Starting phenix.real_space_refine on Thu Jun 5 07:27:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwb_32865/06_2025/7wwb_32865.cif" } resolution = 3.86 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= 0.018 sd= 0.094 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 60 5.16 5 C 3682 2.51 5 N 834 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5428 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.05, per 1000 atoms: 0.75 Number of scatterers: 5428 At special positions: 0 Unit cell: (107.613, 120.657, 82.612, 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 60 16.00 O 852 8.00 N 834 7.00 C 3682 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: 1.32 Conformation dependent library (CDL) restraints added in 647.8 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 228 through 245 removed outlier: 5.997A pdb=" N ARG A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 310 through 331 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 337 through 356 removed outlier: 3.515A pdb=" N THR A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 416 removed outlier: 3.614A pdb=" N ILE A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.545A pdb=" N VAL A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 479 through 508 Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 525 through 554 Processing helix chain 'A' and resid 573 through 607 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 228 through 245 removed outlier: 5.997A pdb=" N ARG B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 337 through 356 removed outlier: 3.516A pdb=" N THR B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 416 removed outlier: 3.615A pdb=" N ILE B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.544A pdb=" N VAL B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 479 through 508 Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 525 through 554 Processing helix chain 'B' and resid 573 through 607 428 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 756 1.30 - 1.43: 1504 1.43 - 1.56: 3180 1.56 - 1.68: 34 1.68 - 1.81: 90 Bond restraints: 5564 Sorted by residual: bond pdb=" C GLN B 337 " pdb=" O GLN B 337 " ideal model delta sigma weight residual 1.243 1.177 0.066 9.90e-03 1.02e+04 4.38e+01 bond pdb=" C GLN A 337 " pdb=" O GLN A 337 " ideal model delta sigma weight residual 1.243 1.178 0.065 9.90e-03 1.02e+04 4.35e+01 bond pdb=" C PHE B 339 " pdb=" O PHE B 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" C PHE A 339 " pdb=" O PHE A 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.25e+01 bond pdb=" C17 CLR A 702 " pdb=" C20 CLR A 702 " ideal model delta sigma weight residual 1.535 1.596 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 5559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 7256 2.16 - 4.32: 268 4.32 - 6.48: 32 6.48 - 8.64: 8 8.64 - 10.80: 4 Bond angle restraints: 7568 Sorted by residual: angle pdb=" C PHE B 339 " pdb=" N TRP B 340 " pdb=" CA TRP B 340 " ideal model delta sigma weight residual 120.31 109.51 10.80 1.52e+00 4.33e-01 5.05e+01 angle pdb=" C PHE A 339 " pdb=" N TRP A 340 " pdb=" CA TRP A 340 " ideal model delta sigma weight residual 120.31 109.53 10.78 1.52e+00 4.33e-01 5.03e+01 angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 113.53 107.83 5.70 9.80e-01 1.04e+00 3.38e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 113.53 107.85 5.68 9.80e-01 1.04e+00 3.36e+01 angle pdb=" C PHE B 336 " pdb=" N GLN B 337 " pdb=" CA GLN B 337 " ideal model delta sigma weight residual 120.58 128.05 -7.47 1.32e+00 5.74e-01 3.20e+01 ... (remaining 7563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3222 17.14 - 34.28: 68 34.28 - 51.42: 6 51.42 - 68.56: 4 68.56 - 85.70: 4 Dihedral angle restraints: 3304 sinusoidal: 1350 harmonic: 1954 Sorted by residual: dihedral pdb=" CA TYR