Starting phenix.real_space_refine on Thu Oct 22 18:25:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sf5_54814/10_2026/9sf5_54814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sf5_54814/10_2026/9sf5_54814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sf5_54814/10_2026/9sf5_54814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sf5_54814/10_2026/9sf5_54814.map" model { file = "/net/cci-nas-00/data/ceres_data/9sf5_54814/10_2026/9sf5_54814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sf5_54814/10_2026/9sf5_54814.cif" } resolution = 3.7 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= 0.000 sd= 0.010 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 16 5.16 5 C 2156 2.51 5 N 567 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1607 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 14, 'TRANS': 185} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 960 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.89, per 1000 atoms: 0.26 Number of scatterers: 3388 At special positions: 0 Unit cell: (52.5816, 95.6693, 97.8602, 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 16 16.00 O 649 8.00 N 567 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 340 " " NAG A1302 " - " ASN A 351 " Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 134.9 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 11.9% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.728A pdb=" N PHE A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.661A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.179A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.645A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'L' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.850A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.660A pdb=" N CYS A 358 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.522A pdb=" N ALA H 33 " --> pdb=" O TYR H 101 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.286A pdb=" N ILE H 113 " --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.492A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 23 124 hydrogen bonds defined for protein. 282 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: 0.48 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1070 1.34 - 1.46: 888 1.46 - 1.58: 1504 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3482 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 3477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4468 0.92 - 1.85: 205 1.85 - 2.77: 42 2.77 - 3.69: 18 3.69 - 4.62: 2 Bond angle restraints: 4735 Sorted by residual: angle pdb=" N THR L 51 " pdb=" CA THR L 51 " pdb=" C THR L 51 " ideal model delta sigma weight residual 110.80 115.11 -4.31 2.13e+00 2.20e-01 4.09e+00 angle pdb=" C TYR L 86 " pdb=" N CYS L 87 " pdb=" CA CYS L 87 " ideal model delta sigma weight residual 122.65 120.16 2.49 1.49e+00 4.50e-01 2.79e+00 angle pdb=" C PHE H 111 " pdb=" N ASP H 112 " pdb=" CA ASP H 112 " ideal model delta sigma weight residual 122.79 119.96 2.83 1.70e+00 3.46e-01 2.77e+00 angle pdb=" N VAL L 46 " pdb=" CA VAL L 46 " pdb=" C VAL L 46 " ideal model delta sigma weight residual 109.34 112.75 -3.41 2.08e+00 2.31e-01 2.69e+00 angle pdb=" CA VAL L 46 " pdb=" C VAL L 46 " pdb=" N ILE L 47 " ideal model delta sigma weight residual 116.60 118.89 -2.29 1.45e+00 4.76e-01 2.49e+00 ... (remaining 4730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.15: 1938 13.15 - 26.30: 98 26.30 - 39.45: 24 39.45 - 52.60: 8 52.60 - 65.75: 1 Dihedral angle restraints: 2069 sinusoidal: 829 harmonic: 1240 Sorted by residual: dihedral pdb=" N HIS A 336 " pdb=" CA HIS A 336 " pdb=" CB HIS A 336 " pdb=" CG HIS A 336 " ideal model delta sinusoidal sigma weight residual -180.00 -127.71 -52.29 3 1.50e+01 4.44e-03 9.10e+00 dihedral pdb=" N LYS A 480 " pdb=" CA LYS A 480 " pdb=" CB LYS A 480 " pdb=" CG LYS A 480 " ideal model delta sinusoidal sigma weight residual -180.00 -133.75 -46.25 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" N ASN A 483 " pdb=" CA ASN A 483 " pdb=" CB ASN A 483 " pdb=" CG ASN A 483 " ideal model delta sinusoidal sigma weight residual -180.00 -134.42 -45.58 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 2066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 284 0.024 - 0.049: 134 0.049 - 0.073: 42 0.073 - 0.097: 15 0.097 - 0.122: 34 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA VAL A 379 " pdb=" N VAL A 379 " pdb=" C VAL A 379 " pdb=" CB