Starting phenix.real_space_refine on Thu Sep 10 19:50:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzu_22574/09_2026/7jzu_22574.cif" } resolution = 3.1 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= 0.031 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 11 5.16 5 C 1270 2.51 5 N 325 2.21 5 O 381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1987 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1512 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.78, per 1000 atoms: 0.39 Number of scatterers: 1987 At special positions: 0 Unit cell: (59.85, 71.4, 66.15, 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 11 16.00 O 381 8.00 N 325 7.00 C 1270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.16 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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 BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN B 343 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 70.0 milliseconds 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 462 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 36.7% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.566A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.781A pdb=" N LEU A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 removed outlier: 4.251A pdb=" N GLU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.716A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.979A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.459A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.944A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.591A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 80 hydrogen bonds defined for protein. 204 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: 0.34 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 571 1.33 - 1.46: 603 1.46 - 1.59: 846 1.59 - 1.73: 0 1.73 - 1.86: 14 Bond restraints: 2034 Sorted by residual: bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ASN B 487 " pdb=" CG ASN B 487 " ideal model delta sigma weight residual 1.516 1.442 0.074 2.50e-02 1.60e+03 8.85e+00 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.03e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" C5 FUC C 3 " pdb=" O5 FUC C 3 " ideal model delta sigma weight residual 1.423 1.476 -0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 2029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 2134 1.42 - 2.85: 499 2.85 - 4.27: 87 4.27 - 5.70: 31 5.70 - 7.12: 9 Bond angle restraints: 2760 Sorted by residual: angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.07 -6.51 1.02e+00 9.61e-01 4.08e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.95 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C LEU B 425 " pdb=" N PRO B 426 " pdb=" CA PRO B 426 " ideal model delta sigma weight residual 120.03 126.20 -6.17 9.90e-01 1.02e+00 3.89e+01 angle pdb=" C THR B 478 " pdb=" N PRO B 479 " pdb=" CA PRO B 479 " ideal model delta sigma weight residual 119.78 126.05 -6.27 1.03e+00 9.43e-01 3.71e+01 angle pdb=" C ALA B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 119.76 125.81 -6.05 1.03e+00 9.43e-01 3.45e+01 ... (remaining 2755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 1111 13.82 - 27.64: 51 27.64 - 41.46: 17 41.46 - 55.27: 4 55.27 - 69.09: 2 Dihedral angle restraints: 1185 sinusoidal: 460 harmonic: 725 Sorted by residual: dihedral pdb=" C TYR B 495 " pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " ideal model delta harmonic sigma weight residual -122.60 -114.96 -7.64 0 2.50e+00 1.60e-01 9.34e+00 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 116.81 -23.81 1 1.00e+01 1.00e-02 8.17e+00 dihedral pdb=" CB GLU B 484 " pdb=" CG GLU B 484 " pdb=" CD GLU B 484 " pdb=" OE1 GLU B 484 " ideal model delta sinusoidal sigma weight residual 0.00 69.09 -69.09 1 3.00e+01 1.11e-03 6.86e+00 ... (remaining 1182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 199 0.074 - 0.149: 81 0.149 - 0.223: 18 0.223 - 0.298: 4 0.298 - 0.372: 2 Chirality restraints: 304 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.72e+01 chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.21e+01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.86 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 301 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.043 2.00e-02 2.50e+03 2.19e-02 9.57e+00 pdb=" CG TYR B 495 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " 0.025 2.00e-02 2.50e+03 1.47e-02 4.34e+00 pdb=" CG TYR B 449 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 505 " -0.026 2.00e-02 2.50e+03 1.45e-02 4.23e+00 pdb=" CG TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 505 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 505 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 505 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 505 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 505 " -0.023 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1044 2.99 - 3.47: 1816 3.47 - 3.94: 3369 3.94 - 4.42: 3931 4.42 - 4.90: 6085 Nonbonded interactions: 16245 Sorted by model distance: nonbonded pdb=" N ALA B 520 " pdb=" O ALA B 520 " model vdw 2.509 2.496 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.573 3.120 nonbonded pdb=" N ASN B 440 " pdb=" OD1 ASN B 440 " model vdw 2.586 3.120 nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.597 2.496 nonbonded pdb=" N GLN B 506 " pdb=" O GLN B 506 " model vdw 2.617 2.496 ... (remaining 16240 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.740 Find NCS groups from input model: 0.010 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:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.015 0.126 2041 Z= 0.818 Angle : 1.357 7.124 2777 Z= 0.905 Chirality : 0.085 0.372 304 Planarity : 0.005 0.022 355 Dihedral : 9.687 69.093 711 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.23 (0.52), residues: 244 helix: -1.00 (0.53), residues: 78 sheet: 0.98 (0.75), residues: 49 loop : 0.87 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.043 0.006 TYR B 495 PHE 0.014 0.003 PHE B 497 TRP 0.020 0.006 TRP B 353 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.01477 / 0.80 ( 2034) covalent geometry : angle 1.34354 / 0.90 ( 2760) SS BOND : bond 0.07104 / 3.52 ( 4) SS BOND : angle 2.48932 / 1.34 ( 8) hydrogen bonds : bond 0.18316 / 11.94 ( 80) hydrogen bonds : angle 8.72729 / 6.14 ( 204) link_BETA1-4 : bond 0.07263 / 3.82 ( 1) link_BETA1-4 : angle 3.79002 / 2.15 ( 3) link_BETA1-6 : bond 0.05027 / 2.65 ( 1) link_BETA1-6 : angle 2.19551 / 1.19 ( 3) link_NAG-ASN : bond 0.05641 / 2.97 ( 1) link_NAG-ASN : angle 2.67644 / 2.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.080 Fit side-chains REVERT: B 361 CYS cc_start: 0.6296 (p) cc_final: 0.5722 (p) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0733 time to fit residues: 4.1189 Evaluate side-chains 32 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN B 487 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.158934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145787 restraints weight = 2303.600| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.16 r_work: 0.3508 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2041 Z= 0.148 Angle : 0.581 6.117 2777 Z= 0.303 Chirality : 0.044 0.164 304 Planarity : 0.004 0.038 355 Dihedral : 4.346 13.449 275 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 4.90 % Favored : 93.63 % 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: 0.52 (0.54), residues: 244 helix: 0.02 (0.59), residues: 79 sheet: 0.63 (0.79), residues: 48 loop : 0.69 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.024 0.002 TYR B 505 PHE 0.013 0.001 PHE B 497 TRP 0.007 0.001 TRP B 436 HIS 0.005 0.003 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 2034) covalent geometry : angle 0.57435 / 0.30 ( 2760) SS BOND : bond 0.00105 / 0.05 ( 4) SS BOND : angle 0.42837 / 0.20 ( 8) hydrogen bonds : bond 0.05375 / 3.53 ( 80) hydrogen bonds : angle 6.35161 / 4.58 ( 204) link_BETA1-4 : bond 0.00440 / 0.23 ( 1) link_BETA1-4 : angle 1.79861 / 1.43 ( 3) link_BETA1-6 : bond 0.00034 / 0.02 ( 1) link_BETA1-6 : angle 1.50029 / 1.11 ( 3) link_NAG-ASN : bond 0.00088 / 0.05 ( 1) link_NAG-ASN : angle 1.70362 / 1.