B 438 " pdb=" C TYR B 438 " pdb=" N HIS B 439 " pdb=" CA HIS B 439 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 438 " pdb=" C TYR A 438 " pdb=" N HIS A 439 " pdb=" CA HIS A 439 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " pdb=" CD GLU B 591 " pdb=" OE1 GLU B 591 " ideal model delta sinusoidal sigma weight residual 0.00 -85.70 85.70 1 3.00e+01 1.11e-03 9.87e+00 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 642 0.063 - 0.125: 240 0.125 - 0.188: 32 0.188 - 0.251: 8 0.251 - 0.313: 8 Chirality restraints: 930 Sorted by residual: chirality pdb=" C13 CLR A 702 " pdb=" C12 CLR A 702 " pdb=" C14 CLR A 702 " pdb=" C17 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C14 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C15 CLR B 702 " pdb=" C8 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 927 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 343 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C PHE A 343 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 343 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 344 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 343 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C PHE B 343 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE B 343 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 344 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 493 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LEU B 493 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU B 493 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 494 " 0.013 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2767 2.99 - 3.47: 5843 3.47 - 3.94: 8642 3.94 - 4.42: 9683 4.42 - 4.90: 15145 Nonbonded interactions: 42080 Sorted by model distance: nonbonded pdb=" NZ LYS B 326 " pdb=" OD2 ASP B 619 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS A 326 " pdb=" OD2 ASP A 619 " model vdw 2.512 3.120 nonbonded pdb=" O CYS B 26 " pdb=" OG1 THR B 27 " model vdw 2.531 3.040 nonbonded pdb=" O CYS A 26 " pdb=" OG1 THR A 27 " model vdw 2.531 3.040 nonbonded pdb=" N PHE B 336 " pdb=" N GLN B 337 " model vdw 2.561 2.560 ... (remaining 42075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.008 0.066 5564 Z= 0.476 Angle : 0.969 10.801 7568 Z= 0.650 Chirality : 0.066 0.313 930 Planarity : 0.006 0.026 860 Dihedral : 9.324 85.703 2028 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.31), residues: 642 helix: 0.69 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -2.08 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 386 HIS 0.001 0.000 HIS B 464 PHE 0.001 0.000 PHE B 348 TYR 0.001 0.000 TYR B 415 ARG 0.001 0.000 ARG B 311 Details of bonding type rmsd hydrogen bonds : bond 0.21072 ( 428) hydrogen bonds : angle 6.93898 ( 1260) covalent geometry : bond 0.00825 ( 5564) covalent geometry : angle 0.96944 ( 7568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8669 (mt) cc_final: 0.8421 (mt) REVERT: A 234 ARG cc_start: 0.7483 (ptt180) cc_final: 0.7161 (ptt-90) REVERT: A 326 LYS cc_start: 0.8897 (mttt) cc_final: 0.8603 (ttmm) REVERT: A 342 PHE cc_start: 0.7578 (t80) cc_final: 0.7357 (m-10) REVERT: A 352 TRP cc_start: 0.8852 (t60) cc_final: 0.8616 (t60) REVERT: A 354 MET cc_start: 0.8206 (mmm) cc_final: 0.7948 (tpp) REVERT: A 438 TYR cc_start: 0.7244 (m-80) cc_final: 0.7021 (m-10) REVERT: A 516 LYS cc_start: 0.6466 (mttt) cc_final: 0.6192 (mmtp) REVERT: A 528 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7031 (mpt180) REVERT: A 581 LEU cc_start: 0.8942 (mt) cc_final: 0.8654 (tt) REVERT: B 340 TRP cc_start: 0.6592 (m-10) cc_final: 0.5815 (m100) REVERT: B 437 ARG cc_start: 0.7457 (tpt90) cc_final: 0.6958 (mmt180) REVERT: B 463 ILE cc_start: 0.8796 (mt) cc_final: 0.8568 (mm) REVERT: B 508 SER cc_start: 0.8865 (m) cc_final: 0.8506 (t) REVERT: B 516 LYS cc_start: 0.6949 (mttt) cc_final: 0.6379 (mptt) REVERT: B 534 THR cc_start: 0.8810 (m) cc_final: 0.8596 (p) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1907 time to fit residues: 69.5435 Evaluate side-chains 178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 466 GLN B 439 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120133 restraints weight = 9006.