VAL A 379 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE L 57 " pdb=" N ILE L 57 " pdb=" C ILE L 57 " pdb=" CB ILE L 57 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 506 not shown) Planarity restraints: 609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 370 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 326 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO A 327 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 459 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.73e-01 pdb=" N PRO A 460 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.014 5.00e-02 4.00e+02 ... (remaining 606 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1030 2.82 - 3.34: 2790 3.34 - 3.86: 5448 3.86 - 4.38: 6402 4.38 - 4.90: 11209 Nonbonded interactions: 26879 Sorted by model distance: nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 74 " model vdw 2.303 3.120 nonbonded pdb=" N ASP A 395 " pdb=" OD1 ASP A 395 " model vdw 2.318 3.120 nonbonded pdb=" ND2 ASN A 391 " pdb=" OE1 GLU A 512 " model vdw 2.325 3.120 nonbonded pdb=" NH1 ARG H 52 " pdb=" OG1 THR H 59 " model vdw 2.337 3.120 nonbonded pdb=" NH1 ARG H 69 " pdb=" O SER H 87 " model vdw 2.353 3.120 ... (remaining 26874 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.650 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.630 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.003 0.029 3490 Z= 0.144 Angle : 0.508 5.073 4753 Z= 0.276 Chirality : 0.041 0.122 509 Planarity : 0.004 0.037 607 Dihedral : 8.952 65.746 1267 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.64 % Allowed : 4.66 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.57 (0.43), residues: 424 helix: -2.30 (1.37), residues: 12 sheet: 1.11 (0.44), residues: 143 loop : 0.17 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.009 0.001 TYR A 450 PHE 0.011 0.001 PHE H 50 TRP 0.005 0.001 TRP A 350 HIS 0.002 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 3482) covalent geometry : angle 0.49425 / 0.27 ( 4735) SS BOND : bond 0.00201 / 0.10 ( 6) SS BOND : angle 0.59265 / 0.47 ( 12) hydrogen bonds : bond 0.24203 / 16.87 ( 114) hydrogen bonds : angle 9.40156 / 6.54 ( 282) link_NAG-ASN : bond 0.00425 / 0.22 ( 2) link_NAG-ASN : angle 3.29980 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8872 (ttm170) cc_final: 0.8649 (ttm170) REVERT: A 375 LYS cc_start: 0.7691 (mtpm) cc_final: 0.7368 (mtmt) REVERT: A 380 SER cc_start: 0.9178 (t) cc_final: 0.8794 (p) REVERT: A 464 ASP cc_start: 0.7471 (t0) cc_final: 0.7255 (t0) REVERT: H 37 VAL cc_start: 0.9172 (t) cc_final: 0.8887 (m) REVERT: H 96 TYR cc_start: 0.8288 (m-80) cc_final: 0.8040 (m-80) REVERT: L 35 TYR cc_start: 0.8443 (m-80) cc_final: 0.7726 (m-80) outliers start: 6 outliers final: 2 residues processed: 124 average time/residue: 0.0710 time to fit residues: 10.4688 Evaluate side-chains 84 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 395 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143189 restraints weight = 4620.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147263 restraints weight = 5737.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148632 restraints weight = 4084.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148929 restraints weight = 2642.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150030 restraints weight = 2599.693| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3490 Z= 0.247 Angle : 0.651 6.581 4753 Z= 0.337 Chirality : 0.048 0.240 509 Planarity : 0.005 0.043 607 Dihedral : 5.481 34.663 521 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.29 % Allowed : 14.79 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.41 (0.43), residues: 424 helix: -2.69 (1.14), residues: 12 sheet: 1.08 (0.45), residues: 142 loop : 0.02 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 343 TYR 0.016 0.002 TYR A 450 PHE 0.013 0.002 PHE H 50 TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 ( 3482) covalent geometry : angle 0.63535 / 0.33 ( 4735) SS BOND : bond 0.00291 / 0.15 ( 6) SS BOND : angle 1.51277 / 1.14 ( 12) hydrogen bonds : bond 0.04407 / 2.83 ( 114) hydrogen bonds : angle 6.70649 / 4.68 ( 282) link_NAG-ASN : bond 0.00238 / 0.12 ( 2) link_NAG-ASN : angle 3.61276 / 1.