Starting phenix.real_space_refine on Tue Mar 11 18:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdb_61387/03_2025/9jdb_61387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdb_61387/03_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_61387/03_2025/9jdb_61387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdb_61387/03_2025/9jdb_61387.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdb_61387/03_2025/9jdb_61387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdb_61387/03_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-5624/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: 4.22, per 1000 atoms: 0.64 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: 1.51 Conformation dependent library (CDL) restraints added in 811.5 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: 0.67 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: 1.68 Time building geometry restraints manager: 1.78 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.780 Find NCS groups from input model: 0.200 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:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- 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 : 0.688 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 1.6422 time to fit residues: 126.4493 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 : 0.711 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116461 restraints weight = 7899.467| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.49 r_work: 0.3305 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.799 Fit side-chains REVERT: A 304 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8421 (mmtp) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 1.6917 time to fit residues: 140.6313 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 : 0.686 ------------------------------------------------------------------------------- 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: 0.0770 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.134462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115778 restraints weight = 7910.613| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.46 r_work: 0.3289 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6792 Z= 0.278 Angle : 0.687 16.437 9264 Z= 0.303 Chirality : 0.046 0.135 960 Planarity : 0.005 0.039 1204 Dihedral : 7.039 72.286 888 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.12 % Allowed : 19.49 % 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: 0.00 (0.29), residues: 796 helix: 1.03 (0.31), residues: 296 sheet: 0.57 (0.40), residues: 148 loop : -1.13 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 161 HIS 0.005 0.001 HIS B 349 PHE 0.011 0.002 PHE B 178 TYR 0.010 0.001 TYR B 209 ARG 0.003 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 81 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.694 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 78 average time/residue: 1.8181 time to fit residues: 147.2544 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 : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 427 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.132992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114090 restraints weight = 8038.357| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.50 r_work: 0.3266 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6792 Z= 0.389 Angle : 0.768 18.562 9264 Z= 0.340 Chirality : 0.049 0.136 960 Planarity : 0.006 0.042 1204 Dihedral : 7.561 78.400 888 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.12 % Allowed : 19.35 % 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: -0.22 (0.29), residues: 796 helix: 0.76 (0.31), residues: 296 sheet: 0.60 (0.38), residues: 148 loop : -1.26 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.006 0.001 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 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 77 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.688 Fit side-chains REVERT: A 329 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: B 329 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7474 (mt-10) outliers start: 15 outliers final: 6 residues processed: 73 average time/residue: 1.7532 time to fit residues: 132.9963 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 : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 GLU 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 256 THR Chi-restraints excluded: chain B residue 329 GLU 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: 2.9990 chunk 12 optimal weight: 0.7980 chunk 71 optimal weight: 0.0020 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.136994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118434 restraints weight = 7874.932| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.45 r_work: 0.3329 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0879 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= 0.160 Angle : 0.566 10.939 9264 Z= 0.260 Chirality : 0.043 0.136 960 Planarity : 0.005 0.038 1204 Dihedral : 6.318 67.428 888 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 0.16 (0.29), residues: 796 helix: 1.20 (0.32), residues: 296 sheet: 0.70 (0.40), residues: 146 loop : -1.10 (0.31), residues: 354 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 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 85 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.684 Fit side-chains REVERT: A 310 TYR cc_start: 0.8415 (t80) cc_final: 0.8211 (t80) REVERT: A 450 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7347 (tttp) outliers start: 10 outliers final: 4 residues processed: 81 average time/residue: 1.6961 time to fit residues: 143.2667 Evaluate side-chains 72 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.135982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117384 restraints weight = 7908.919| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.46 r_work: 0.3319 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6792 Z= 0.194 Angle : 0.616 13.758 9264 Z= 0.274 Chirality : 0.044 0.136 960 Planarity : 0.005 0.038 1204 Dihedral : 6.567 67.987 888 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 0.27 (0.29), residues: 796 helix: 1.27 (0.32), residues: 296 sheet: 0.82 (0.40), residues: 146 loop : -1.04 (0.31), residues: 354 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 B 91 TYR 0.008 0.001 TYR A 209 ARG 0.002 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 78 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.742 Fit side-chains REVERT: A 305 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7893 (tptt) REVERT: A 450 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7385 (tttp) outliers start: 11 outliers final: 1 residues processed: 75 average time/residue: 1.6400 time to fit residues: 128.1787 Evaluate side-chains 67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 1.1520 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.135999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117249 restraints weight = 7959.081| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.46 r_work: 0.3310 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6792 Z= 0.206 Angle : 0.634 13.918 9264 Z= 0.281 Chirality : 0.044 0.135 960 Planarity : 0.005 0.038 1204 Dihedral : 6.608 67.987 888 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.41 % Allowed : 20.34 % 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: 0.27 (0.29), residues: 796 helix: 1.26 (0.32), residues: 296 sheet: 0.83 (0.40), residues: 146 loop : -1.05 (0.31), residues: 354 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 B 91 TYR 0.008 0.001 TYR B 209 ARG 0.002 0.000 ARG B 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 80 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.808 Fit side-chains REVERT: A 329 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: A 450 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7400 (tttp) REVERT: B 329 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: B 450 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7381 (tttp) outliers start: 10 outliers final: 2 residues processed: 74 average time/residue: 1.7457 time to fit residues: 134.3110 Evaluate side-chains 76 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.136814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118131 restraints weight = 7902.251| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.47 r_work: 0.3326 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6792 Z= 0.181 Angle : 0.616 12.613 9264 Z= 0.274 Chirality : 0.044 0.136 960 Planarity : 0.004 0.037 1204 Dihedral : 6.430 67.723 888 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.27 % Allowed : 20.48 % 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: 0.32 (0.30), residues: 796 helix: 1.30 (0.32), residues: 296 sheet: 0.83 (0.40), residues: 146 loop : -1.01 (0.31), residues: 354 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 B 91 TYR 0.008 0.001 TYR A 244 ARG 0.002 0.000 ARG A 55 *********************** 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 85 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.708 Fit side-chains REVERT: A 450 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7398 (tttp) REVERT: B 305 LYS cc_start: 0.8113 (tptt) cc_final: 0.7895 (tptt) REVERT: B 450 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7307 (tttp) outliers start: 9 outliers final: 2 residues processed: 81 average time/residue: 1.6282 time to fit residues: 137.5291 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 : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.137488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118754 restraints weight = 8017.576| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.48 r_work: 0.3334 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6792 Z= 0.169 Angle : 0.602 11.942 9264 Z= 0.267 Chirality : 0.043 0.135 960 Planarity : 0.004 0.037 1204 Dihedral : 6.340 67.555 888 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.85 % Allowed : 20.90 % 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: 0.39 (0.30), residues: 796 helix: 1.39 (0.32), residues: 294 sheet: 0.71 (0.40), residues: 150 loop : -0.92 (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 91 TYR 0.010 0.001 TYR B 244 ARG 0.001 0.000 ARG B 55 *********************** 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: 6 poor density : 72 time to evaluate : 0.760 Fit side-chains REVERT: A 305 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7793 (tptt) REVERT: A 450 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7363 (tttp) REVERT: B 305 LYS cc_start: 0.8024 (tptt) cc_final: 0.7789 (tptt) REVERT: B 450 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7296 (tttp) outliers start: 6 outliers final: 2 residues processed: 76 average time/residue: 1.6869 time to fit residues: 133.5720 Evaluate side-chains 76 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU 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 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 73 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.138411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119555 restraints weight = 8042.717| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.49 r_work: 0.3346 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6792 Z= 0.157 Angle : 0.581 10.849 9264 Z= 0.259 Chirality : 0.043 0.135 960 Planarity : 0.004 0.037 1204 Dihedral : 6.194 67.681 888 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.99 % Allowed : 20.76 % 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: 0.50 (0.30), residues: 796 helix: 1.49 (0.32), residues: 294 sheet: 0.75 (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 A 178 TYR 0.012 0.001 TYR B 244 ARG 0.002 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 83 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.718 Fit side-chains REVERT: A 450 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7384 (tttp) REVERT: B 450 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7298 (tttp) outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 1.6045 time to fit residues: 135.3669 Evaluate side-chains 76 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 130 MET 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: 4.9990 chunk 3 optimal weight: 0.4980 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.135360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116367 restraints weight = 8057.347| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.50 r_work: 0.3330 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6792 Z= 0.198 Angle : 0.648 13.775 9264 Z= 0.286 Chirality : 0.044 0.135 960 Planarity : 0.005 0.038 1204 Dihedral : 6.554 67.915 888 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.13 % Allowed : 21.05 % 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: 0.47 (0.30), residues: 796 helix: 1.41 (0.31), residues: 294 sheet: 0.93 (0.41), residues: 146 loop : -0.89 (0.32), residues: 356 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 A 209 ARG 0.001 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.71 seconds wall clock time: 83 minutes 30.76 seconds (5010.76 seconds total)