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123419 restraints weight = 5596.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125573 restraints weight = 4252.766| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5564 Z= 0.162 Angle : 0.680 7.472 7568 Z= 0.344 Chirality : 0.039 0.184 930 Planarity : 0.004 0.028 860 Dihedral : 4.735 31.905 836 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.38 % Allowed : 14.93 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.34), residues: 642 helix: 2.65 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -2.41 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.002 0.001 HIS B 330 PHE 0.020 0.001 PHE B 44 TYR 0.012 0.001 TYR B 415 ARG 0.006 0.001 ARG B 614 Details of bonding type rmsd hydrogen bonds : bond 0.05651 ( 428) hydrogen bonds : angle 4.24186 ( 1260) covalent geometry : bond 0.00339 ( 5564) covalent geometry : angle 0.68032 ( 7568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.7205 (m-80) cc_final: 0.6991 (m-80) REVERT: A 342 PHE cc_start: 0.7881 (t80) cc_final: 0.7448 (m-10) REVERT: A 397 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: A 433 ASN cc_start: 0.7526 (p0) cc_final: 0.7158 (m-40) REVERT: A 445 LYS cc_start: 0.8190 (tptm) cc_final: 0.7895 (tptm) REVERT: A 528 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7077 (mpt180) REVERT: A 538 PHE cc_start: 0.8627 (t80) cc_final: 0.7727 (t80) REVERT: A 542 LEU cc_start: 0.8732 (mp) cc_final: 0.8500 (mp) REVERT: A 578 PHE cc_start: 0.8200 (t80) cc_final: 0.7780 (t80) REVERT: A 581 LEU cc_start: 0.9001 (mt) cc_final: 0.8772 (tt) REVERT: B 21 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7092 (pp) REVERT: B 22 GLU cc_start: 0.7800 (mp0) cc_final: 0.7587 (mp0) REVERT: B 234 ARG cc_start: 0.8782 (ptp90) cc_final: 0.8494 (ptp90) REVERT: B 340 TRP cc_start: 0.6946 (m-10) cc_final: 0.6652 (m-10) REVERT: B 508 SER cc_start: 0.8822 (m) cc_final: 0.8609 (t) REVERT: B 516 LYS cc_start: 0.7089 (mttt) cc_final: 0.6312 (mmtt) outliers start: 38 outliers final: 26 residues processed: 216 average time/residue: 0.1989 time to fit residues: 55.4400 Evaluate side-chains 181 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 603 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.159459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123423 restraints weight = 9078.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126961 restraints weight = 5712.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129253 restraints weight = 4368.214| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5564 Z= 0.149 Angle : 0.638 6.932 7568 Z= 0.321 Chirality : 0.038 0.177 930 Planarity : 0.004 0.031 860 Dihedral : 4.747 34.753 836 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.38 % Allowed : 17.28 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.34), residues: 642 helix: 2.65 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.20 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 352 HIS 0.004 0.001 HIS A 439 PHE 0.022 0.001 PHE B 48 TYR 0.027 0.002 TYR A 438 ARG 0.005 0.001 ARG B 614 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 428) hydrogen bonds : angle 4.06187 ( 1260) covalent geometry : bond 0.00333 ( 5564) covalent geometry : angle 0.63752 ( 7568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.583 Fit side-chains REVERT: A 230 MET cc_start: 0.7991 (mmp) cc_final: 0.7639 (mmp) REVERT: A 307 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7627 (tpt) REVERT: A 342 