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.7627 (mtpm) cc_final: 0.7355 (mtmt) REVERT: A 380 SER cc_start: 0.9166 (t) cc_final: 0.8865 (p) REVERT: A 497 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8509 (m-10) REVERT: H 36 TRP cc_start: 0.8440 (m100) cc_final: 0.8109 (m100) REVERT: H 37 VAL cc_start: 0.9092 (t) cc_final: 0.8845 (m) REVERT: L 88 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8582 (tm-30) REVERT: L 102 LYS cc_start: 0.8619 (tppt) cc_final: 0.7980 (tttm) outliers start: 12 outliers final: 10 residues processed: 99 average time/residue: 0.0741 time to fit residues: 8.7592 Evaluate side-chains 96 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [5, 37, 25, 8, 36, 39, 33, 12, 17, 18, 10] chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.0570 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 ASN H 86 ASN H 102 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146157 restraints weight = 4604.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150232 restraints weight = 6016.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152888 restraints weight = 4261.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152715 restraints weight = 2797.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153517 restraints weight = 2945.601| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3490 Z= 0.121 Angle : 0.558 5.931 4753 Z= 0.289 Chirality : 0.045 0.168 509 Planarity : 0.004 0.040 607 Dihedral : 5.010 33.857 519 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.84 % Allowed : 15.62 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.18 (0.42), residues: 424 helix: -2.50 (1.25), residues: 12 sheet: 0.67 (0.43), residues: 154 loop : -0.02 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 69 TYR 0.010 0.001 TYR L 86 PHE 0.022 0.002 PHE H 29 TRP 0.016 0.001 TRP H 47 HIS 0.002 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 3482) covalent geometry : angle 0.53890 / 0.28 ( 4735) SS BOND : bond 0.00151 / 0.09 ( 6) SS BOND : angle 1.84199 / 1.50 ( 12) hydrogen bonds : bond 0.03417 / 2.18 ( 114) hydrogen bonds : angle 6.12526 / 4.25 ( 282) link_NAG-ASN : bond 0.00325 / 0.17 ( 2) link_NAG-ASN : angle 3.30858 / 1.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 SER cc_start: 0.9116 (t) cc_final: 0.8786 (p) REVERT: L 35 TYR cc_start: 0.8469 (m-80) cc_final: 0.7542 (m-80) REVERT: L 37 GLN cc_start: 0.7696 (tt0) cc_final: 0.7399 (tt0) REVERT: L 88 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8465 (tm-30) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.0699 time to fit residues: 8.7018 Evaluate side-chains 100 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [26, 3, 10, 16, 18, 34, 27, 37, 0, 41, 31] chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 27 optimal weight: 0.1980 chunk 37 optimal weight: 0.0670 chunk 0 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** L 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145653 restraints weight = 4455.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144989 restraints weight = 4767.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148870 restraints weight = 3949.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149055 restraints weight = 2473.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149800 restraints weight = 2520.174| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3490 Z= 0.106 Angle : 0.556 5.993 4753 Z= 0.284 Chirality : 0.044 0.136 509 Planarity : 0.005 0.050 607 Dihedral : 4.826 34.563 519 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.29 % Allowed : 18.63 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.12 (0.41), residues: 424 helix: -2.31 (1.34), residues: 12 sheet: 0.69 (0.43), residues: 152 loop : -0.12 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.007 0.001 TYR H 32 PHE 0.021 0.001 PHE H 29 TRP 0.023 0.002 TRP H 36 HIS 0.001 0.000 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 3482) covalent geometry : angle 0.54264 / 0.28 ( 4735) SS BOND : bond 0.00117 / 0.07 ( 6) SS BOND : angle 1.25709 / 0.96 ( 12) hydrogen bonds : bond 0.03099 / 1.91 ( 114) hydrogen bonds : angle 5.70759 / 3.96 ( 282) link_NAG-ASN : bond 0.00335 / 0.17 ( 2) link_NAG-ASN : angle 3.10139 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8739 (ttm170) cc_final: 0.8490 (ttm170) REVERT: A 380 SER cc_start: 0.9161 (t) cc_final: 0.8799 (p) REVERT: A 497 TYR cc_start: 0.8850 (m-10) cc_final: 0.8495 (m-10) REVERT: L 37 GLN cc_start: 0.7752 (tt0) cc_final: 0.7509 (tt0) REVERT: L 88 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.0561 time to fit residues: 7.0219 Evaluate side-chains 98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [31, 30, 15, 7, 8, 9, 17, 20, 2, 36, 32] chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.180921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147480 restraints weight = 4492.