Starting phenix.real_space_refine on Thu Mar 13 08:11:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rez_19113/03_2025/8rez_19113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rez_19113/03_2025/8rez_19113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rez_19113/03_2025/8rez_19113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rez_19113/03_2025/8rez_19113.map" model { file = "/net/cci-nas-00/data/ceres_data/8rez_19113/03_2025/8rez_19113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rez_19113/03_2025/8rez_19113.cif" } resolution = 3.3 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= 0.002 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5650 2.51 5 N 1468 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8802 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4401 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain: "B" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4401 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Time building chain proxies: 5.42, per 1000 atoms: 0.62 Number of scatterers: 8802 At special positions: 0 Unit cell: (72.993, 111.587, 131.723, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1648 8.00 N 1468 7.00 C 5650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 995.9 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 67.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 4.551A pdb=" N PHE A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 59 through 108 removed outlier: 3.838A pdb=" N SER A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.950A pdb=" N PHE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 140 removed outlier: 3.537A pdb=" N VAL A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 163 Processing helix chain 'A' and resid 165 through 210 removed outlier: 3.938A pdb=" N VAL A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 175 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 221 through 276 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 280 through 321 Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.511A pdb=" N ASN A 434 " --> pdb=" O THR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.808A pdb=" N ARG A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 removed outlier: 4.039A pdb=" N SER A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'B' and resid 11 through 21 removed outlier: 4.552A pdb=" N PHE B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 59 through 108 removed outlier: 3.838A pdb=" N SER B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 removed outlier: 3.922A pdb=" N PHE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 140 removed outlier: 3.536A pdb=" N VAL B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 163 Processing helix chain 'B' and resid 165 through 210 removed outlier: 3.938A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 221 through 276 Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 280 through 321 Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 409 through 416 Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.512A pdb=" N ASN B 434 " --> pdb=" O THR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.798A pdb=" N ARG B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 525 removed outlier: 3.954A pdb=" N SER B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 570 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364 removed outlier: 7.832A pdb=" N ALA A 362 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP A 344 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 364 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN A 342 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420 removed outlier: 6.044A pdb=" N GLY A 418 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR A 370 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 369 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 558 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 548 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY A 556 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 550 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE A 554 " --> pdb=" O GLU A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364 removed outlier: 7.833A pdb=" N ALA B 362 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASP B 344 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 364 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN B 342 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 420 removed outlier: 6.044A pdb=" N GLY B 418 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 370 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 369 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 547 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 371 