PHE cc_start: 0.7823 (t80) cc_final: 0.7163 (m-10) REVERT: A 349 TRP cc_start: 0.9064 (m-10) cc_final: 0.8861 (m-10) REVERT: A 397 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: A 466 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 501 TYR cc_start: 0.9220 (m-10) cc_final: 0.8962 (m-10) REVERT: A 528 ARG cc_start: 0.7656 (mtt90) cc_final: 0.7207 (mpt180) REVERT: A 538 PHE cc_start: 0.8664 (t80) cc_final: 0.7809 (t80) REVERT: A 581 LEU cc_start: 0.9021 (mt) cc_final: 0.8666 (tt) REVERT: B 244 LEU cc_start: 0.9091 (tt) cc_final: 0.8799 (mm) REVERT: B 397 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8502 (mm-30) REVERT: B 454 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8396 (ttpt) REVERT: B 516 LYS cc_start: 0.7327 (mttt) cc_final: 0.6772 (mmtt) outliers start: 38 outliers final: 20 residues processed: 199 average time/residue: 0.1477 time to fit residues: 38.7487 Evaluate side-chains 167 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 5 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.161369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128546 restraints weight = 9303.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131537 restraints weight = 6288.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.133257 restraints weight = 4232.360| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5564 Z= 0.132 Angle : 0.632 8.842 7568 Z= 0.319 Chirality : 0.038 0.201 930 Planarity : 0.004 0.029 860 Dihedral : 4.639 29.025 836 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.53 % Allowed : 22.65 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.34), residues: 642 helix: 2.58 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.21 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 352 HIS 0.001 0.000 HIS B 330 PHE 0.025 0.001 PHE B 343 TYR 0.023 0.002 TYR A 438 ARG 0.004 0.000 ARG B 614 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 428) hydrogen bonds : angle 3.87735 ( 1260) covalent geometry : bond 0.00275 ( 5564) covalent geometry : angle 0.63244 ( 7568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7640 (tpt) REVERT: A 342 PHE cc_start: 0.7797 (t80) cc_final: 0.7159 (m-10) REVERT: A 349 TRP cc_start: 0.9036 (m-10) cc_final: 0.8675 (m-10) REVERT: A 384 MET cc_start: 0.5125 (mpp) cc_final: 0.4709 (mpp) REVERT: A 393 ILE cc_start: 0.8039 (mm) cc_final: 0.7783 (mt) REVERT: A 397 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: A 445 LYS cc_start: 0.8314 (tptm) cc_final: 0.7828 (tptm) REVERT: A 449 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8907 (mp) REVERT: A 501 TYR cc_start: 0.9212 (m-10) cc_final: 0.8998 (m-10) REVERT: A 528 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7319 (mpt180) REVERT: A 538 PHE cc_start: 0.8568 (t80) cc_final: 0.8172 (t80) REVERT: A 581 LEU cc_start: 0.8949 (mt) cc_final: 0.8579 (tt) REVERT: A 599 LEU cc_start: 0.8806 (tp) cc_final: 0.8491 (tp) REVERT: B 42 MET cc_start: 0.8572 (tpt) cc_final: 0.8065 (tpp) REVERT: B 242 TRP cc_start: 0.7607 (OUTLIER) cc_final: 0.6975 (t60) REVERT: B 244 LEU cc_start: 0.8884 (tt) cc_final: 0.8628 (mm) REVERT: B 419 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7044 (p0) REVERT: B 438 TYR cc_start: 0.7773 (m-80) cc_final: 0.7272 (m-10) REVERT: B 454 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8310 (ttmt) REVERT: B 516 LYS cc_start: 0.7278 (mttt) cc_final: 0.6837 (mmtt) outliers start: 27 outliers final: 15 residues processed: 187 average time/residue: 0.1705 time to fit residues: 42.4916 Evaluate side-chains 177 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116578 restraints weight = 9263.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118314 restraints weight = 6736.