Starting phenix.real_space_refine on Sat Aug 23 00:22:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rez_19113/08_2025/8rez_19113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rez_19113/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rez_19113/08_2025/8rez_19113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rez_19113/08_2025/8rez_19113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rez_19113/08_2025/8rez_19113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rez_19113/08_2025/8rez_19113.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.94, per 1000 atoms: 0.22 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: 0.68 Conformation dependent library (CDL) restraints added in 268.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 0.92 Time building geometry restraints manager: 0.93 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: 0.02 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: 1.400 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.750 ------------------------------------------------------------------------------- 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= 0.310 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 399 TYR 0.033 0.002 TYR B 408 PHE 0.014 0.001 PHE A 303 TRP 0.008 0.001 TRP B 413 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8936) covalent geometry : angle 0.92581 (12094) hydrogen bonds : bond 0.12694 ( 599) hydrogen bonds : angle 6.50434 ( 1785) *********************** 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 : 0.333 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: 0.0731 time to fit residues: 7.9184 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 : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 272 GLN B 77 GLN B 91 ASN 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 = 0.4632 r_free = 0.4632 target = 0.249794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.176117 restraints weight = 8650.272| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.98 r_work: 0.3295 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 8936 Z= 0.294 Angle : 0.836 9.212 12094 Z= 0.435 Chirality : 0.049 0.179 1464 Planarity : 0.008 0.120 1518 Dihedral : 6.066 42.950 1224 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.02 % Rotamer: Outliers : 6.02 % Allowed : 17.95 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.25), residues: 1140 helix: 1.28 (0.18), residues: 744 sheet: 0.61 (0.65), residues: 70 loop : -3.63 (0.29), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 399 TYR 0.030 0.002 TYR B 408 PHE 0.016 0.002 PHE B 237 TRP 0.010 0.002 TRP A 164 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 8936) covalent geometry : angle 0.83569 (12094) hydrogen bonds : bond 0.07314 ( 599) hydrogen bonds : angle 5.24377 ( 1785) *********************** 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 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 73 time to evaluate : 0.210 Fit side-chains REVERT: A 59 MET cc_start: 0.3950 (pmm) cc_final: 0.3210 (ppp) REVERT: A 180 ILE cc_start: 0.6835 (tt) cc_final: 0.6611 (tp) REVERT: A 339 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7032 (mm) REVERT: B 20 ARG cc_start: 0.7625 (tpt-90) cc_final: 0.6621 (tmm160) REVERT: B 59 MET cc_start: 0.4338 (pmm) cc_final: 0.3466 (ppp) REVERT: B 339 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6983 (mm) REVERT: B 411 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 58 outliers final: 28 residues processed: 123 average time/residue: 0.0534 time to fit residues: 10.4258 Evaluate side-chains 97 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 175 PRO 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 402 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 175 PRO Chi-restraints excluded: chain B residue 182 VAL 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 339 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 A 434 ASN B 91 ASN B 163 ASN B 220 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.257686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.186428 restraints weight = 8635.618| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.06 r_work: 0.3362 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8936 Z= 0.160 Angle : 0.632 6.947 12094 Z= 0.335 Chirality : 0.041 0.147 1464 Planarity : 0.006 0.113 1518 Dihedral : 5.727 38.439 1224 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.37 % Favored : 92.46 % Rotamer: Outliers : 2.70 % Allowed : 21.