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 549 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 558 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 548 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY B 556 " --> pdb=" O PHE B 548 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU B 550 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1785 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: 2.64 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1542 1.32 - 1.45: 2074 1.45 - 1.57: 5250 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8936 Sorted by residual: bond pdb=" C GLU A 403 " pdb=" N PRO A 404 " ideal model delta sigma weight residual 1.337 1.389 -0.052 1.11e-02 8.12e+03 2.21e+01 bond pdb=" C GLU B 403 " pdb=" N PRO B 404 " ideal model delta sigma weight residual 1.337 1.389 -0.052 1.11e-02 8.12e+03 2.20e+01 bond pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.27e-02 6.20e+03 1.31e+01 bond pdb=" N VAL B 443 " pdb=" CA VAL B 443 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" N VAL A 443 " pdb=" CA VAL A 443 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.17e+01 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11725 2.46 - 4.91: 321 4.91 - 7.37: 42 7.37 - 9.83: 3 9.83 - 12.28: 3 Bond angle restraints: 12094 Sorted by residual: angle pdb=" C GLN A 512 " pdb=" CA GLN A 512 " pdb=" CB GLN A 512 " ideal model delta sigma weight residual 110.74 121.69 -10.95 1.66e+00 3.63e-01 4.35e+01 angle pdb=" N SER A 513 " pdb=" CA SER A 513 " pdb=" CB SER A 513 " ideal model delta sigma weight residual 110.47 101.85 8.62 1.46e+00 4.69e-01 3.48e+01 angle pdb=" N SER A 513 " pdb=" CA SER A 513 " pdb=" C SER A 513 " ideal model delta sigma weight residual 113.41 120.07 -6.66 1.22e+00 6.72e-01 2.98e+01 angle pdb=" C VAL B 420 " pdb=" N SER B 421 " pdb=" CA SER B 421 " ideal model delta sigma weight residual 122.44 116.25 6.19 1.19e+00 7.06e-01 2.70e+01 angle pdb=" C VAL A 420 " pdb=" N SER A 421 " pdb=" CA SER A 421 " ideal model delta sigma weight residual 122.44 116.31 6.13 1.19e+00 7.06e-01 2.65e+01 ... (remaining 12089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 4684 16.86 - 33.71: 539 33.71 - 50.57: 146 50.57 - 67.42: 31 67.42 - 84.28: 8 Dihedral angle restraints: 5408 sinusoidal: 2132 harmonic: 3276 Sorted by residual: dihedral pdb=" CA GLU A 403 " pdb=" C GLU A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual 180.00 126.74 53.26 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA GLU B 403 " pdb=" C GLU B 403 " pdb=" N PRO B 404 " pdb=" CA PRO B 404 " ideal model delta harmonic sigma weight residual 180.00 126.75 53.25 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA LEU B 400 " pdb=" C LEU B 400 " pdb=" N GLY B 401 " pdb=" CA GLY B 401 " ideal model delta harmonic sigma weight residual 180.00 143.27 36.73 0 5.00e+00 4.00e-02 5.40e+01 ... (remaining 5405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1264 0.064 - 0.128: 159 0.128 - 0.192: 31 0.192 - 0.257: 6 0.257 - 0.321: 4 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CB VAL B 443 " pdb=" CA VAL B 443 " pdb=" CG1 VAL B 443 " pdb=" CG2 VAL B 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB VAL A 443 " pdb=" CA VAL A 443 " pdb=" CG1 VAL A 443 " pdb=" CG2 VAL A 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN B 118 " pdb=" N ASN B 118 " pdb=" C ASN B 118 " pdb=" CB ASN B 118 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1461 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 403 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 404 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 403 " -0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 404 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 401 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C GLY B 401 " 0.059 2.00e-02 2.50e+03 pdb=" O GLY B 401 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 402 " -0.020 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 573 2.73 - 3.27: 9650 3.27 - 3.82: 14655 3.82 - 4.36: 16688 4.36 - 4.90: 28515 Nonbonded interactions: 70081 Sorted by model distance: nonbonded pdb=" OH TYR A 437 " pdb=" OE2 GLU B 225 " model vdw 2.191 3.040 nonbonded pdb=" OG SER A 428 " pdb=" NE2 GLN B 208 " model vdw 2.192 3.120 nonbonded pdb=" OE2 GLU A 225 " pdb=" OH TYR B 437 " model vdw 2.251 3.040 nonbonded pdb=" OG SER A 43 " pdb=" NE2 GLN A 77 " model vdw 2.272 3.120 nonbonded pdb=" OG SER B 43 " pdb=" NE2 GLN B 77 " model vdw 2.272 3.120 ... (remaining 70076 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: 0.04 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.810 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.004 0.067 8936 Z= 0.301 Angle : 0.926 12.284 12094 Z= 0.593 Chirality : 0.049 0.321 1464 Planarity : 0.007 0.113 1518 