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120285 restraints weight = 5216.580| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5564 Z= 0.166 Angle : 0.660 7.827 7568 Z= 0.339 Chirality : 0.040 0.245 930 Planarity : 0.004 0.029 860 Dihedral : 5.242 41.099 836 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.54 % Allowed : 21.81 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.34), residues: 642 helix: 2.65 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.06 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 386 HIS 0.003 0.001 HIS B 330 PHE 0.024 0.002 PHE B 343 TYR 0.026 0.002 TYR A 438 ARG 0.003 0.001 ARG B 614 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 428) hydrogen bonds : angle 4.04487 ( 1260) covalent geometry : bond 0.00384 ( 5564) covalent geometry : angle 0.66043 ( 7568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.585 Fit side-chains REVERT: A 242 TRP cc_start: 0.7651 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: A 307 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7680 (tpt) REVERT: A 342 PHE cc_start: 0.7845 (t80) cc_final: 0.7098 (m-10) REVERT: A 349 TRP cc_start: 0.9127 (m-10) cc_final: 0.8896 (m-10) REVERT: A 384 MET cc_start: 0.5364 (mpp) cc_final: 0.5109 (mpp) REVERT: A 393 ILE cc_start: 0.8567 (mm) cc_final: 0.8131 (mt) REVERT: A 397 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 445 LYS cc_start: 0.8360 (tptm) cc_final: 0.7911 (tptm) REVERT: A 449 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8826 (mp) REVERT: A 458 MET cc_start: 0.7796 (tpt) cc_final: 0.7376 (tpt) REVERT: A 538 PHE cc_start: 0.8678 (t80) cc_final: 0.8369 (t80) REVERT: A 581 LEU cc_start: 0.9030 (mt) cc_final: 0.8633 (tt) REVERT: B 42 MET cc_start: 0.8724 (tpt) cc_final: 0.8303 (tpp) REVERT: B 242 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.6762 (t60) REVERT: B 244 LEU cc_start: 0.8967 (tt) cc_final: 0.8764 (mm) REVERT: B 516 LYS cc_start: 0.7267 (mttt) cc_final: 0.6712 (mmtt) REVERT: B 604 ASP cc_start: 0.8933 (t70) cc_final: 0.8690 (t0) outliers start: 39 outliers final: 25 residues processed: 184 average time/residue: 0.1493 time to fit residues: 36.6960 Evaluate side-chains 174 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117997 restraints weight = 9267.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120019 restraints weight = 6693.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121777 restraints weight = 5077.045| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5564 Z= 0.148 Angle : 0.651 7.651 7568 Z= 0.329 Chirality : 0.039 0.220 930 Planarity : 0.004 0.027 860 Dihedral : 5.081 38.726 836 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.54 % Allowed : 24.16 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 2.82 (0.34), residues: 642 helix: 2.66 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.98 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 386 HIS 0.003 0.001 HIS B 330 PHE 0.023 0.001 PHE B 343 TYR 0.026 0.002 TYR A 438 ARG 0.003 0.001 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 428) hydrogen bonds : angle 3.94250 ( 1260) covalent geometry : bond 0.00340 ( 5564) covalent geometry : angle 0.65076 ( 7568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.571 Fit side-chains REVERT: A 242 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: A 307 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7630 (tpt) REVERT: A 342 PHE cc_start: 0.7825 (t80) cc_final: 0.7159 (m-10) REVERT: A 349 TRP cc_start: 0.9140 (m-10) cc_final: 0.8932 (m-10) REVERT: A 393 ILE cc_start: 0.8459 (mm) cc_final: 0.8019 (mt) REVERT: A 397 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: A 445 LYS cc_start: 0.8264 (tptm) cc_final: 0.7850 (tptm) REVERT: A 449 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8800 (mp) REVERT: A 458 MET cc_start: 0.7812 (tpt) cc_final: 0.7388 (tpt) REVERT: A 581 LEU cc_start: 0.9006 (mt) cc_final: 0.8615 (tt) REVERT: A 599 LEU cc_start: 