Starting phenix.real_space_refine on Wed Jan 15 20:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rez_19113/01_2025/8rez_19113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rez_19113/01_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_19113/01_2025/8rez_19113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rez_19113/01_2025/8rez_19113.map" model { file = "/net/cci-nas-00/data/ceres_data/8rez_19113/01_2025/8rez_19113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rez_19113/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.75, per 1000 atoms: 0.65 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.90 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: 2.61 Time building geometry restraints manager: 2.88 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.520 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- 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 : 0.931 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: 0.1978 time to fit residues: 21.6825 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 : 1.062 ------------------------------------------------------------------------------- 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 = 0.264810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.208970 restraints weight = 8724.178| |-----------------------------------------------------------------------------| r_work (start): 0.4095 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: 0.7383 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 46.453 1224 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.64 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 : 0.974 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7384 (tpt-90) cc_final: 0.6408 (tmm160) REVERT: A 249 LEU cc_start: 0.7476 (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: 0.7374 (m-10) cc_final: 0.7061 (m-10) REVERT: B 20 ARG cc_start: 0.7135 (tpt-90) cc_final: 0.6106 (tmm160) REVERT: B 59 MET cc_start: 0.4813 (pmm) cc_final: 0.3943 (ppp) REVERT: B 249 LEU cc_start: 0.7429 (tp) cc_final: 0.7085 (tp) REVERT: B 339 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6929 (mm) REVERT: B 391 TYR cc_start: 0.6984 (m-10) cc_final: 0.6730 (m-10) REVERT: B 411 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7374 (tm-30) outliers start: 28 outliers final: 6 residues processed: 91 average time/residue: 0.1819 time to fit residues: 24.5970 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 : 0.954 ------------------------------------------------------------------------------- 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: 6.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 33 optimal weight: 50.0000 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 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 = 0.4584 r_free = 0.4584 target = 0.247351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142223 restraints weight = 8888.049| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.16 r_work: 0.3337 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8936 Z= 0.246 Angle : 0.639 7.732 12094 Z= 0.337 Chirality : 0.042 0.178 1464 Planarity : 0.006 0.109 1518 Dihedral : 5.557 38.004 1224 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.54 % Favored : 92.28 % 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: 1.93 (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 0.007 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 0.004 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 : 0.947 Fit side-chains REVERT: A 20 ARG cc_start: 0.7426 (tpt-90) cc_final: 0.6365 (tmm160) REVERT: A 180 ILE cc_start: 0.5954 (tt) cc_final: 0.5490 (mm) REVERT: A 249 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6923 (tp) REVERT: B 20 ARG cc_start: 0.7332 (tpt-90) cc_final: 0.6319 (tmm160) REVERT: B 59 MET cc_start: 0.4349 (pmm) cc_final: 0.3536 (ppp) REVERT: B 120 SER cc_start: 0.8047 (t) cc_final: 0.7618 (m) REVERT: B 180 ILE cc_start: 0.5887 (tt) cc_final: 0.5448 (mm) REVERT: B 249 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6938 (tp) REVERT: B 411 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7350 (tm-30) outliers start: 41 outliers final: 20 residues processed: 96 average time/residue: 0.1691 time to fit residues: 24.7259 Evaluate side-chains 82 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 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 448 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: 0.9980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 33 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4743 r_free = 0.4743 target = 0.263185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.196577 restraints weight = 8757.466| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.26 r_work: 0.3399 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8936 Z= 0.188 Angle : 0.596 8.199 12094 Z= 0.315 Chirality : 0.041 0.236 1464 Planarity : 0.006 0.106 1518 Dihedral : 5.413 36.526 1224 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.02 % Rotamer: Outliers : 3.11 % Allowed : 20.95 % Favored : 75.93 % 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: 0.75 (0.26), residues: 1140 helix: 2.03 (0.19), residues: 750 sheet: 0.41 (0.78), residues: 