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.086 Fit side-chains REVERT: A 13 MET cc_start: 0.8530 (ptm) cc_final: 0.8037 (ptt) REVERT: A 29 SER cc_start: 0.8227 (t) cc_final: 0.7774 (p) REVERT: B 361 CYS cc_start: 0.7406 (p) cc_final: 0.6765 (p) outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 0.0582 time to fit residues: 3.1037 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 0 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS B 487 ASN B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.157160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147245 restraints weight = 2283.576| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 0.80 r_work: 0.3564 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2041 Z= 0.193 Angle : 0.586 4.759 2777 Z= 0.304 Chirality : 0.045 0.145 304 Planarity : 0.005 0.051 355 Dihedral : 4.305 13.337 275 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.45 % Allowed : 6.37 % Favored : 91.18 % 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: 0.42 (0.55), residues: 244 helix: 0.34 (0.61), residues: 81 sheet: 0.26 (0.75), residues: 48 loop : 0.44 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 403 TYR 0.026 0.002 TYR B 495 PHE 0.011 0.002 PHE B 456 TRP 0.007 0.001 TRP B 436 HIS 0.004 0.002 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 2034) covalent geometry : angle 0.57362 / 0.30 ( 2760) SS BOND : bond 0.00259 / 0.13 ( 4) SS BOND : angle 0.94325 / 0.72 ( 8) hydrogen bonds : bond 0.04663 / 3.15 ( 80) hydrogen bonds : angle 5.94900 / 4.27 ( 204) link_BETA1-4 : bond 0.00357 / 0.19 ( 1) link_BETA1-4 : angle 2.18560 / 1.59 ( 3) link_BETA1-6 : bond 0.00005 / 0.00 ( 1) link_BETA1-6 : angle 1.56654 / 0.96 ( 3) link_NAG-ASN : bond 0.00321 / 0.17 ( 1) link_NAG-ASN : angle 2.38869 / 2.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.077 Fit side-chains REVERT: A 29 SER cc_start: 0.8330 (t) cc_final: 0.7857 (p) REVERT: B 361 CYS cc_start: 0.7376 (p) cc_final: 0.6768 (p) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.0707 time to fit residues: 3.2771 Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0870 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 20 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 22 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 overall best weight: 0.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.166340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150246 restraints weight = 2300.055| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.64 r_work: 0.3595 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2041 Z= 0.125 Angle : 0.505 3.715 2777 Z= 0.261 Chirality : 0.043 0.130 304 Planarity : 0.004 0.050 355 Dihedral : 4.047 13.858 275 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 7.84 % Favored : 90.20 % 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: 0.75 (0.55), residues: 244 helix: 1.04 (0.65), residues: 73 sheet: 0.12 (0.74), residues: 48 loop : 0.50 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.017 0.001 TYR B 495 PHE 0.004 0.001 PHE B 497 TRP 0.008 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2034) covalent geometry : angle 0.49646 / 0.26 ( 2760) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.83760 / 0.70 ( 8) hydrogen bonds : bond 0.03846 / 2.62 ( 80) hydrogen bonds : angle 5.62052 / 4.08 ( 204) link_BETA1-4 : bond 0.00371 / 0.20 ( 1) link_BETA1-4 : angle 1.57466 / 1.19 ( 3) link_BETA1-6 : bond 0.00195 / 0.10 ( 1) link_BETA1-6 : angle 1.25838 / 0.82 ( 3) link_NAG-ASN : bond 0.00092 / 0.05 ( 1) link_NAG-ASN : angle 1.82597 / 1.