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150845 restraints weight = 5509.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153760 restraints weight = 3890.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155766 restraints weight = 2647.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156373 restraints weight = 2454.686| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3490 Z= 0.156 Angle : 0.569 5.002 4753 Z= 0.294 Chirality : 0.044 0.131 509 Planarity : 0.005 0.048 607 Dihedral : 4.895 35.727 519 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.38 % Allowed : 19.18 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.06 (0.41), residues: 424 helix: -2.29 (1.34), residues: 12 sheet: 0.86 (0.44), residues: 140 loop : -0.27 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.009 0.001 TYR H 32 PHE 0.015 0.002 PHE H 70 TRP 0.031 0.002 TRP H 36 HIS 0.002 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 3482) covalent geometry : angle 0.55243 / 0.29 ( 4735) SS BOND : bond 0.00288 / 0.15 ( 6) SS BOND : angle 1.69436 / 1.31 ( 12) hydrogen bonds : bond 0.03200 / 1.95 ( 114) hydrogen bonds : angle 5.66523 / 3.95 ( 282) link_NAG-ASN : bond 0.00268 / 0.14 ( 2) link_NAG-ASN : angle 3.15849 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8377 (ttm170) REVERT: A 380 SER cc_start: 0.9172 (t) cc_final: 0.8833 (p) REVERT: A 497 TYR cc_start: 0.8806 (m-10) cc_final: 0.8426 (m-10) REVERT: L 88 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8272 (tm-30) outliers start: 16 outliers final: 15 residues processed: 94 average time/residue: 0.0641 time to fit residues: 7.5569 Evaluate side-chains 99 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [4, 9, 12, 14, 34, 2, 41, 31, 7, 29, 15] chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.0010 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146882 restraints weight = 4444.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146085 restraints weight = 5362.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150131 restraints weight = 4372.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150077 restraints weight = 2716.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151404 restraints weight = 2783.086| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3490 Z= 0.106 Angle : 0.533 5.004 4753 Z= 0.274 Chirality : 0.043 0.130 509 Planarity : 0.004 0.048 607 Dihedral : 4.670 35.934 519 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.38 % Allowed : 19.45 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.16 (0.41), residues: 424 helix: -1.19 (2.21), residues: 6 sheet: 0.70 (0.44), residues: 144 loop : -0.15 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.007 0.001 TYR H 32 PHE 0.014 0.001 PHE H 29 TRP 0.027 0.002 TRP H 36 HIS 0.001 0.000 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 3482) covalent geometry : angle 0.52013 / 0.27 ( 4735) SS BOND : bond 0.00209 / 0.10 ( 6) SS BOND : angle 1.24472 / 0.94 ( 12) hydrogen bonds : bond 0.02902 / 1.81 ( 114) hydrogen bonds : angle 5.42017 / 3.76 ( 282) link_NAG-ASN : bond 0.00300 / 0.16 ( 2) link_NAG-ASN : angle 2.86802 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8553 (ttm170) REVERT: A 380 SER cc_start: 0.9138 (t) cc_final: 0.8789 (p) REVERT: A 497 TYR cc_start: 0.8839 (m-10) cc_final: 0.8470 (m-10) REVERT: H 19 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7647 (mmm160) REVERT: L 88 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8421 (tm-30) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.0579 time to fit residues: 6.8880 Evaluate side-chains 97 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [37, 22, 28, 19, 4, 14, 36, 34, 24, 21, 17] chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145584 restraints weight = 4590.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149387 restraints weight = 5113.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150854 restraints weight = 3958.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151100 restraints weight = 2694.