Starting phenix.real_space_refine on Wed Jul 1 21:03:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uhb_26511/07_2026/7uhb_26511.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.069 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 1373 2.51 5 N 358 2.21 5 O 399 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2141 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1510 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 593 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" 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: 0.82, per 1000 atoms: 0.38 Number of scatterers: 2141 At special positions: 0 Unit cell: (57, 57, 77, 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 399 8.00 N 358 7.00 C 1373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.08 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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 A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN C 343 " Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 50.5 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 37.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.874A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.387A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'K' and resid 2 through 20 removed outlier: 3.780A pdb=" N VAL K 9 " --> pdb=" O GLN K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 23 No H-bonds generated for 'chain 'K' and resid 21 through 23' Processing helix chain 'K' and resid 26 through 49 removed outlier: 4.041A pdb=" N LEU K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 74 removed outlier: 3.624A pdb=" N GLU K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU K 72 " --> pdb=" O HIS K 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 94 hydrogen bonds defined for protein. 243 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: 0.18 Time building geometry restraints manager: 0.19 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: 461 1.33 - 1.45: 585 1.45 - 1.58: 1133 1.58 - 1.71: 0 1.71 - 1.84: 14 Bond restraints: 2193 Sorted by residual: bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" CA CYS C 336 " pdb=" C CYS C 336 " ideal model delta sigma weight residual 1.528 1.497 0.030 1.08e-02 8.57e+03 7.78e+00 bond pdb=" C5 FUC A 3 " pdb=" O5 FUC A 3 " ideal model delta sigma weight residual 1.423 1.476 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" CG ASP K 11 " pdb=" OD1 ASP K 11 " ideal model delta sigma weight residual 1.249 1.199 0.050 1.90e-02 2.77e+03 6.98e+00 bond pdb=" CA LYS K 48 " pdb=" C LYS K 48 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.35e-02 5.49e+03 6.70e+00 ... (remaining 2188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 2925 3.61 - 7.22: 49 7.22 - 10.83: 6 10.83 - 14.43: 2 14.43 - 18.04: 2 Bond angle restraints: 2984 Sorted by residual: angle pdb=" N ASN C 388 " pdb=" CA ASN C 388 " pdb=" C ASN C 388 " ideal model delta sigma weight residual 113.01 126.98 -13.97 1.20e+00 6.94e-01 1.36e+02 angle pdb=" C LEU C 387 " pdb=" CA LEU C 387 " pdb=" CB LEU C 387 " ideal model delta sigma weight residual 110.68 128.72 -18.04 1.70e+00 3.46e-01 1.13e+02 angle pdb=" N ASN C 388 " pdb=" CA ASN C 388 " pdb=" CB ASN C 388 " ideal model delta sigma weight residual 110.39 93.68 16.71 1.75e+00 3.27e-01 9.12e+01 angle pdb=" N LYS K 48 " pdb=" CA LYS K 48 " pdb=" C LYS K 48 " ideal model delta sigma weight residual 111.82 121.75 -9.93 1.16e+00 7.43e-01 7.33e+01 angle pdb=" N SER K 49 " pdb=" CA SER K 49 " pdb=" C SER K 49 " ideal model delta sigma weight residual 110.35 120.84 -10.49 1.38e+00 5.25e-01 5.77e+01 ... (remaining 2979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 1213 16.63 - 33.25: 51 33.25 - 49.88: 8 49.88 - 66.51: 1 66.51 - 83.14: 2 Dihedral angle restraints: 1275 sinusoidal: 483 harmonic: 792 Sorted by residual: dihedral pdb=" C LYS K 48 " pdb=" N LYS K 48 " pdb=" CA LYS K 48 " pdb=" CB LYS K 48 " ideal model delta harmonic sigma weight residual -122.60 -156.03 33.43 0 2.50e+00 1.60e-01 1.79e+02 dihedral pdb=" C LEU C 387 " pdb=" N LEU C 387 " pdb=" CA LEU C 387 " pdb=" CB LEU C 387 " ideal model delta harmonic sigma weight residual -122.60 -153.09 30.49 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N LYS K 48 " pdb=" C LYS K 48 " pdb=" CA LYS K 48 " pdb=" CB LYS K 48 " ideal model delta harmonic sigma weight residual 122.80 152.94 -30.14 0 2.50e+00 1.60e-01 1.45e+02 ... (remaining 1272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 331 0.275 - 0.550: 1 0.550 - 0.825: 0 0.825 - 1.100: 0 1.100 - 1.375: 2 Chirality restraints: 334 