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.083 Fit side-chains REVERT: A 29 SER cc_start: 0.8360 (t) cc_final: 0.7761 (p) REVERT: B 361 CYS cc_start: 0.7770 (p) cc_final: 0.7147 (p) REVERT: B 380 TYR cc_start: 0.8566 (m-80) cc_final: 0.8355 (m-80) REVERT: B 467 ASP cc_start: 0.7001 (t0) cc_final: 0.6761 (t0) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.0594 time to fit residues: 2.8966 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.0770 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.2980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147501 restraints weight = 2284.889| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.62 r_work: 0.3576 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2041 Z= 0.165 Angle : 0.556 6.583 2777 Z= 0.281 Chirality : 0.044 0.131 304 Planarity : 0.004 0.052 355 Dihedral : 4.159 13.660 275 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 8.33 % Favored : 89.71 % 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: 0.66 (0.56), residues: 244 helix: 1.16 (0.64), residues: 73 sheet: -0.18 (0.75), residues: 50 loop : 0.42 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 14 TYR 0.023 0.002 TYR B 495 PHE 0.009 0.001 PHE B 456 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 2034) covalent geometry : angle 0.54371 / 0.28 ( 2760) SS BOND : bond 0.00347 / 0.17 ( 4) SS BOND : angle 1.01750 / 0.82 ( 8) hydrogen bonds : bond 0.04026 / 2.70 ( 80) hydrogen bonds : angle 5.69969 / 4.12 ( 204) link_BETA1-4 : bond 0.00339 / 0.18 ( 1) link_BETA1-4 : angle 2.27648 / 1.71 ( 3) link_BETA1-6 : bond 0.00225 / 0.12 ( 1) link_BETA1-6 : angle 1.19932 / 0.76 ( 3) link_NAG-ASN : bond 0.00331 / 0.17 ( 1) link_NAG-ASN : angle 2.29669 / 2.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7169 (m-30) cc_final: 0.6594 (m-30) REVERT: A 29 SER cc_start: 0.8422 (t) cc_final: 0.7845 (p) REVERT: B 380 TYR cc_start: 0.8578 (m-80) cc_final: 0.8375 (m-80) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.0491 time to fit residues: 2.5145 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.0970 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.0020 chunk 4 optimal weight: 0.6980 chunk 23 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.3307 > 50:) chunk 12 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 overall best weight: 0.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149308 restraints weight = 2292.756| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.65 r_work: 0.3597 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2041 Z= 0.115 Angle : 0.509 7.454 2777 Z= 0.254 Chirality : 0.043 0.121 304 Planarity : 0.004 0.049 355 Dihedral : 3.905 13.695 275 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.96 % Allowed : 10.78 % Favored : 87.25 % 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: 0.89 (0.56), residues: 244 helix: 1.88 (0.68), residues: 67 sheet: -0.27 (0.75), residues: 51 loop : 0.39 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.014 0.001 TYR B 495 PHE 0.005 0.001 PHE B 400 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 2034) covalent geometry : angle 0.50051 / 0.25 ( 2760) SS BOND : bond 0.00174 / 0.08 ( 4) SS BOND : angle 0.90582 / 0.82 ( 8) hydrogen bonds : bond 0.03463 / 2.35 ( 80) hydrogen bonds : angle 5.58484 / 4.04 ( 204) link_BETA1-4 : bond 0.00400 / 0.21 ( 1) link_BETA1-4 : angle 1.73591 / 1.31 ( 3) link_BETA1-6 : bond 0.00302 / 0.16 ( 1) link_BETA1-6 : angle 1.08919 / 0.79 ( 3) link_NAG-ASN : bond 0.00038 / 0.02 ( 1) link_NAG-ASN : angle 1.69841 / 1.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.076 Fit side-chains REVERT: A 17 ASP cc_start: 0.7106 (m-30) cc_final: 0.6533 (m-30) REVERT: A 29 SER cc_start: 0.8317 (t) cc_final: 0.7838 (p) REVERT: A 55 GLU cc_start: 0.5995 (mt-10) cc_final: 0.5598 (mt-10) REVERT: B 361 CYS cc_start: 0.7773 (p) cc_final: 0.7153 (p) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.0586 time to fit residues: 2.9587 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 9 optimal weight: 0.1980 chunk 12 optimal weight: 0.0970 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 overall best weight: 0.1496 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.165432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148919 restraints weight = 2284.653| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.65 r_work: 0.3593 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2041 Z= 0.120 Angle : 0.504 7.842 2777 Z= 0.252 Chirality : 0.043 0.122 304 Planarity : 0.004 0.050 355 Dihedral : 3.870 13.795 275 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 10.78 % Favored : 87.75 % 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: 0.90 (0.57), residues: 244 helix: 2.02 (0.69), residues: 67 