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152022 restraints weight = 2646.966| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3490 Z= 0.168 Angle : 0.580 5.941 4753 Z= 0.300 Chirality : 0.046 0.324 509 Planarity : 0.005 0.044 607 Dihedral : 4.874 36.811 519 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.84 % Allowed : 21.10 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.09 (0.41), residues: 424 helix: -2.35 (1.30), residues: 12 sheet: 0.64 (0.43), residues: 144 loop : -0.32 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.016 0.001 TYR H 32 PHE 0.015 0.002 PHE H 70 TRP 0.035 0.002 TRP H 36 HIS 0.003 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 3482) covalent geometry : angle 0.56580 / 0.30 ( 4735) SS BOND : bond 0.00325 / 0.16 ( 6) SS BOND : angle 1.43160 / 1.15 ( 12) hydrogen bonds : bond 0.03169 / 1.96 ( 114) hydrogen bonds : angle 5.47862 / 3.82 ( 282) link_NAG-ASN : bond 0.00203 / 0.11 ( 2) link_NAG-ASN : angle 3.06129 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8802 (ttm170) cc_final: 0.7924 (ttm170) REVERT: A 380 SER cc_start: 0.9176 (t) cc_final: 0.8850 (p) REVERT: A 497 TYR cc_start: 0.8870 (m-10) cc_final: 0.8455 (m-10) REVERT: H 6 GLU cc_start: 0.7914 (mp0) cc_final: 0.7637 (mt-10) outliers start: 14 outliers final: 13 residues processed: 93 average time/residue: 0.0629 time to fit residues: 7.1903 Evaluate side-chains 97 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [1, 9, 34, 28, 15, 17, 38, 21, 22, 19, 33] chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** 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 = 0.4097 r_free = 0.4097 target = 0.182659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149166 restraints weight = 4563.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151129 restraints weight = 5277.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153540 restraints weight = 4318.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153682 restraints weight = 2788.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154489 restraints weight = 2775.691| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3490 Z= 0.123 Angle : 0.584 7.112 4753 Z= 0.296 Chirality : 0.046 0.312 509 Planarity : 0.005 0.048 607 Dihedral : 4.767 36.434 519 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.11 % Allowed : 20.55 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.41), residues: 424 helix: -2.29 (1.34), residues: 12 sheet: 0.65 (0.44), residues: 142 loop : -0.33 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 19 TYR 0.014 0.001 TYR H 32 PHE 0.013 0.001 PHE H 70 TRP 0.025 0.002 TRP H 36 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 3482) covalent geometry : angle 0.57343 / 0.29 ( 4735) SS BOND : bond 0.00269 / 0.13 ( 6) SS BOND : angle 1.17011 / 0.91 ( 12) hydrogen bonds : bond 0.03045 / 1.92 ( 114) hydrogen bonds : angle 5.38235 / 3.74 ( 282) link_NAG-ASN : bond 0.00257 / 0.13 ( 2) link_NAG-ASN : angle 2.88644 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8767 (ttm170) cc_final: 0.8367 (ttm170) REVERT: A 380 SER cc_start: 0.9150 (t) cc_final: 0.8831 (p) REVERT: A 403 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 497 TYR cc_start: 0.8806 (m-10) cc_final: 0.8456 (m-10) REVERT: L 35 TYR cc_start: 0.8373 (m-80) cc_final: 0.7708 (m-80) outliers start: 15 outliers final: 14 residues processed: 91 average time/residue: 0.0582 time to fit residues: 6.7013 Evaluate side-chains 97 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [10, 33, 23, 12, 36, 0, 13, 39, 5, 34, 4] chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 102 HIS ** 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 = 0.4081 r_free = 0.4081 target = 0.181097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145935 restraints weight = 4520.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151023 restraints weight = 5192.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152970 restraints weight = 3802.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153130 restraints weight = 2524.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154178 restraints weight = 2470.029| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3490 Z= 0.150 Angle : 0.583 6.418 4753 Z= 0.300 Chirality : 0.046 0.301 509 Planarity : 0.005 0.045 607 Dihedral : 4.839 36.822 519 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.38 % Allowed : 19.73 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.20 (0.40), residues: 424 helix: -2.26 (1.34), residues: 12 sheet: 0.62 (0.44), residues: 141 loop : -0.41 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.014 0.001 TYR H 32 PHE 0.012 0.002 PHE H 29 TRP 0.036 0.002 TRP H 36 HIS 0.003 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 3482) covalent geometry : angle 0.57080 / 0.30 ( 4735) SS BOND : bond 0.00291 / 0.14 ( 6) SS BOND : angle 1.27201 / 1.00 ( 12) hydrogen bonds : bond 0.03139 / 1.97 ( 114) hydrogen bonds : angle 5.40421 / 3.76 ( 282) link_NAG-ASN : bond 0.00216 / 0.11 ( 2) link_NAG-ASN : angle 2.96128 / 1.