bond restraints: 6792 Sorted by residual: bond pdb=" CB PRO A 418 " pdb=" CG PRO A 418 " ideal model delta sigma weight residual 1.492 1.003 0.489 5.00e-02 4.00e+02 9.57e+01 bond pdb=" CG PRO A 418 " pdb=" CD PRO A 418 " ideal model delta sigma weight residual 1.503 1.234 0.269 3.40e-02 8.65e+02 6.28e+01 bond pdb=" CA PRO A 418 " pdb=" CB PRO A 418 " ideal model delta sigma weight residual 1.533 1.584 -0.051 1.42e-02 4.96e+03 1.28e+01 bond pdb=" N PRO A 418 " pdb=" CA PRO A 418 " ideal model delta sigma weight residual 1.469 1.509 -0.041 1.28e-02 6.10e+03 1.01e+01 bond pdb=" N PRO A 418 " pdb=" CD PRO A 418 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.73e+00 ... (remaining 6787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 9259 14.76 - 29.53: 4 29.53 - 44.29: 0 44.29 - 59.05: 0 59.05 - 73.82: 1 Bond angle restraints: 9264 Sorted by residual: angle pdb=" CB PRO A 418 " pdb=" CG PRO A 418 " pdb=" CD PRO A 418 " ideal model delta sigma weight residual 106.10 179.92 -73.82 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO A 418 " pdb=" CD PRO A 418 " pdb=" CG PRO A 418 " ideal model delta sigma weight residual 103.20 75.83 27.37 1.50e+00 4.44e-01 3.33e+02 angle pdb=" CA PRO A 418 " pdb=" CB PRO A 418 " pdb=" CG PRO A 418 " ideal model delta sigma weight residual 104.50 75.80 28.70 1.90e+00 2.77e-01 2.28e+02 angle pdb=" CA PRO A 418 " pdb=" N PRO A 418 " pdb=" CD PRO A 418 " ideal model delta sigma weight residual 112.00 105.67 6.33 1.40e+00 5.10e-01 2.04e+01 angle pdb=" CA LYS B 305 " pdb=" CB LYS B 305 " pdb=" CG LYS B 305 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 ... (remaining 9259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 3671 24.98 - 49.95: 286 49.95 - 74.93: 49 74.93 - 99.91: 8 99.91 - 124.88: 2 Dihedral angle restraints: 4016 sinusoidal: 1656 harmonic: 2360 Sorted by residual: dihedral pdb=" N PRO A 418 " pdb=" CG PRO A 418 " pdb=" CD PRO A 418 " pdb=" CB PRO A 418 " ideal model delta sinusoidal sigma weight residual -30.00 -154.88 124.88 1 1.50e+01 4.44e-03 6.71e+01 dihedral pdb=" CA PRO A 418 " pdb=" CB PRO A 418 " pdb=" CG PRO A 418 " pdb=" CD PRO A 418 " ideal model delta sinusoidal sigma weight residual -38.00 -144.01 106.01 1 2.00e+01 2.50e-03 3.06e+01 dihedral pdb=" CA THR A 94 " pdb=" C THR A 94 " pdb=" N ALA A 95 " pdb=" CA ALA A 95 " ideal model delta harmonic sigma weight residual -180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 4013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 812 0.059 - 0.118: 139 0.118 - 0.177: 8 0.177 - 0.236: 0 0.236 - 0.295: 1 Chirality restraints: 960 Sorted by residual: chirality pdb=" CG LEU A 466 " pdb=" CB LEU A 466 " pdb=" CD1 LEU A 466 " pdb=" CD2 LEU A 466 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ILE B 293 " pdb=" N ILE B 293 " pdb=" C ILE B 293 " pdb=" CB ILE B 293 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE A 47 " pdb=" N ILE A 47 " pdb=" C ILE A 47 " pdb=" CB ILE A 47 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 957 not shown) Planarity restraints: 1204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 417 " 0.032 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 418 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 416 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C ALA A 416 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA A 416 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 417 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 128 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO B 129 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.020 5.00e-02 4.00e+02 ... (remaining 1201 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1355 2.78 - 3.31: 5531 3.31 - 3.84: 10961 3.84 - 4.37: 13499 4.37 - 4.90: 22956 Nonbonded interactions: 54302 Sorted by model distance: nonbonded pdb=" OD2 ASP B 217 " pdb=" NZ LYS B 300 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP A 217 " pdb=" NZ LYS A 300 " model vdw 2.252 3.120 nonbonded pdb=" NE2 HIS A 172 " pdb=" OH TYR A 286 " model vdw 2.300 3.120 nonbonded pdb=" NE2 HIS B 172 " pdb=" OH TYR B 286 " model vdw 2.300 3.120 nonbonded pdb=" OG1 THR A 94 " pdb=" O VAL A 107 " model vdw 2.322 3.040 ... (remaining 54297 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.010 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.810 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.007 0.489 6792 Z= 0.492 Angle : 1.097 73.817 9264 Z= 0.452 Chirality : 0.044 0.295 960 Planarity : 0.005 0.046 1204 Dihedral : 18.082 124.882 2480 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.41 % Allowed : 20.06 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.01 (0.30), residues: 796 helix: 1.09 (0.32), residues: 290 sheet: 0.04 (0.44), residues: 140 loop : -0.86 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 161 HIS 0.004 0.001 HIS A 349 PHE 0.007 0.001 PHE A 425 TYR 0.009 0.001 TYR B 209 ARG 0.005 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.756 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 1.7855 time to fit residues: 137.4763 Evaluate side-chains 72 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 315 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116429 restraints weight = 7899.467| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.49 r_work: 0.3303 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6792 Z= 0.233 Angle : 0.652 14.957 9264 Z= 0.291 Chirality : 0.045 