Dihedral : 15.795 84.281 3304 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.54 % Favored : 91.75 % Rotamer: Outliers : 0.52 % Allowed : 19.92 % Favored : 79.56 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.36 % 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: 0.15 (0.25), residues: 1140 helix: 1.45 (0.19), residues: 750 sheet: 0.52 (0.81), residues: 50 loop : -3.24 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 413 HIS 0.002 0.001 HIS B 141 PHE 0.014 0.001 PHE A 303 TYR 0.033 0.002 TYR B 408 ARG 0.007 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.027 Fit side-chains REVERT: A 20 ARG cc_start: 0.7294 (tpt-90) cc_final: 0.6488 (tmm160) REVERT: A 59 MET cc_start: 0.4740 (pmm) cc_final: 0.3871 (ppp) REVERT: A 247 GLN cc_start: 0.8076 (tt0) cc_final: 0.7589 (mt0) REVERT: A 249 LEU cc_start: 0.7464 (tp) cc_final: 0.7064 (tp) REVERT: A 427 MET cc_start: 0.6825 (mtp) cc_final: 0.5531 (mmm) REVERT: A 580 MET cc_start: 0.3414 (mtm) cc_final: 0.2944 (mmm) REVERT: B 20 ARG cc_start: 0.6998 (tpt-90) cc_final: 0.6178 (tmm160) REVERT: B 59 MET cc_start: 0.5012 (pmm) cc_final: 0.4634 (pmm) REVERT: B 247 GLN cc_start: 0.7977 (tt0) cc_final: 0.7519 (mt0) REVERT: B 249 LEU cc_start: 0.7385 (tp) cc_final: 0.7018 (tp) outliers start: 5 outliers final: 0 residues processed: 73 average time/residue: 0.1887 time to fit residues: 20.6428 Evaluate side-chains 58 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 46 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 208 GLN B 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.264811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.208961 restraints weight = 8724.171| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.27 r_work: 0.3422 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8936 Z= 0.195 Angle : 0.660 7.903 12094 Z= 0.344 Chirality : 0.041 0.162 1464 Planarity : 0.007 0.124 1518 Dihedral : 5.848 46.451 1224 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.19 % Favored : 92.63 % Rotamer: Outliers : 2.90 % Allowed : 19.50 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.18 % 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: 0.72 (0.26), residues: 1140 helix: 2.03 (0.19), residues: 754 sheet: 0.55 (0.82), residues: 50 loop : -3.44 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.003 0.001 HIS B 567 PHE 0.015 0.001 PHE B 303 TYR 0.030 0.001 TYR B 408 ARG 0.004 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7384 (tpt-90) cc_final: 0.6409 (tmm160) REVERT: A 249 LEU cc_start: 0.7475 (tp) cc_final: 0.7084 (tp) REVERT: A 339 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6921 (mm) REVERT: A 391 TYR cc_start: 0.7373 (m-10) cc_final: 0.7060 (m-10) REVERT: B 20 ARG cc_start: 0.7136 (tpt-90) cc_final: 0.6108 (tmm160) REVERT: B 59 MET cc_start: 0.4814 (pmm) cc_final: 0.3944 (ppp) REVERT: B 249 LEU cc_start: 0.7428 (tp) cc_final: 0.7084 (tp) REVERT: B 339 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6928 (mm) REVERT: B 391 TYR cc_start: 0.6985 (m-10) cc_final: 0.6730 (m-10) REVERT: B 411 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7374 (tm-30) outliers start: 28 outliers final: 6 residues processed: 91 average time/residue: 0.1666 time to fit residues: 22.9996 Evaluate side-chains 66 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 TYR Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 163 ASN A 208 GLN A 220 ASN A 272 GLN B 77 GLN B 163 ASN B 208 GLN B 220 ASN B 272 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.260163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191600 restraints weight = 8861.084| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.04 r_work: 0.3409 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8936 Z= 0.247 Angle : 0.638 8.289 12094 Z= 0.336 Chirality : 0.042 0.185 1464 Planarity : 0.006 0.109 1518 Dihedral : 5.557 37.834 1224 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.46 % Favored : 92.37 % Rotamer: Outliers : 4.25 % Allowed : 19.50 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.18 % 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: 0.62 (0.25), residues: 1140 helix: 1.92 (0.18), residues: 750 sheet: 0.38 (0.78), residues: 50 loop : -3.30 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 164 HIS 0.004 0.001 HIS A 141 PHE 0.015 0.001 PHE B 303 TYR 0.027 0.001 TYR B 408 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.855 Fit side-chains REVERT: A 20 ARG cc_start: 0.7520 (tpt-90) cc_final: 0.6527 (tmm160) REVERT: A 180 ILE cc_start: 0.6073 (tt) cc_final: 0.5599 (mm) REVERT: A 249 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7006 (tp) REVERT: B 20 ARG cc_start: 0.7401 (tpt-90) cc_final: 0.6450 (tmm160) REVERT: B 59 MET cc_start: 0.4640 (pmm) cc_final: 0.3790 (ppp) REVERT: B 120 SER