50 loop : -3.27 (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 A 567 PHE 0.014 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 94 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.919 Fit side-chains REVERT: A 20 ARG cc_start: 0.7447 (tpt-90) cc_final: 0.6443 (tmm160) REVERT: A 180 ILE cc_start: 0.6124 (tt) cc_final: 0.5719 (mm) REVERT: A 249 LEU cc_start: 0.7425 (tp) cc_final: 0.7002 (tp) REVERT: A 339 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6940 (mm) REVERT: B 20 ARG cc_start: 0.7395 (tpt-90) cc_final: 0.6449 (tmm160) REVERT: B 59 MET cc_start: 0.4403 (pmm) cc_final: 0.3577 (ppp) REVERT: B 108 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 180 ILE cc_start: 0.6030 (tt) cc_final: 0.5664 (mm) REVERT: B 249 LEU cc_start: 0.7403 (tp) cc_final: 0.6962 (tp) REVERT: B 339 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6907 (mm) REVERT: B 391 TYR cc_start: 0.7343 (m-10) cc_final: 0.7098 (m-10) outliers start: 30 outliers final: 11 residues processed: 91 average time/residue: 0.1848 time to fit residues: 25.2305 Evaluate side-chains 74 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 243 GLU 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 448 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 132 MET 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 559 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.254813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184863 restraints weight = 8660.258| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.04 r_work: 0.3338 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8936 Z= 0.321 Angle : 0.649 7.286 12094 Z= 0.345 Chirality : 0.043 0.170 1464 Planarity : 0.006 0.100 1518 Dihedral : 5.411 35.649 1224 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.93 % Favored : 92.89 % Rotamer: Outliers : 4.67 % Allowed : 20.02 % Favored : 75.31 % 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: 0.42 (0.25), residues: 1140 helix: 1.72 (0.18), residues: 744 sheet: 0.09 (0.75), residues: 50 loop : -3.12 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 164 HIS 0.006 0.001 HIS B 141 PHE 0.015 0.001 PHE B 303 TYR 0.021 0.001 TYR B 408 ARG 0.003 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 110 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7672 (tpt-90) cc_final: 0.6640 (tmm160) REVERT: A 249 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7092 (tp) REVERT: A 339 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7013 (mm) REVERT: A 447 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5785 (tm-30) REVERT: B 20 ARG cc_start: 0.7593 (tpt-90) cc_final: 0.6609 (tmm160) REVERT: B 249 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7093 (tp) REVERT: B 339 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6987 (mm) REVERT: B 411 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7329 (tm-30) outliers start: 45 outliers final: 15 residues processed: 102 average time/residue: 0.1643 time to fit residues: 25.6885 Evaluate side-chains 83 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 113 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 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 447 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 132 MET 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 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: 5.9990 chunk 52 optimal weight: 0.3980 chunk 37 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.257187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.187066 restraints weight = 8607.189| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.05 r_work: 0.3386 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8936 Z= 0.183 Angle : 0.574 6.929 12094 Z= 0.306 Chirality : 0.040 0.164 1464 Planarity : 0.005 0.095 1518 Dihedral : 5.249 34.869 1224 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.11 % Favored : 92.72 % Rotamer: Outliers : 3.01 % Allowed : 21.99 % Favored : 75.00 % 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: 0.79 (0.26), residues: 1140 helix: 2.02 (0.19), residues: 750 sheet: 0.25 (0.75), residues: 50 loop : -3.09 (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 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 91 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7555 (tpt-90) cc_final: 0.6521 (tmm160) REVERT: A 249 LEU cc_start: 0.7536 (tp) cc_final: 0.7126 (tp) REVERT: A 339 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6889 (mm) REVERT: A 391 TYR cc_start: 0.7772 (m-10) cc_final: 0.7504 (m-10) REVERT: B 20 ARG cc_start: 0.7532 (tpt-90) cc_final: 0.6560 (tmm160) REVERT: B 59 MET cc_start: 0.4368 (pmm) cc_final: 0.3497 (ppp) REVERT: B 101 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: B 249 LEU cc_start: 0.7525 (tp) cc_final: 0.7106 (tp) REVERT: B 339 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6911 (mm) REVERT: B 411 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 29 outliers final: 11 residues processed: 90 average time/residue: 0.1865 time to fit residues: 25.0285 Evaluate side-chains 71 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER 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 A residue 448 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 