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1140 helix: 1.73 (0.19), residues: 750 sheet: 0.12 (0.78), residues: 50 loop : -3.28 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.024 0.001 TYR B 408 PHE 0.014 0.001 PHE A 303 TRP 0.006 0.001 TRP A 413 HIS 0.002 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8936) covalent geometry : angle 0.63151 (12094) hydrogen bonds : bond 0.06137 ( 599) hydrogen bonds : angle 4.86846 ( 1785) *********************** 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 93 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7593 (tpt-90) cc_final: 0.6542 (tmm160) REVERT: A 59 MET cc_start: 0.3869 (pmm) cc_final: 0.3161 (ppp) REVERT: A 120 SER cc_start: 0.8140 (t) cc_final: 0.7786 (m) REVERT: A 180 ILE cc_start: 0.6592 (tt) cc_final: 0.6386 (tp) REVERT: A 249 LEU cc_start: 0.7459 (tp) cc_final: 0.7065 (tp) REVERT: B 20 ARG cc_start: 0.7533 (tpt-90) cc_final: 0.6521 (tmm160) REVERT: B 59 MET cc_start: 0.4220 (pmm) cc_final: 0.3400 (ppp) REVERT: B 120 SER cc_start: 0.8118 (t) cc_final: 0.7717 (m) REVERT: B 249 LEU cc_start: 0.7523 (tp) cc_final: 0.7124 (tp) outliers start: 26 outliers final: 12 residues processed: 89 average time/residue: 0.0631 time to fit residues: 8.7377 Evaluate side-chains 77 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 501 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 408 TYR 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 29 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 0.0770 chunk 26 optimal weight: 0.0980 chunk 102 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 163 ASN B 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.246231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150311 restraints weight = 8723.309| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.48 r_work: 0.3366 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2309 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= 0.137 Angle : 0.586 9.176 12094 Z= 0.313 Chirality : 0.040 0.229 1464 Planarity : 0.006 0.104 1518 Dihedral : 5.474 35.380 1224 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.02 % Rotamer: Outliers : 3.53 % Allowed : 20.64 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 1140 helix: 2.01 (0.19), residues: 750 sheet: 0.19 (0.77), residues: 50 loop : -3.22 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.025 0.001 TYR B 408 PHE 0.014 0.001 PHE A 303 TRP 0.006 0.001 TRP A 413 HIS 0.002 0.001 HIS A 567 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8936) covalent geometry : angle 0.58566 (12094) hydrogen bonds : bond 0.05473 ( 599) hydrogen bonds : angle 4.58049 ( 1785) *********************** 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 100 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7393 (tpt-90) cc_final: 0.6319 (tmm160) REVERT: A 59 MET cc_start: 0.3566 (pmm) cc_final: 0.2940 (ppp) REVERT: A 101 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: A 180 ILE cc_start: 0.6170 (tt) cc_final: 0.5759 (mm) REVERT: A 249 LEU cc_start: 0.7252 (tp) cc_final: 0.6857 (tp) REVERT: A 339 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6895 (mm) REVERT: A 437 TYR cc_start: 0.4004 (OUTLIER) cc_final: 0.2925 (m-10) REVERT: B 20 ARG cc_start: 0.7388 (tpt-90) cc_final: 0.6358 (tmm160) REVERT: B 180 ILE cc_start: 0.5874 (tp) cc_final: 0.5575 (mm) REVERT: B 249 LEU cc_start: 0.7303 (tp) cc_final: 0.6921 (tp) REVERT: B 339 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6934 (mm) REVERT: B 391 TYR cc_start: 0.7276 (m-10) cc_final: 0.6978 (m-10) REVERT: B 411 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 427 MET cc_start: 0.5487 (mtp) cc_final: 0.5126 (mtm) outliers start: 34 outliers final: 8 residues processed: 100 average time/residue: 0.0680 time to fit residues: 10.0550 Evaluate side-chains 68 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 408 TYR Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain B residue 81 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 113 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.0770 chunk 43 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 A 247 GLN B 163 ASN B 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.260608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.191903 restraints weight = 8716.157| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.09 r_work: 0.3421 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8936 Z= 0.133 Angle : 0.563 7.073 12094 Z= 0.301 Chirality : 0.039 0.147 1464 Planarity : 0.006 0.098 1518 Dihedral : 5.298 33.797 1224 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.07 % Rotamer: Outliers : 4.67 % Allowed : 19.61 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1140 helix: 2.09 (0.19), residues: 750 sheet: 0.21 (0.76), residues: 50 loop : -3.09 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.022 0.001 TYR B 408 PHE 0.013 0.001 PHE A 303 TRP 0.007 0.001 TRP A 164 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8936) covalent geometry : angle 0.56340 (12094) hydrogen bonds : bond 0.05286 ( 599) hydrogen bonds : angle 4.48213 ( 1785) *********************** 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 103 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 