0.8954 (tp) cc_final: 0.8443 (tt) REVERT: B 42 MET cc_start: 0.8677 (tpt) cc_final: 0.8229 (tpp) REVERT: B 230 MET cc_start: 0.8915 (mmm) cc_final: 0.8705 (mmt) REVERT: B 242 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.6749 (t60) REVERT: B 354 MET cc_start: 0.7193 (ttp) cc_final: 0.6799 (tmm) REVERT: B 438 TYR cc_start: 0.7869 (m-80) cc_final: 0.7658 (m-10) REVERT: B 516 LYS cc_start: 0.7407 (mttt) cc_final: 0.6894 (mmtt) outliers start: 39 outliers final: 28 residues processed: 173 average time/residue: 0.1500 time to fit residues: 34.5545 Evaluate side-chains 175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.157152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121979 restraints weight = 9178.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125394 restraints weight = 5801.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127437 restraints weight = 4415.936| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.7477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5564 Z= 0.134 Angle : 0.645 7.346 7568 Z= 0.324 Chirality : 0.038 0.222 930 Planarity : 0.004 0.027 860 Dihedral : 4.934 36.295 836 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.38 % Allowed : 24.66 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.34), residues: 642 helix: 2.79 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.90 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 386 HIS 0.002 0.001 HIS B 330 PHE 0.024 0.001 PHE B 342 TYR 0.025 0.002 TYR A 438 ARG 0.004 0.001 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 428) hydrogen bonds : angle 3.85044 ( 1260) covalent geometry : bond 0.00297 ( 5564) covalent geometry : angle 0.64477 ( 7568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.8426 (ttm) cc_final: 0.8211 (ttt) REVERT: A 242 TRP cc_start: 0.7710 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: A 307 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7694 (tpt) REVERT: A 349 TRP cc_start: 0.9126 (m-10) cc_final: 0.8771 (m-10) REVERT: A 393 ILE cc_start: 0.8341 (mm) cc_final: 0.7894 (mt) REVERT: A 397 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 445 LYS cc_start: 0.8151 (tptm) cc_final: 0.7748 (tptm) REVERT: A 449 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 458 MET cc_start: 0.7882 (tpt) cc_final: 0.7457 (tpt) REVERT: A 460 LEU cc_start: 0.8554 (mp) cc_final: 0.8338 (tt) REVERT: A 508 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8668 (t) REVERT: A 516 LYS cc_start: 0.5961 (mmtp) cc_final: 0.5552 (mmtt) REVERT: A 581 LEU cc_start: 0.8985 (mt) cc_final: 0.8612 (tt) REVERT: A 599 LEU cc_start: 0.8842 (tp) cc_final: 0.8583 (tp) REVERT: B 42 MET cc_start: 0.8662 (tpt) cc_final: 0.8226 (tpp) REVERT: B 230 MET cc_start: 0.8887 (mmm) cc_final: 0.8628 (mmt) REVERT: B 242 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.7003 (t60) REVERT: B 354 MET cc_start: 0.7220 (ttp) cc_final: 0.6861 (tmm) REVERT: B 438 TYR cc_start: 0.7908 (m-80) cc_final: 0.7506 (m-10) REVERT: B 462 TYR cc_start: 0.8537 (t80) cc_final: 0.8057 (t80) REVERT: B 516 LYS cc_start: 0.7369 (mttt) cc_final: 0.6898 (mmtt) outliers start: 38 outliers final: 28 residues processed: 177 average time/residue: 0.1299 time to fit residues: 31.1777 Evaluate side-chains 173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.157783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125263 restraints weight = 9199.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127818 restraints weight = 6264.