cc_start: 0.8078 (t) cc_final: 0.7682 (m) REVERT: B 180 ILE cc_start: 0.6002 (tt) cc_final: 0.5551 (mm) REVERT: B 249 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6998 (tp) REVERT: B 411 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7488 (tm-30) outliers start: 41 outliers final: 19 residues processed: 96 average time/residue: 0.1660 time to fit residues: 24.3239 Evaluate side-chains 81 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 434 ASN B 247 GLN B 434 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.257011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.185528 restraints weight = 8662.901| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.95 r_work: 0.3375 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8936 Z= 0.286 Angle : 0.645 8.406 12094 Z= 0.341 Chirality : 0.043 0.242 1464 Planarity : 0.006 0.106 1518 Dihedral : 5.507 36.392 1224 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.98 % Favored : 91.84 % Rotamer: Outliers : 4.25 % Allowed : 20.23 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.27 % 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 (0.25), residues: 1140 helix: 1.77 (0.19), residues: 750 sheet: 0.21 (0.76), residues: 50 loop : -3.24 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.004 0.001 HIS A 141 PHE 0.015 0.001 PHE B 303 TYR 0.024 0.001 TYR B 408 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7572 (tpt-90) cc_final: 0.6558 (tmm160) REVERT: A 180 ILE cc_start: 0.6408 (tt) cc_final: 0.5963 (mm) REVERT: A 249 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7004 (tp) REVERT: A 339 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6973 (mm) REVERT: B 20 ARG cc_start: 0.7517 (tpt-90) cc_final: 0.6563 (tmm160) REVERT: B 180 ILE cc_start: 0.6315 (tt) cc_final: 0.5886 (mm) REVERT: B 249 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7066 (tp) REVERT: B 339 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6996 (mm) outliers start: 41 outliers final: 14 residues processed: 99 average time/residue: 0.1619 time to fit residues: 24.4286 Evaluate side-chains 79 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 TYR Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 26 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 207 ASN B 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.259660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.190594 restraints weight = 8720.949| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.05 r_work: 0.3381 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8936 Z= 0.196 Angle : 0.578 7.274 12094 Z= 0.309 Chirality : 0.040 0.161 1464 Planarity : 0.006 0.100 1518 Dihedral : 5.334 34.756 1224 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.28 % Favored : 92.54 % Rotamer: Outliers : 3.53 % Allowed : 20.54 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.18 % 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: 0.69 (0.26), residues: 1140 helix: 1.94 (0.19), residues: 750 sheet: 0.25 (0.76), residues: 50 loop : -3.16 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.002 0.001 HIS B 141 PHE 0.014 0.001 PHE A 303 TYR 0.023 0.001 TYR B 408 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 1.083 Fit side-chains REVERT: A 20 ARG cc_start: 0.7543 (tpt-90) cc_final: 0.6506 (tmm160) REVERT: A 59 MET cc_start: 0.3681 (pmm) cc_final: 0.2992 (ppp) REVERT: A 180 ILE cc_start: 0.6314 (tt) cc_final: 0.5919 (mm) REVERT: A 249 LEU cc_start: 0.7461 (tp) cc_final: 0.7043 (tp) REVERT: A 339 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6923 (mm) REVERT: A 391 TYR cc_start: 0.7812 (m-10) cc_final: 0.7592 (m-10) REVERT: A 447 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5815 (tm-30) REVERT: B 20 ARG cc_start: 0.7510 (tpt-90) cc_final: 0.6536 (tmm160) REVERT: B 59 MET cc_start: 0.4261 (pmm) cc_final: 0.3378 (ppp) REVERT: B 180 ILE cc_start: 0.6227 (tt) cc_final: 0.5862 (mm) REVERT: B 249 LEU cc_start: 0.7412 (tp) cc_final: 0.7007 (tp) REVERT: B 339 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6947 (mm) REVERT: B 411 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7291 (tm-30) outliers start: 34 outliers final: 13 residues processed: 95 average time/residue: 0.2073 time to fit residues: 29.6860 Evaluate side-chains 77 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 52 optimal weight: 0.0060 chunk 37 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.260330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.191725 restraints weight = 8628.918| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.03 r_work: 0.3399 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8936 Z= 0.185 Angle : 0.577 7.489 12094 Z= 0.306 Chirality : 0.040 0.164 1464 Planarity : 0.005 0.096 1518 Dihedral : 5.221 34.412 1224 