58 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.4124 (pmm) cc_final: 0.3889 (pmm) REVERT: A 101 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 180 ILE cc_start: 0.6388 (tt) cc_final: 0.5919 (mm) REVERT: A 249 LEU cc_start: 0.7424 (tp) cc_final: 0.6995 (tp) REVERT: A 339 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6930 (mm) REVERT: A 437 TYR cc_start: 0.4306 (OUTLIER) cc_final: 0.2965 (m-10) REVERT: A 447 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5865 (tm-30) REVERT: B 20 ARG cc_start: 0.7519 (tpt-90) cc_final: 0.6509 (tmm160) REVERT: B 59 MET cc_start: 0.4411 (pmm) cc_final: 0.3522 (ppp) REVERT: B 180 ILE cc_start: 0.5858 (tp) cc_final: 0.5474 (mm) REVERT: B 249 LEU cc_start: 0.7439 (tp) cc_final: 0.7010 (tp) REVERT: B 339 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6962 (mm) REVERT: B 391 TYR cc_start: 0.7564 (m-10) cc_final: 0.7309 (m-10) REVERT: B 411 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7291 (tm-30) outliers start: 45 outliers final: 15 residues processed: 95 average time/residue: 0.0627 time to fit residues: 9.3072 Evaluate side-chains 75 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 208 GLN Chi-restraints excluded: chain A residue 247 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 427 MET Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 448 ILE 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 317 MET 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 82 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.243175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141163 restraints weight = 8787.046| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.81 r_work: 0.3240 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8936 Z= 0.215 Angle : 0.635 6.988 12094 Z= 0.338 Chirality : 0.042 0.156 1464 Planarity : 0.006 0.093 1518 Dihedral : 5.382 35.090 1224 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.02 % Rotamer: Outliers : 4.88 % Allowed : 18.98 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.25), residues: 1140 helix: 1.87 (0.18), residues: 750 sheet: 0.02 (0.74), residues: 50 loop : -3.05 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.020 0.001 TYR A 408 PHE 0.012 0.001 PHE B 303 TRP 0.010 0.002 TRP A 164 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 8936) covalent geometry : angle 0.63550 (12094) hydrogen bonds : bond 0.06056 ( 599) hydrogen bonds : angle 4.69455 ( 1785) *********************** 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 111 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 64 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.3639 (pmm) cc_final: 0.3401 (pmm) REVERT: A 171 LEU cc_start: 0.8174 (tp) cc_final: 0.7741 (tp) REVERT: A 180 ILE cc_start: 0.6434 (tt) cc_final: 0.6199 (tp) REVERT: A 249 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7047 (tp) REVERT: A 339 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6779 (mm) REVERT: A 437 TYR cc_start: 0.4647 (OUTLIER) cc_final: 0.3042 (m-10) REVERT: A 447 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5757 (tm-30) REVERT: B 20 ARG cc_start: 0.7565 (tpt-90) cc_final: 0.6463 (tmm160) REVERT: B 59 MET cc_start: 0.4020 (pmm) cc_final: 0.3724 (pmm) REVERT: B 171 LEU cc_start: 0.8272 (tp) cc_final: 0.7879 (tp) REVERT: B 249 LEU cc_start: 0.7437 (tp) cc_final: 0.7049 (tp) REVERT: B 339 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6908 (mm) REVERT: B 411 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7179 (tm-30) REVERT: B 478 MET cc_start: 0.6655 (pmm) cc_final: 0.6073 (pmm) outliers start: 47 outliers final: 21 residues processed: 106 average time/residue: 0.0706 time to fit residues: 11.7480 Evaluate side-chains 89 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 151 SER 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 408 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 247 GLN 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 494 LEU 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 88 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.253960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183000 restraints weight = 8708.421| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.98 r_work: 0.3339 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8936 Z= 0.179 Angle : 0.608 8.447 12094 Z= 0.323 Chirality : 0.041 0.191 1464 Planarity : 0.006 0.087 1518 Dihedral : 5.322 35.169 1224 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.93 % Favored : 92.89 % Rotamer: Outliers : 4.15 % Allowed : 19.81 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1140 helix: 1.87 (0.18), residues: 750 sheet: 0.04 (0.73), residues: 50 loop : -3.03 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.020 0.001 TYR A 408 PHE 0.012 0.001 PHE B 303 TRP 0.008 0.001 TRP A 164 