sheet: -0.29 (0.75), residues: 51 loop : 0.33 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.017 0.001 TYR B 495 PHE 0.007 0.001 PHE B 456 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 2034) covalent geometry : angle 0.49412 / 0.25 ( 2760) SS BOND : bond 0.00182 / 0.09 ( 4) SS BOND : angle 0.98747 / 0.88 ( 8) hydrogen bonds : bond 0.03388 / 2.30 ( 80) hydrogen bonds : angle 5.54478 / 4.01 ( 204) link_BETA1-4 : bond 0.00352 / 0.19 ( 1) link_BETA1-4 : angle 1.90812 / 1.45 ( 3) link_BETA1-6 : bond 0.00353 / 0.19 ( 1) link_BETA1-6 : angle 1.05805 / 0.78 ( 3) link_NAG-ASN : bond 0.00105 / 0.06 ( 1) link_NAG-ASN : angle 1.80756 / 1.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7025 (m-30) cc_final: 0.6497 (m-30) REVERT: A 29 SER cc_start: 0.8317 (t) cc_final: 0.7847 (p) REVERT: A 55 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5760 (mt-10) outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.0495 time to fit residues: 2.6455 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.0060 chunk 8 optimal weight: 0.1980 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 20 optimal weight: 0.0770 overall best weight: 0.0952 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.167195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150766 restraints weight = 2266.309| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.63 r_work: 0.3613 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2041 Z= 0.095 Angle : 0.486 8.327 2777 Z= 0.240 Chirality : 0.042 0.121 304 Planarity : 0.004 0.050 355 Dihedral : 3.737 13.869 275 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.98 % Allowed : 12.25 % Favored : 86.76 % 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: 0.92 (0.57), residues: 244 helix: 2.00 (0.68), residues: 67 sheet: -0.31 (0.74), residues: 51 loop : 0.37 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.013 0.001 TYR B 495 PHE 0.004 0.001 PHE B 456 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 2034) covalent geometry : angle 0.47848 / 0.24 ( 2760) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 0.93838 / 0.86 ( 8) hydrogen bonds : bond 0.03147 / 2.15 ( 80) hydrogen bonds : angle 5.46816 / 3.97 ( 204) link_BETA1-4 : bond 0.00370 / 0.19 ( 1) link_BETA1-4 : angle 1.60280 / 1.23 ( 3) link_BETA1-6 : bond 0.00371 / 0.20 ( 1) link_BETA1-6 : angle 1.07941 / 0.85 ( 3) link_NAG-ASN : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : angle 1.44593 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.081 Fit side-chains REVERT: A 17 ASP cc_start: 0.7013 (m-30) cc_final: 0.6495 (m-30) REVERT: A 29 SER cc_start: 0.8257 (t) cc_final: 0.7801 (p) REVERT: A 38 LYS cc_start: 0.5858 (mmmt) cc_final: 0.4568 (tptp) REVERT: B 361 CYS cc_start: 0.7715 (p) cc_final: 0.7098 (p) REVERT: B 423 TYR cc_start: 0.8794 (t80) cc_final: 0.8457 (t80) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.0575 time to fit residues: 2.8107 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 1 optimal weight: 0.0980 chunk 13 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.164876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148468 restraints weight = 2257.015| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.64 r_work: 0.3600 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2041 Z= 0.131 Angle : 0.515 8.513 2777 Z= 0.255 Chirality : 0.043 0.120 304 Planarity : 0.004 0.050 355 Dihedral : 3.832 13.704 275 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 10.78 % Favored : 87.25 % 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: 0.97 (0.56), residues: 244 helix: 2.00 (0.69), residues: 67 sheet: 0.02 (0.85), residues: 41 loop : 0.25 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.017 0.002 TYR B 495 PHE 0.007 0.001 PHE B 456 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 2034) covalent geometry : angle 0.50350 / 0.25 ( 2760) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 1.16360 / 1.01 ( 8) hydrogen bonds : bond 0.03379 / 2.30 ( 80) hydrogen bonds : angle 5.56918 / 4.03 ( 204) link_BETA1-4 : bond 0.00340 / 0.18 ( 1) link_BETA1-4 : angle 1.96742 / 1.49 ( 3) link_BETA1-6 : bond 0.00368 / 0.19 ( 1) link_BETA1-6 : angle 0.96064 / 0.76 ( 3) link_NAG-ASN : bond 0.00163 / 0.09 ( 1) link_NAG-ASN : angle 1.91052 / 1.