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.11 % Favored : 92.72 % Rotamer: Outliers : 3.94 % Allowed : 20.95 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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: 0.82 (0.25), residues: 1140 helix: 2.04 (0.19), residues: 750 sheet: 0.34 (0.75), residues: 50 loop : -3.09 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 413 HIS 0.002 0.001 HIS B 141 PHE 0.014 0.001 PHE B 303 TYR 0.021 0.001 TYR B 408 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7538 (tpt-90) cc_final: 0.6495 (tmm160) REVERT: A 59 MET cc_start: 0.3734 (pmm) cc_final: 0.3076 (ppp) REVERT: A 180 ILE cc_start: 0.6282 (tt) cc_final: 0.5901 (mm) REVERT: A 249 LEU cc_start: 0.7458 (tp) cc_final: 0.7045 (tp) REVERT: A 339 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6948 (mm) REVERT: A 391 TYR cc_start: 0.7793 (m-10) cc_final: 0.7558 (m-10) REVERT: A 447 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5791 (tm-30) REVERT: B 20 ARG cc_start: 0.7501 (tpt-90) cc_final: 0.6535 (tmm160) REVERT: B 59 MET cc_start: 0.4384 (pmm) cc_final: 0.3560 (ppp) REVERT: B 180 ILE cc_start: 0.6161 (tt) cc_final: 0.5805 (mm) REVERT: B 249 LEU cc_start: 0.7455 (tp) cc_final: 0.7032 (tp) REVERT: B 339 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6914 (mm) REVERT: B 411 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7251 (tm-30) outliers start: 38 outliers final: 14 residues processed: 93 average time/residue: 0.2357 time to fit residues: 31.6827 Evaluate side-chains 75 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 TYR Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 55 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 434 ASN B 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.260192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.191721 restraints weight = 8721.998| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.99 r_work: 0.3403 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8936 Z= 0.191 Angle : 0.569 6.927 12094 Z= 0.302 Chirality : 0.039 0.153 1464 Planarity : 0.005 0.090 1518 Dihedral : 5.134 34.131 1224 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.07 % Rotamer: Outliers : 3.22 % Allowed : 20.85 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.85 (0.26), residues: 1140 helix: 2.05 (0.18), residues: 750 sheet: 0.38 (0.75), residues: 50 loop : -3.06 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 413 HIS 0.003 0.001 HIS B 141 PHE 0.014 0.001 PHE B 303 TYR 0.021 0.001 TYR B 408 ARG 0.005 0.000 ARG B 484 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7544 (tpt-90) cc_final: 0.6499 (tmm160) REVERT: A 59 MET cc_start: 0.3783 (pmm) cc_final: 0.3150 (ppp) REVERT: A 101 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: A 171 LEU cc_start: 0.8074 (tp) cc_final: 0.7802 (tp) REVERT: A 180 ILE cc_start: 0.6291 (tt) cc_final: 0.5908 (mm) REVERT: A 249 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7056 (tp) REVERT: A 339 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6925 (mm) REVERT: B 20 ARG cc_start: 0.7533 (tpt-90) cc_final: 0.6557 (tmm160) REVERT: B 59 MET cc_start: 0.4400 (pmm) cc_final: 0.4092 (pmm) REVERT: B 180 ILE cc_start: 0.6180 (tt) cc_final: 0.5817 (mm) REVERT: B 249 LEU cc_start: 0.7477 (tp) cc_final: 0.7053 (tp) REVERT: B 339 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6893 (mm) REVERT: B 411 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7231 (tm-30) outliers start: 31 outliers final: 15 residues processed: 86 average time/residue: 0.1829 time to fit residues: 23.9657 Evaluate side-chains 77 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 TYR Chi-restraints excluded: chain B residue 420 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 220 ASN B 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.251084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179887 restraints weight = 8703.087| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.16 r_work: 0.3266 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 8936 Z= 0.383 Angle : 0.684 8.416 12094 Z= 0.365 Chirality : 0.045 0.264 1464 Planarity : 0.006 0.086 1518 Dihedral : 5.343 35.844 1224 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.93 % Favored : 92.89 % Rotamer: Outliers : 3.84 % Allowed : 20.85 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1140 helix: 1.61 (0.18), residues: 744 sheet: 0.16 (0.73), residues: 50 loop : -2.99 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 164 HIS 0.005 0.001 HIS B 141 PHE 0.013 0.002 PHE B 303 TYR 0.020 0.002 TYR B 408 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.877 Fit side-chains REVERT: A 59 MET cc_start: 0.3914 (pmm) cc_final: 0.3253 (ppp) REVERT: A 171 LEU cc_start: 0.8330 (tp) cc_final: 0.7981 (tp) REVERT: A 249 