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8936) covalent geometry : angle 0.60819 (12094) hydrogen bonds : bond 0.05929 ( 599) hydrogen bonds : angle 4.66343 ( 1785) *********************** 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 106 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 66 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 22 THR cc_start: 0.5202 (OUTLIER) cc_final: 0.4695 (m) REVERT: A 59 MET cc_start: 0.4135 (pmm) cc_final: 0.3871 (pmm) REVERT: A 171 LEU cc_start: 0.8231 (tp) cc_final: 0.7701 (tp) REVERT: A 180 ILE cc_start: 0.6640 (tt) cc_final: 0.6393 (tp) REVERT: A 249 LEU cc_start: 0.7520 (tp) cc_final: 0.7117 (tp) REVERT: A 339 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6862 (mm) REVERT: A 437 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.3377 (m-10) REVERT: B 20 ARG cc_start: 0.7677 (tpt-90) cc_final: 0.6680 (tmm160) REVERT: B 22 THR cc_start: 0.5162 (OUTLIER) cc_final: 0.4604 (m) REVERT: B 59 MET cc_start: 0.4465 (pmm) cc_final: 0.4172 (pmm) REVERT: B 171 LEU cc_start: 0.8339 (tp) cc_final: 0.7888 (tp) REVERT: B 249 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7163 (tp) REVERT: B 339 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6996 (mm) REVERT: B 478 MET cc_start: 0.6705 (pmm) cc_final: 0.6016 (pmm) outliers start: 40 outliers final: 18 residues processed: 101 average time/residue: 0.0718 time to fit residues: 11.2132 Evaluate side-chains 88 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 147 THR Chi-restraints excluded: chain A residue 149 ILE 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 427 MET Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 22 THR 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 149 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.243623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139811 restraints weight = 8747.426| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.17 r_work: 0.3310 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8936 Z= 0.144 Angle : 0.581 9.024 12094 Z= 0.311 Chirality : 0.040 0.161 1464 Planarity : 0.005 0.084 1518 Dihedral : 5.223 34.622 1224 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.11 % Favored : 92.72 % Rotamer: Outliers : 3.01 % Allowed : 20.64 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1140 helix: 2.06 (0.19), residues: 750 sheet: 0.25 (0.72), residues: 50 loop : -3.03 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.020 0.001 TYR A 408 PHE 0.012 0.001 PHE A 303 TRP 0.005 0.001 TRP A 413 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8936) covalent geometry : angle 0.58110 (12094) hydrogen bonds : bond 0.05524 ( 599) hydrogen bonds : angle 4.52784 ( 1785) *********************** 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 93 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 22 THR cc_start: 0.4951 (OUTLIER) cc_final: 0.4512 (m) REVERT: A 101 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: A 171 LEU cc_start: 0.8019 (tp) cc_final: 0.7506 (tp) REVERT: A 180 ILE cc_start: 0.6502 (tt) cc_final: 0.6235 (tp) REVERT: A 249 LEU cc_start: 0.7388 (tp) cc_final: 0.6985 (tp) REVERT: A 339 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6928 (mm) REVERT: A 437 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.3137 (m-10) REVERT: B 20 ARG cc_start: 0.7607 (tpt-90) cc_final: 0.6525 (tmm160) REVERT: B 59 MET cc_start: 0.4168 (pmm) cc_final: 0.3875 (pmm) REVERT: B 171 LEU cc_start: 0.8103 (tp) cc_final: 0.7668 (tp) REVERT: B 212 GLU cc_start: 0.7799 (pt0) cc_final: 0.7461 (pt0) REVERT: B 249 LEU cc_start: 0.7388 (tp) cc_final: 0.6993 (tp) REVERT: B 339 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6884 (mm) REVERT: B 411 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7336 (tm-30) outliers start: 29 outliers final: 12 residues processed: 91 average time/residue: 0.0719 time to fit residues: 10.1389 Evaluate side-chains 79 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 427 MET Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ILE 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 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 50 optimal weight: 9.