0.135 960 Planarity : 0.005 0.036 1204 Dihedral : 7.214 69.139 902 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.41 % Allowed : 20.20 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.06 (0.30), residues: 796 helix: 1.07 (0.31), residues: 296 sheet: 0.40 (0.41), residues: 148 loop : -1.00 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 161 HIS 0.004 0.001 HIS B 349 PHE 0.009 0.002 PHE B 178 TYR 0.007 0.001 TYR B 209 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.743 Fit side-chains REVERT: A 304 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8419 (mmtp) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 1.7753 time to fit residues: 147.7452 Evaluate side-chains 74 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 427 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114123 restraints weight = 7913.928| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.49 r_work: 0.3268 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6792 Z= 0.399 Angle : 0.774 18.664 9264 Z= 0.344 Chirality : 0.050 0.140 960 Planarity : 0.006 0.042 1204 Dihedral : 7.551 78.640 888 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.40 % Allowed : 19.63 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.21 (0.29), residues: 796 helix: 0.77 (0.31), residues: 296 sheet: 0.51 (0.39), residues: 148 loop : -1.20 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 161 HIS 0.006 0.002 HIS B 349 PHE 0.013 0.002 PHE B 91 TYR 0.012 0.002 TYR A 209 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.895 Fit side-chains REVERT: B 329 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7506 (mt-10) outliers start: 17 outliers final: 6 residues processed: 75 average time/residue: 2.0815 time to fit residues: 161.7748 Evaluate side-chains 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 329 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116664 restraints weight = 8036.080| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.43 r_work: 0.3298 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6792 Z= 0.222 Angle : 0.630 14.285 9264 Z= 0.283 Chirality : 0.045 0.136 960 Planarity : 0.005 0.039 1204 Dihedral : 6.746 68.386 888 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.26 % Allowed : 19.49 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.03 (0.29), residues: 796 helix: 1.03 (0.31), residues: 296 sheet: 0.72 (0.39), residues: 148 loop : -1.17 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS B 349 PHE 0.009 0.001 PHE A 91 TYR 0.008 0.001 TYR B 209 ARG 0.002 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.779 Fit side-chains REVERT: A 450 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7294 (tttp) outliers start: 16 outliers final: 7 residues processed: 76 average time/residue: 1.7967 time to fit residues: 142.0338 Evaluate side-chains 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 71 optimal weight: 0.0170 chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.138162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119597 restraints weight = 7885.550| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.46 r_work: 0.3340 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6792 Z= 0.150 Angle : 0.550 10.226 9264 Z= 0.252 Chirality : 0.043 0.135 960 Planarity : 0.004 0.037 1204 Dihedral : 6.173 67.116 888 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.55 % Allowed : 20.06 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.31 (0.30), residues: 796 helix: 1.36 (0.32), residues: 296 sheet: 0.59 (0.39), residues: 150 loop : -0.98 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.003 0.001 HIS B 349 PHE 0.006 0.001 PHE A 91 TYR 0.006 0.001 TYR B 449 ARG 0.001 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.704 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 89 average time/residue: 1.5501 time to fit residues: 143.9636 Evaluate side-chains 74 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.137710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119080 restraints weight = 7925.182| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.48 r_work: 0.3335 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6792 Z= 0.162 Angle : 0.579 12.001 9264 Z= 0.258 Chirality : 0.043 0.136 960 Planarity : 0.004 0.035 1204 Dihedral : 6.304 67.668 888 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.98 % Allowed : 19.77 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.48 (0.30), residues: 796 helix: 1.47 (0.32), residues: 296 sheet: 0.77 (0.40), residues: 150 loop : -0.90 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.003 0.001 HIS B 349 PHE 0.007 0.001 PHE A 178 TYR 0.006 0.001 TYR A 209 ARG 0.001 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.799 Fit side-chains REVERT: A 450 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7365 (tttp) outliers start: 14 outliers final: 3 residues processed: 83 average time/residue: 1.5945 time to fit residues: 138.5870 Evaluate side-chains 75 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.137038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118307 restraints weight = 7973.873| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.48 r_work: 0.3328 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6792 Z= 0.183 Angle : 0.607 13.081 9264 Z= 0.268 Chirality : 0.044 0.136 960 Planarity : 0.004 0.036 1204 Dihedral : 6.438 67.919 888 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.84 % Allowed : 20.20 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.44 (0.30), residues: 796 helix: 1.45 (0.31), residues: 296 sheet: 0.77 (0.40), residues: 150 loop : -0.93 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS B 349 PHE 0.008 0.001 PHE A 178 TYR 0.007 0.001 TYR B 209 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.725 Fit side-chains REVERT: A 329 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: A 450 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7393 (tttp) REVERT: B 329 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: B 450 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7318 (tttp) outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 1.5665 time to fit residues: 127.6888 Evaluate side-chains 76 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 450 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.134093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115268 restraints weight = 7926.504| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.47 r_work: 0.3284 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6792 Z= 0.321 Angle : 0.733 17.264 9264 Z= 0.322 Chirality : 0.048 0.134 960 Planarity : 0.005 0.039 1204 Dihedral : 7.251 75.351 888 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.69 % Allowed : 20.62 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.12 (0.29), residues: 796 helix: 1.03 (0.31), residues: 296 sheet: 0.85 (0.39), residues: 148 loop : -1.08 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 161 HIS 0.005 0.001 HIS B 349 PHE 0.012 0.002 PHE B 178 TYR 0.010 0.002 TYR B 209 ARG 0.004 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.715 Fit side-chains REVERT: A 329 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: A 450 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7450 (tttp) REVERT: B 329 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: B 450 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7421 (tttp) outliers start: 12 outliers final: 2 residues processed: 72 average time/residue: 1.6781 time to fit residues: 125.8923 Evaluate side-chains 69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 450 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.137455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118530 restraints weight = 7999.056| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.50 r_work: 0.3334 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6792 Z= 0.164 Angle : 0.600 11.033 9264 Z= 0.271 Chirality : 0.043 0.136 960 Planarity : 0.004 0.036 1204 Dihedral : 6.323 67.372 888 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.42 % Allowed : 22.18 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.36 (0.30), residues: 796 helix: 1.35 (0.32), residues: 294 sheet: 0.71 (0.40), residues: 150 loop : -0.94 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.003 0.001 HIS B 349 PHE 0.007 0.001 PHE B 178 TYR 0.008 0.001 TYR B 244 ARG 0.001 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.782 Fit side-chains REVERT: B 450 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7361 (tttp) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 1.8099 time to fit residues: 145.1465 Evaluate side-chains 71 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 450 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.137763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119211 restraints weight = 8034.699| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.45 r_work: 0.3334 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6792 Z= 0.166 Angle : 0.610 11.793 9264 Z= 0.273 Chirality : 0.043 0.135 960 Planarity : 0.004 0.036 1204 Dihedral : 6.350 67.460 888 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.85 % Allowed : 21.33 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.46 (0.30), residues: 796 helix: 1.43 (0.32), residues: 294 sheet: 0.72 (0.40), residues: 150 loop : -0.85 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.003 0.001 HIS B 349 PHE 0.007 0.001 PHE B 91 TYR 0.010 0.001 TYR B 244 ARG 0.001 0.000 ARG B 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.861 Fit side-chains REVERT: A 450 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7297 (tttp) REVERT: B 450 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7220 (tttp) outliers start: 6 outliers final: 1 residues processed: 73 average time/residue: 1.6521 time to fit residues: 125.6998 Evaluate side-chains 72 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 450 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.132391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113249 restraints weight = 8099.341| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.51 r_work: 0.3286 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6792 Z= 0.351 Angle : 0.772 17.578 9264 Z= 0.342 Chirality : 0.049 0.168 960 Planarity : 0.005 0.039 1204 Dihedral : 7.381 76.430 888 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.13 % Allowed : 21.19 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.06 (0.29), residues: 796 helix: 0.99 (0.31), residues: 294 sheet: 0.78 (0.39), residues: 146 loop : -1.08 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 161 HIS 0.005 0.001 HIS B 349 PHE 0.012 0.002 PHE B 178 TYR 0.010 0.002 TYR B 209 ARG 0.005 0.000 ARG B 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4702.63 seconds wall clock time: 84 minutes 43.71 seconds (5083.71 seconds total)