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.04e+01 chirality pdb=" CA LYS K 48 " pdb=" N LYS K 48 " pdb=" C LYS K 48 " pdb=" CB LYS K 48 " both_signs ideal model delta sigma weight residual False 2.51 1.14 1.38 2.00e-01 2.50e+01 4.73e+01 chirality pdb=" CA LEU C 387 " pdb=" N LEU C 387 " pdb=" C LEU C 387 " pdb=" CB LEU C 387 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.56e+01 ... (remaining 331 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 495 " 0.034 2.00e-02 2.50e+03 1.74e-02 6.07e+00 pdb=" CG TYR C 495 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 495 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 495 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 495 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 495 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 505 " 0.024 2.00e-02 2.50e+03 1.26e-02 3.16e+00 pdb=" CG TYR C 505 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 505 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 505 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 505 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 505 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 505 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 505 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 505 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C TYR C 505 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR C 505 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN C 506 " -0.008 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1220 3.03 - 3.50: 1963 3.50 - 3.96: 3487 3.96 - 4.43: 4061 4.43 - 4.90: 6324 Nonbonded interactions: 17055 Sorted by model distance: nonbonded pdb=" N ASN C 334 " pdb=" OD1 ASN C 334 " model vdw 2.562 3.120 nonbonded pdb=" N ASN C 370 " pdb=" N SER C 371 " model vdw 2.580 2.560 nonbonded pdb=" N SER C 373 " pdb=" N PHE C 374 " model vdw 2.585 2.560 nonbonded pdb=" N LYS C 386 " pdb=" N LEU C 387 " model vdw 2.598 2.560 nonbonded pdb=" N ASP C 428 " pdb=" OD1 ASP C 428 " model vdw 2.599 3.120 ... (remaining 17050 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: 5.530 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: 0.000 Process input model: 3.260 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: 0.000 Load rotamer database and sin/cos tables:5.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 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 : 0.012 0.072 2200 Z= 0.636 Angle : 1.377 18.043 3001 Z= 0.926 Chirality : 0.123 1.375 334 Planarity : 0.005 0.017 384 Dihedral : 9.917 83.136 755 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.62 % Rotamer: Outliers : 1.42 % Allowed : 1.42 % Favored : 97.16 % Cbeta Deviations : 1.18 % 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 (0.47), residues: 266 helix: -1.36 (0.48), residues: 93 sheet: 1.09 (0.73), residues: 49 loop : 0.06 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 509 TYR 0.034 0.005 TYR C 495 PHE 0.014 0.003 PHE C 392 TRP 0.015 0.004 TRP C 353 HIS 0.003 0.001 HIS K 8 Details of bonding type rmsd/Z covalent geometry : bond 0.01136 / 0.63 ( 2193) covalent geometry : angle 1.36429 / 0.92 ( 2984) SS BOND : bond 0.02642 / 1.26 ( 4) SS BOND : angle 3.25619 / 1.85 ( 8) hydrogen bonds : bond 0.20539 / 13.24 ( 94) hydrogen bonds : angle 7.17655 / 4.80 ( 243) link_BETA1-4 : bond 0.07207 / 3.79 ( 1) link_BETA1-4 : angle 2.70408 / 1.30 ( 3) link_BETA1-6 : bond 0.03473 / 1.83 ( 1) link_BETA1-6 : angle 0.48289 / 0.28 ( 3) link_NAG-ASN : bond 0.05175 / 2.72 ( 1) link_NAG-ASN : angle 2.96894 / 1.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 55 average time/residue: 0.3856 time to fit residues: 21.6150 Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.0770 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.155208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130310 restraints weight = 2392.466| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.95 r_work: 0.3222 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 2200 Z= 0.257 Angle : 0.833 8.183 3001 Z= 0.424 Chirality : 0.048 0.156 334 Planarity : 0.007 0.054 384 Dihedral : 5.112 17.719 297 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.84 % Allowed : 9.48 % Favored : 87.68 % 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: -0.32 (0.48), residues: 266 helix: -0.83 (0.54), residues: 92 sheet: 1.36 (0.74), residues: 46 loop : -0.20 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 457 TYR 0.029 0.003 TYR C 495 PHE 0.017 0.003 PHE C 392 TRP 0.018 0.002 TRP C 436 HIS 0.009 0.003 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 ( 2193) covalent geometry : angle 0.82748 / 0.42 ( 2984) SS BOND : bond 0.00648 / 0.31 ( 4) SS BOND : angle 1.52932 / 0.85 ( 8) hydrogen bonds : bond 0.04952 / 3.15 ( 94) hydrogen bonds : angle 5.94304 / 3.87 ( 243) link_BETA1-4 : bond 0.00018 / 0.01 ( 1) link_BETA1-4 : angle 1.33023 / 0.66 ( 3) link_BETA1-6 : bond 0.01076 / 0.57 ( 1) link_BETA1-6 : angle 1.21303 / 0.62 ( 3) link_NAG-ASN : bond 0.00870 / 0.46 ( 1) link_NAG-ASN : angle 1.89357 / 1.