THR 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 559 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 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 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.259800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191366 restraints weight = 8666.343| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.00 r_work: 0.3425 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8936 Z= 0.188 Angle : 0.572 7.989 12094 Z= 0.304 Chirality : 0.039 0.157 1464 Planarity : 0.005 0.089 1518 Dihedral : 5.112 34.422 1224 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.49 % Favored : 93.33 % Rotamer: Outliers : 3.42 % Allowed : 21.37 % Favored : 75.21 % 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: 0.89 (0.26), residues: 1140 helix: 2.10 (0.18), residues: 750 sheet: 0.31 (0.75), residues: 50 loop : -3.07 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 164 HIS 0.003 0.001 HIS B 141 PHE 0.014 0.001 PHE B 303 TYR 0.020 0.001 TYR B 408 ARG 0.003 0.000 ARG B 536 *********************** 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 91 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.3965 (pmm) cc_final: 0.3215 (ppp) REVERT: A 101 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: A 249 LEU cc_start: 0.7519 (tp) cc_final: 0.7093 (tp) REVERT: A 339 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6880 (mm) REVERT: A 357 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7237 (tp) REVERT: A 391 TYR cc_start: 0.7863 (m-10) cc_final: 0.7627 (m-10) REVERT: B 20 ARG cc_start: 0.7529 (tpt-90) cc_final: 0.6571 (tmm160) REVERT: B 59 MET cc_start: 0.4483 (pmm) cc_final: 0.3613 (ppp) REVERT: B 101 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: B 249 LEU cc_start: 0.7506 (tp) cc_final: 0.7072 (tp) REVERT: B 339 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6919 (mm) REVERT: B 411 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7286 (tm-30) outliers start: 33 outliers final: 12 residues processed: 87 average time/residue: 0.1822 time to fit residues: 23.6127 Evaluate side-chains 73 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 147 THR 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 A residue 448 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 THR 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 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: 0.0010 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 90 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.4286 ------------------------------------------------------------------------------- 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 = 0.4723 r_free = 0.4723 target = 0.261513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.194426 restraints weight = 8769.164| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.04 r_work: 0.3425 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8936 Z= 0.174 Angle : 0.558 6.837 12094 Z= 0.297 Chirality : 0.039 0.154 1464 Planarity : 0.005 0.085 1518 Dihedral : 5.012 33.467 1224 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.67 % Favored : 93.16 % Rotamer: Outliers : 2.28 % Allowed : 22.10 % 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: 0.98 (0.26), residues: 1140 helix: 2.17 (0.19), residues: 750 sheet: 0.48 (0.74), 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 0.002 0.001 HIS B 141 PHE 0.013 0.001 PHE B 303 TYR 0.020 0.001 TYR B 408 ARG 0.002 0.000 ARG A 399 *********************** 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 81 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.3927 (pmm) cc_final: 0.3192 (ppp) REVERT: A 101 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 180 ILE cc_start: 0.5967 (tp) cc_final: 0.5734 (mm) REVERT: A 249 LEU cc_start: 0.7444 (tp) cc_final: 0.7029 (tp) REVERT: A 339 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6917 (mm) REVERT: A 357 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7269 (tp) REVERT: B 20 ARG cc_start: 0.7467 (tpt-90) cc_final: 0.6494 (tmm160) REVERT: B 59 MET cc_start: 0.4311 (pmm) cc_final: 0.3496 (ppp) REVERT: B 101 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: B 180 ILE cc_start: 0.5900 (tp) cc_final: 0.5680 (mm) REVERT: B 249 LEU cc_start: 0.7438 (tp) cc_final: 0.7024 (tp) REVERT: B 339 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6875 (mm) REVERT: B 411 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7269 (tm-30) outliers start: 22 outliers final: 12 residues processed: 80 average time/residue: 0.1674 time to fit residues: 20.7782 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 : 1.179 ------------------------------------------------------------------------------- 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 147 THR 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 A residue 448 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 408 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.0570 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.260560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.192217 restraints weight = 8760.409| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.97 r_work: 0.3424 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8936 