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129262 restraints weight = 4518.036| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5564 Z= 0.129 Angle : 0.637 8.516 7568 Z= 0.319 Chirality : 0.038 0.201 930 Planarity : 0.004 0.027 860 Dihedral : 4.792 32.690 836 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.88 % Allowed : 24.83 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.34), residues: 642 helix: 2.89 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.07 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 386 HIS 0.002 0.000 HIS B 330 PHE 0.026 0.001 PHE B 343 TYR 0.021 0.002 TYR A 438 ARG 0.004 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 428) hydrogen bonds : angle 3.79575 ( 1260) covalent geometry : bond 0.00280 ( 5564) covalent geometry : angle 0.63687 ( 7568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 242 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.7238 (m-10) REVERT: A 307 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7703 (tpt) REVERT: A 342 PHE cc_start: 0.7799 (t80) cc_final: 0.7121 (m-10) REVERT: A 349 TRP cc_start: 0.9120 (m-10) cc_final: 0.8763 (m-10) REVERT: A 393 ILE cc_start: 0.8352 (mm) cc_final: 0.7922 (mt) REVERT: A 397 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: A 458 MET cc_start: 0.7765 (tpt) cc_final: 0.7438 (tpt) REVERT: A 460 LEU cc_start: 0.8598 (mp) cc_final: 0.8308 (tt) REVERT: A 508 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8626 (t) REVERT: A 581 LEU cc_start: 0.8969 (mt) cc_final: 0.8558 (tt) REVERT: A 599 LEU cc_start: 0.8871 (tp) cc_final: 0.8289 (tt) REVERT: B 230 MET cc_start: 0.8825 (mmm) cc_final: 0.8592 (mmt) REVERT: B 354 MET cc_start: 0.7303 (ttp) cc_final: 0.6832 (tmm) REVERT: B 438 TYR cc_start: 0.7944 (m-80) cc_final: 0.7720 (m-10) REVERT: B 462 TYR cc_start: 0.8598 (t80) cc_final: 0.8084 (t80) REVERT: B 516 LYS cc_start: 0.7348 (mttt) cc_final: 0.6906 (mmtt) REVERT: B 549 CYS cc_start: 0.8869 (m) cc_final: 0.8611 (m) outliers start: 41 outliers final: 30 residues processed: 177 average time/residue: 0.1258 time to fit residues: 30.8863 Evaluate side-chains 180 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.152262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120557 restraints weight = 9414.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122784 restraints weight = 6377.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123892 restraints weight = 4577.915| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5564 Z= 0.135 Angle : 0.663 10.457 7568 Z= 0.332 Chirality : 0.039 0.240 930 Planarity : 0.004 0.027 860 Dihedral : 4.794 31.392 836 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.54 % Allowed : 25.34 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.34), residues: 642 helix: 2.88 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.84 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 386 HIS 0.003 0.001 HIS B 388 PHE 0.028 0.001 PHE B 342 TYR 0.025 0.002 TYR B 235 ARG 0.003 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 428) hydrogen bonds : angle 3.83715 ( 1260) covalent geometry : bond 0.00300 ( 5564) covalent geometry : angle 0.66276 ( 7568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.584 Fit side-chains REVERT: A 242 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: A 307 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7705 (tpt) REVERT: A 342 PHE cc_start: 0.7801 (t80) cc_final: 0.7119 (m-10) REVERT: A 349 TRP cc_start: 0.9120 (m-10) cc_final: 0.8765 (m-10) REVERT: A 393 ILE cc_start: 0.8393 (mm) cc_final: 0.7965 (mt) REVERT: A 397 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: A 458 MET cc_start: 0.7762 (tpt) cc_final: 0.7464 (tpt) REVERT: A 460 LEU cc_start: 0.8583 (mp) cc_final: 0.8342 (tt) REVERT: A 508 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8606 (t) REVERT: A 538 PHE cc_start: 0.8650 (t80) cc_final: 0.7981 (t80) REVERT: A 581 LEU cc_start: 0.8965 (mt) cc_final: 0.8553 (tt) REVERT: A 599 LEU cc_start: 0.8886 (tp) cc_final: 0.8338 (tt) REVERT: B 438 TYR cc_start: 0.7973 (m-80) cc_final: 0.7561 (m-10) REVERT: B 462 TYR cc_start: 0.8571 (t80) cc_final: 0.8088 (t80) REVERT: B 516 LYS cc_start: 0.7340 (mttt) cc_final: 0.6903 (mmtt) REVERT: B 549 CYS cc_start: 0.8864 (m) cc_final: 0.8584 (m) outliers start: 39 outliers final: 28 residues processed: 179 average time/residue: 0.1313 time to fit residues: 32.5891 Evaluate side-chains 179 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.151833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120204 restraints weight = 9412.