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.243881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140862 restraints weight = 8774.096| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.44 r_work: 0.3269 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8936 Z= 0.150 Angle : 0.582 7.995 12094 Z= 0.311 Chirality : 0.040 0.148 1464 Planarity : 0.005 0.079 1518 Dihedral : 5.179 34.395 1224 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.49 % Favored : 93.33 % Rotamer: Outliers : 2.07 % Allowed : 21.78 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.26), residues: 1140 helix: 2.08 (0.19), residues: 750 sheet: 0.28 (0.72), residues: 50 loop : -3.02 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.019 0.001 TYR A 408 PHE 0.012 0.001 PHE A 303 TRP 0.008 0.001 TRP B 164 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8936) covalent geometry : angle 0.58198 (12094) hydrogen bonds : bond 0.05555 ( 599) hydrogen bonds : angle 4.52799 ( 1785) *********************** 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 81 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 22 THR cc_start: 0.5074 (OUTLIER) cc_final: 0.4598 (m) REVERT: A 171 LEU cc_start: 0.8074 (tp) cc_final: 0.7545 (tp) REVERT: A 180 ILE cc_start: 0.6560 (tt) cc_final: 0.6286 (tp) REVERT: A 249 LEU cc_start: 0.7451 (tp) cc_final: 0.7056 (tp) REVERT: A 339 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6965 (mm) REVERT: A 437 TYR cc_start: 0.5182 (OUTLIER) cc_final: 0.3209 (m-10) REVERT: B 20 ARG cc_start: 0.7609 (tpt-90) cc_final: 0.6548 (tmm160) REVERT: B 59 MET cc_start: 0.4147 (pmm) cc_final: 0.3857 (pmm) REVERT: B 171 LEU cc_start: 0.8140 (tp) cc_final: 0.7706 (tp) REVERT: B 212 GLU cc_start: 0.7840 (pt0) cc_final: 0.7497 (pt0) REVERT: B 249 LEU cc_start: 0.7421 (tp) cc_final: 0.7035 (tp) REVERT: B 339 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6899 (mm) REVERT: B 411 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7334 (tm-30) outliers start: 20 outliers final: 10 residues processed: 79 average time/residue: 0.0772 time to fit residues: 9.5436 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 427 MET Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 437 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4583 r_free = 0.4583 target = 0.246200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.172749 restraints weight = 8782.829| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.17 r_work: 0.3346 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8936 Z= 0.144 Angle : 0.582 8.071 12094 Z= 0.311 Chirality : 0.040 0.146 1464 Planarity : 0.005 0.076 1518 Dihedral : 5.083 34.174 1224 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % Rotamer: Outliers : 1.66 % Allowed : 22.10 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1140 helix: 2.11 (0.19), residues: 750 sheet: 0.33 (0.72), residues: 50 loop : -2.97 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.018 0.001 TYR A 408 PHE 0.012 0.001 PHE B 303 TRP 0.007 0.001 TRP B 164 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8936) covalent geometry : angle 0.58187 (12094) hydrogen bonds : bond 0.05464 ( 599) hydrogen bonds : angle 4.50778 ( 1785) ********************** 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 77 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 22 THR cc_start: 0.5297 (OUTLIER) cc_final: 0.4766 (m) REVERT: A 171 LEU cc_start: 0.8116 (tp) cc_final: 0.7586 (tp) REVERT: A 180 ILE cc_start: 0.6654 (tt) cc_final: 0.6447 (tt) REVERT: A 249 LEU cc_start: 0.7534 (tp) cc_final: 0.7127 (tp) REVERT: A 339 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6994 (mm) REVERT: A 437 TYR cc_start: 0.5276 (OUTLIER) cc_final: 0.3156 (m-10) REVERT: B 20 ARG cc_start: 0.7636 (tpt-90) cc_final: 0.6625 (tmm160) REVERT: B 59 MET cc_start: 0.4400 (pmm) cc_final: 0.4128 (pmm) REVERT: B 171 LEU cc_start: 0.8200 (tp) cc_final: 0.7730 (tp) REVERT: B 212 GLU cc_start: 0.7872 (pt0) cc_final: 0.7565 (pt0) REVERT: B 249 LEU cc_start: 0.7519 (tp) cc_final: 0.7126 (tp) REVERT: B 339 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6985 (mm) REVERT: B 411 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7444 (tm-30) outliers start: 16 outliers final: 10 residues processed: 75 average time/residue: 0.0745 time to fit residues: 8.7658 Evaluate side-chains 73 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 427 MET Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.4673 r_free = 0.4673 target = 0.255544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.186973 restraints weight = 8692.920| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.01 r_work: 0.3398 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3341 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= 0.133 Angle : 0.569 8.145 12094 Z= 0.303 Chirality : 0.039 0.143 1464 Planarity : 0.005 0.075 1518 Dihedral : 4.979 33.483 1224 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 1.66 % Allowed : 22.51 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1140 helix: 2.19 (0.19), residues: 750 sheet: 0.40 (0.73), residues: 50 loop : -2.95 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.021 0.001 TYR B 437 PHE 0.013 0.001 PHE A 303 TRP 0.007 0.001 TRP B 164 HIS 0.002 0.000 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8936) covalent geometry : angle 0.56931 (12094) hydrogen bonds : bond 0.05270 ( 599) hydrogen bonds : angle 4.44626 ( 1785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.51 seconds wall clock time: 48 minutes 2.22 seconds (2882.22 seconds total)