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.061 Fit side-chains REVERT: A 17 ASP cc_start: 0.7048 (m-30) cc_final: 0.6536 (m-30) REVERT: A 29 SER cc_start: 0.8315 (t) cc_final: 0.7848 (p) REVERT: B 361 CYS cc_start: 0.7764 (p) cc_final: 0.7135 (p) REVERT: B 423 TYR cc_start: 0.8833 (t80) cc_final: 0.8538 (t80) outliers start: 4 outliers final: 4 residues processed: 40 average time/residue: 0.0458 time to fit residues: 2.2476 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 chunk 5 optimal weight: 0.0770 chunk 4 optimal weight: 0.0670 chunk 17 optimal weight: 0.0870 overall best weight: 0.0972 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.171171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157238 restraints weight = 2263.957| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.36 r_work: 0.3688 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2041 Z= 0.095 Angle : 0.492 8.680 2777 Z= 0.243 Chirality : 0.042 0.120 304 Planarity : 0.004 0.050 355 Dihedral : 3.720 13.747 275 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.96 % Allowed : 11.27 % Favored : 86.76 % 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: 0.93 (0.56), residues: 244 helix: 2.00 (0.68), residues: 67 sheet: -0.09 (0.84), residues: 41 loop : 0.24 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.013 0.001 TYR B 495 PHE 0.004 0.001 PHE B 456 TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 2034) covalent geometry : angle 0.48386 / 0.24 ( 2760) SS BOND : bond 0.00171 / 0.08 ( 4) SS BOND : angle 1.03002 / 0.95 ( 8) hydrogen bonds : bond 0.03120 / 2.13 ( 80) hydrogen bonds : angle 5.49707 / 3.99 ( 204) link_BETA1-4 : bond 0.00413 / 0.22 ( 1) link_BETA1-4 : angle 1.62889 / 1.27 ( 3) link_BETA1-6 : bond 0.00377 / 0.20 ( 1) link_BETA1-6 : angle 1.04815 / 0.85 ( 3) link_NAG-ASN : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : angle 1.55842 / 1.40 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.044 Fit side-chains REVERT: A 13 MET cc_start: 0.8060 (ttp) cc_final: 0.7821 (ttp) REVERT: A 17 ASP cc_start: 0.7027 (m-30) cc_final: 0.6525 (m-30) REVERT: A 29 SER cc_start: 0.8224 (t) cc_final: 0.7785 (p) REVERT: A 38 LYS cc_start: 0.5844 (mmmt) cc_final: 0.4600 (tptp) REVERT: B 361 CYS cc_start: 0.7560 (p) cc_final: 0.6931 (p) REVERT: B 423 TYR cc_start: 0.8739 (t80) cc_final: 0.8454 (t80) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.0501 time to fit residues: 2.5127 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 5 optimal weight: 0.0770 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 0.0770 overall best weight: 0.0812 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.172591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158648 restraints weight = 2264.508| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.38 r_work: 0.3700 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2041 Z= 0.087 Angle : 0.467 7.990 2777 Z= 0.232 Chirality : 0.042 0.124 304 Planarity : 0.004 0.051 355 Dihedral : 3.600 13.698 275 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.98 % Allowed : 11.76 % Favored : 87.25 % 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: 1.03 (0.55), residues: 244 helix: 2.07 (0.69), residues: 67 sheet: 0.14 (0.86), residues: 39 loop : 0.24 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.013 0.001 TYR B 495 PHE 0.004 0.001 PHE B 377 TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 2034) covalent geometry : angle 0.45923 / 0.23 ( 2760) SS BOND : bond 0.00173 / 0.08 ( 4) SS BOND : angle 0.98320 / 0.88 ( 8) hydrogen bonds : bond 0.02921 / 2.02 ( 80) hydrogen bonds : angle 5.35603 / 3.90 ( 204) link_BETA1-4 : bond 0.00331 / 0.17 ( 1) link_BETA1-4 : angle 1.51236 / 1.22 ( 3) link_BETA1-6 : bond 0.00356 / 0.19 ( 1) link_BETA1-6 : angle 1.06959 / 0.87 ( 3) link_NAG-ASN : bond 0.00042 / 0.02 ( 1) link_NAG-ASN : angle 1.28363 / 1.15 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 942.16 seconds wall clock time: 16 minutes 58.10 seconds (1018.10 seconds total)