Z= 0.187 Angle : 0.571 8.379 12094 Z= 0.303 Chirality : 0.040 0.274 1464 Planarity : 0.005 0.081 1518 Dihedral : 4.957 32.868 1224 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.88 % Favored : 93.95 % Rotamer: Outliers : 2.59 % Allowed : 22.10 % 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: 1.00 (0.26), residues: 1140 helix: 2.18 (0.18), residues: 750 sheet: 0.57 (0.74), residues: 50 loop : -3.04 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 164 HIS 0.002 0.001 HIS B 141 PHE 0.013 0.001 PHE B 303 TYR 0.019 0.001 TYR B 408 ARG 0.003 0.000 ARG A 389 *********************** 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: 25 poor density : 58 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.4054 (pmm) cc_final: 0.3388 (ppp) REVERT: A 101 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 180 ILE cc_start: 0.5808 (tp) cc_final: 0.5582 (mm) REVERT: A 249 LEU cc_start: 0.7444 (tp) cc_final: 0.7029 (tp) REVERT: A 339 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6925 (mm) REVERT: A 357 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7350 (tp) REVERT: B 20 ARG cc_start: 0.7492 (tpt-90) cc_final: 0.6519 (tmm160) REVERT: B 101 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: B 180 ILE cc_start: 0.5892 (tp) cc_final: 0.5653 (mm) REVERT: B 249 LEU cc_start: 0.7417 (tp) cc_final: 0.7005 (tp) REVERT: B 339 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6831 (mm) outliers start: 25 outliers final: 10 residues processed: 80 average time/residue: 0.1659 time to fit residues: 20.6219 Evaluate side-chains 73 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU 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 A residue 357 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 220 ASN 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 357 LEU Chi-restraints excluded: chain B residue 408 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 43 optimal weight: 0.0170 chunk 102 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 434 ASN B 220 ASN B 434 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.260181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.190137 restraints weight = 8750.589| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.86 r_work: 0.3420 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8936 Z= 0.192 Angle : 0.582 8.434 12094 Z= 0.308 Chirality : 0.041 0.306 1464 Planarity : 0.005 0.078 1518 Dihedral : 4.931 32.985 1224 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 1.66 % Allowed : 22.61 % Favored : 75.73 % 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: 1.01 (0.26), residues: 1140 helix: 2.18 (0.18), residues: 750 sheet: 0.63 (0.73), residues: 50 loop : -3.03 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.003 0.001 HIS B 141 PHE 0.013 0.001 PHE B 303 TYR 0.018 0.001 TYR B 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 75 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.4178 (pmm) cc_final: 0.3490 (ppp) REVERT: A 101 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: A 180 ILE cc_start: 0.5926 (tp) cc_final: 0.5663 (mm) REVERT: A 249 LEU cc_start: 0.7484 (tp) cc_final: 0.7077 (tp) REVERT: A 339 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6890 (mm) REVERT: A 357 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7351 (tp) REVERT: B 20 ARG cc_start: 0.7499 (tpt-90) cc_final: 0.6523 (tmm160) REVERT: B 59 MET cc_start: 0.4385 (pmm) cc_final: 0.3606 (ppp) REVERT: B 101 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: B 180 ILE cc_start: 0.5886 (tp) cc_final: 0.5639 (mm) REVERT: B 249 LEU cc_start: 0.7438 (tp) cc_final: 0.7036 (tp) REVERT: B 339 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6814 (mm) REVERT: B 411 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7423 (tm-30) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.1804 time to fit residues: 20.6770 Evaluate side-chains 71 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 147 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 220 ASN 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 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: 0.6980 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 102 optimal weight: 0.0020 chunk 9 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.260634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.192333 restraints weight = 8766.672| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.98 r_work: 0.3423 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3220 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= 0.183 Angle : 0.575 8.481 12094 Z= 0.305 Chirality : 0.040 0.297 1464 Planarity : 0.005 0.077 1518 Dihedral : 4.890 32.964 1224 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 1.97 % Allowed : 22.61 % Favored : 75.41 % 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: 1.06 (0.26), residues: 1140 helix: 2.22 (0.18), residues: 748 sheet: 0.71 (0.74), residues: 50 loop : -3.00 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 164 HIS 0.003 0.000 HIS B 141 PHE 0.013 0.001 PHE B 303 TYR 0.018 0.001 TYR B 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: 5505.29 seconds wall clock time: 98 minutes 1.98 seconds (5881.98 seconds total)