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 SER cc_start: 0.9171 (t) cc_final: 0.8836 (p) REVERT: A 403 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 497 TYR cc_start: 0.8865 (m-10) cc_final: 0.8411 (m-10) REVERT: L 35 TYR cc_start: 0.8413 (m-80) cc_final: 0.7726 (m-80) outliers start: 16 outliers final: 16 residues processed: 90 average time/residue: 0.0636 time to fit residues: 7.0776 Evaluate side-chains 100 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [4, 13, 7, 35, 21, 6, 30, 1, 22, 8, 14] chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** 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 = 0.4078 r_free = 0.4078 target = 0.180907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146528 restraints weight = 4438.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151269 restraints weight = 5351.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153643 restraints weight = 3748.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153529 restraints weight = 2524.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154340 restraints weight = 2563.128| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3490 Z= 0.143 Angle : 0.590 6.596 4753 Z= 0.302 Chirality : 0.046 0.294 509 Planarity : 0.005 0.047 607 Dihedral : 4.808 36.470 519 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.38 % Allowed : 20.27 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.40), residues: 424 helix: -2.28 (1.33), residues: 12 sheet: 0.54 (0.43), residues: 141 loop : -0.44 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 19 TYR 0.013 0.001 TYR H 32 PHE 0.012 0.002 PHE H 70 TRP 0.033 0.002 TRP H 36 HIS 0.002 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 3482) covalent geometry : angle 0.57837 / 0.30 ( 4735) SS BOND : bond 0.00286 / 0.14 ( 6) SS BOND : angle 1.21493 / 0.95 ( 12) hydrogen bonds : bond 0.03105 / 1.95 ( 114) hydrogen bonds : angle 5.40315 / 3.76 ( 282) link_NAG-ASN : bond 0.00195 / 0.10 ( 2) link_NAG-ASN : angle 2.90168 / 1.45 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ARG cc_start: 0.8767 (ttm170) cc_final: 0.7930 (ttm170) REVERT: A 380 SER cc_start: 0.9159 (t) cc_final: 0.8837 (p) REVERT: A 497 TYR cc_start: 0.8841 (m-10) cc_final: 0.8389 (m-10) REVERT: L 35 TYR cc_start: 0.8387 (m-80) cc_final: 0.7724 (m-80) outliers start: 16 outliers final: 15 residues processed: 96 average time/residue: 0.0605 time to fit residues: 7.1306 Evaluate side-chains 101 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [13, 31, 11, 1, 41, 33, 36, 25, 32, 14, 39] chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.177990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144255 restraints weight = 4571.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144931 restraints weight = 5705.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148366 restraints weight = 4505.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148595 restraints weight = 2936.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149574 restraints weight = 3172.728| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 3490 Z= 0.249 Angle : 0.660 6.255 4753 Z= 0.343 Chirality : 0.048 0.302 509 Planarity : 0.006 0.067 607 Dihedral : 5.236 37.566 519 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.11 % Allowed : 20.82 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.47 (0.40), residues: 424 helix: -2.94 (0.94), residues: 20 sheet: 0.68 (0.43), residues: 139 loop : -0.64 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 19 TYR 0.014 0.002 TYR H 32 PHE 0.013 0.002 PHE A 426 TRP 0.039 0.003 TRP H 47 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 ( 3482) covalent geometry : angle 0.64600 / 0.34 ( 4735) SS BOND : bond 0.00419 / 0.22 ( 6) SS BOND : angle 1.62070 / 1.26 ( 12) hydrogen bonds : bond 0.03538 / 2.18 ( 114) hydrogen bonds : angle 5.68381 / 3.97 ( 282) link_NAG-ASN : bond 0.00046 / 0.02 ( 2) link_NAG-ASN : angle 3.28238 / 1.68 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 959.47 seconds wall clock time: 17 minutes 5.32 seconds (1025.32 seconds total)