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122588 restraints weight = 6332.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123688 restraints weight = 4524.353| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5564 Z= 0.137 Angle : 0.681 10.404 7568 Z= 0.336 Chirality : 0.039 0.236 930 Planarity : 0.004 0.031 860 Dihedral : 4.793 30.031 836 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.87 % Allowed : 25.84 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.34), residues: 642 helix: 2.84 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.90 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 385 HIS 0.002 0.001 HIS B 330 PHE 0.017 0.001 PHE A 578 TYR 0.020 0.002 TYR A 438 ARG 0.004 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 428) hydrogen bonds : angle 3.86220 ( 1260) covalent geometry : bond 0.00307 ( 5564) covalent geometry : angle 0.68107 ( 7568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 242 TRP cc_start: 0.7735 (OUTLIER) cc_final: 0.7213 (m-10) REVERT: A 307 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7706 (tpt) REVERT: A 342 PHE cc_start: 0.7777 (t80) cc_final: 0.7083 (m-10) REVERT: A 349 TRP cc_start: 0.9130 (m-10) cc_final: 0.8771 (m-10) REVERT: A 393 ILE cc_start: 0.8428 (mm) cc_final: 0.7990 (mt) REVERT: A 397 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 458 MET cc_start: 0.7778 (tpt) cc_final: 0.7494 (tpt) REVERT: A 460 LEU cc_start: 0.8564 (mp) cc_final: 0.8322 (tt) REVERT: A 508 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8609 (t) REVERT: A 538 PHE cc_start: 0.8634 (t80) cc_final: 0.8179 (t80) REVERT: A 581 LEU cc_start: 0.8978 (mt) cc_final: 0.8602 (tt) REVERT: A 599 LEU cc_start: 0.8860 (tp) cc_final: 0.8297 (tt) REVERT: B 354 MET cc_start: 0.7432 (ttp) cc_final: 0.6864 (tmm) REVERT: B 438 TYR cc_start: 0.7907 (m-80) cc_final: 0.7516 (m-10) REVERT: B 462 TYR cc_start: 0.8583 (t80) cc_final: 0.8097 (t80) REVERT: B 516 LYS cc_start: 0.7345 (mttt) cc_final: 0.6910 (mmtt) REVERT: B 539 MET cc_start: 0.8817 (mtp) cc_final: 0.8561 (ttm) REVERT: B 549 CYS cc_start: 0.8831 (m) cc_final: 0.8485 (m) outliers start: 35 outliers final: 29 residues processed: 175 average time/residue: 0.1415 time to fit residues: 34.4306 Evaluate side-chains 175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122996 restraints weight = 9225.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126341 restraints weight = 5814.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128325 restraints weight = 4420.372| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.8012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5564 Z= 0.133 Angle : 0.669 10.366 7568 Z= 0.331 Chirality : 0.039 0.236 930 Planarity : 0.004 0.025 860 Dihedral : 4.755 30.978 836 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.20 % Allowed : 26.85 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.34), residues: 642 helix: 2.93 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.00 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.002 0.000 HIS B 330 PHE 0.030 0.001 PHE B 342 TYR 0.020 0.002 TYR B 351 ARG 0.004 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 428) hydrogen bonds : angle 3.84315 ( 1260) covalent geometry : bond 0.00295 ( 5564) covalent geometry : angle 0.66887 ( 7568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.27 seconds wall clock time: 35 minutes 56.99 seconds (2156.99 seconds total)