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7287 (tp) REVERT: A 339 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6944 (mm) REVERT: B 59 MET cc_start: 0.4442 (pmm) cc_final: 0.4132 (pmm) REVERT: B 249 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7352 (tp) REVERT: B 339 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6952 (mm) outliers start: 37 outliers final: 18 residues processed: 97 average time/residue: 0.1612 time to fit residues: 23.9257 Evaluate side-chains 83 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 111 optimal weight: 0.0000 chunk 68 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 96 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.258229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.188494 restraints weight = 8691.793| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.95 r_work: 0.3394 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8936 Z= 0.185 Angle : 0.596 8.321 12094 Z= 0.319 Chirality : 0.041 0.289 1464 Planarity : 0.005 0.086 1518 Dihedral : 5.110 34.509 1224 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 2.18 % Allowed : 22.20 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.83 (0.26), residues: 1140 helix: 2.01 (0.19), residues: 750 sheet: 0.48 (0.72), residues: 50 loop : -3.01 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.002 0.001 HIS B 141 PHE 0.010 0.001 PHE B 303 TYR 0.022 0.001 TYR B 408 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.883 Fit side-chains REVERT: A 59 MET cc_start: 0.4011 (pmm) cc_final: 0.3387 (ppp) REVERT: A 101 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: A 249 LEU cc_start: 0.7528 (tp) cc_final: 0.7137 (tp) REVERT: A 277 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6808 (mt-10) REVERT: A 339 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6968 (mm) REVERT: B 20 ARG cc_start: 0.7554 (tpt-90) cc_final: 0.6589 (tmm160) REVERT: B 59 MET cc_start: 0.4456 (pmm) cc_final: 0.4159 (pmm) REVERT: B 249 LEU cc_start: 0.7538 (tp) cc_final: 0.7144 (tp) REVERT: B 339 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6898 (mm) outliers start: 21 outliers final: 10 residues processed: 81 average time/residue: 0.1702 time to fit residues: 21.4505 Evaluate side-chains 69 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.0370 chunk 12 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 220 ASN B 208 GLN B 220 ASN B 434 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.258593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.190565 restraints weight = 8701.368| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.96 r_work: 0.3403 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8936 Z= 0.192 Angle : 0.596 8.426 12094 Z= 0.320 Chirality : 0.041 0.296 1464 Planarity : 0.005 0.082 1518 Dihedral : 5.054 33.640 1224 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.60 % Rotamer: Outliers : 1.45 % Allowed : 23.03 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.93 (0.26), residues: 1140 helix: 2.09 (0.18), residues: 750 sheet: 0.61 (0.73), residues: 50 loop : -3.00 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.002 0.000 HIS A 141 PHE 0.013 0.001 PHE B 303 TYR 0.019 0.001 TYR A 408 ARG 0.002 0.000 ARG A 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.929 Fit side-chains REVERT: A 59 MET cc_start: 0.4033 (pmm) cc_final: 0.3434 (ppp) REVERT: A 101 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: A 249 LEU cc_start: 0.7483 (tp) cc_final: 0.7088 (tp) REVERT: A 339 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6969 (mm) REVERT: B 20 ARG cc_start: 0.7603 (tpt-90) cc_final: 0.6637 (tmm160) REVERT: B 249 LEU cc_start: 0.7490 (tp) cc_final: 0.7096 (tp) REVERT: B 339 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6888 (mm) outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 0.1929 time to fit residues: 20.4385 Evaluate side-chains 66 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.257867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.194844 restraints weight = 8743.098| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.97 r_work: 0.3423 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8936 Z= 0.257 Angle : 1.044 59.198 12094 Z= 0.633 Chirality : 0.043 0.375 1464 Planarity : 0.006 0.125 1518 Dihedral : 5.071 33.750 1224 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 1.66 % Allowed : 23.34 % Favored : 75.00 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1140 helix: 2.08 (0.18), residues: 750 sheet: 0.61 (0.73), residues: 50 loop : -2.98 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.002 0.000 HIS B 141 PHE 0.012 0.001 PHE B 303 TYR 0.020 0.001 TYR A 408 ARG 0.002 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5549.98 seconds wall clock time: 98 minutes 25.77 seconds (5905.77 seconds total)