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7502 (ptmt) REVERT: C 442 ASP cc_start: 0.7546 (m-30) cc_final: 0.7343 (m-30) REVERT: K 7 MET cc_start: 0.7545 (mmm) cc_final: 0.7315 (tmm) REVERT: K 45 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6147 (mm-30) REVERT: K 70 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7416 (mt-10) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.4402 time to fit residues: 21.4803 Evaluate side-chains 41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.2698 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.154958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126866 restraints weight = 2310.413| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.05 r_work: 0.3103 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.7410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2200 Z= 0.150 Angle : 0.602 7.168 3001 Z= 0.321 Chirality : 0.043 0.146 334 Planarity : 0.005 0.037 384 Dihedral : 4.138 16.080 297 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.74 % Allowed : 14.69 % Favored : 80.57 % 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: 0.39 (0.49), residues: 266 helix: 0.45 (0.56), residues: 90 sheet: 1.38 (0.72), residues: 46 loop : -0.21 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 466 TYR 0.022 0.002 TYR C 495 PHE 0.006 0.001 PHE C 338 TRP 0.009 0.002 TRP C 436 HIS 0.005 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 2193) covalent geometry : angle 0.59926 / 0.32 ( 2984) SS BOND : bond 0.00159 / 0.08 ( 4) SS BOND : angle 0.83081 / 0.41 ( 8) hydrogen bonds : bond 0.04563 / 2.98 ( 94) hydrogen bonds : angle 4.95675 / 3.25 ( 243) link_BETA1-4 : bond 0.00714 / 0.38 ( 1) link_BETA1-4 : angle 1.00083 / 0.49 ( 3) link_BETA1-6 : bond 0.00580 / 0.31 ( 1) link_BETA1-6 : angle 1.11400 / 0.61 ( 3) link_NAG-ASN : bond 0.00061 / 0.03 ( 1) link_NAG-ASN : angle 1.22022 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: C 356 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8239 (tttt) REVERT: C 391 CYS cc_start: 0.7890 (m) cc_final: 0.7574 (m) REVERT: C 409 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: C 442 ASP cc_start: 0.8020 (m-30) cc_final: 0.7731 (m-30) REVERT: K 43 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6677 (mmt) REVERT: K 45 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6338 (mp0) REVERT: K 63 ARG cc_start: 0.7104 (tpp-160) cc_final: 0.6609 (mtt-85) REVERT: K 70 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7603 (mt-10) outliers start: 10 outliers final: 3 residues processed: 42 average time/residue: 0.5654 time to fit residues: 24.1832 Evaluate side-chains 41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.0170 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.142488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114901 restraints weight = 2342.476| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.94 r_work: 0.3073 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.8886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 2200 Z= 0.165 Angle : 0.571 6.681 3001 Z= 0.300 Chirality : 0.042 0.176 334 Planarity : 0.005 0.046 384 Dihedral : 4.352 16.828 297 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.74 % Allowed : 13.27 % Favored : 81.99 % 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: 0.77 (0.49), residues: 266 helix: 0.81 (0.56), residues: 86 sheet: 1.32 (0.72), residues: 46 loop : 0.13 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 466 TYR 0.019 0.002 TYR C 495 PHE 0.013 0.001 PHE C 486 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 2193) covalent geometry : angle 0.56339 / 0.30 ( 2984) SS BOND : bond 0.00198 / 0.10 ( 4) SS BOND : angle 1.35390 / 0.75 ( 8) hydrogen bonds : bond 0.04096 / 2.72 ( 94) hydrogen bonds : angle 4.74878 / 3.13 ( 243) link_BETA1-4 : bond 0.00529 / 0.28 ( 1) link_BETA1-4 : angle 0.99028 / 0.47 ( 3) link_BETA1-6 : bond 0.00247 / 0.13 ( 1) link_BETA1-6 : angle 0.82860 / 0.45 ( 3) link_NAG-ASN : bond 0.00440 / 0.23 ( 1) link_NAG-ASN : angle 2.04609 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: C 472 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7528 (mm) REVERT: C 474 GLN cc_start: 0.8543 (tt0) cc_final: 0.8208 (tt0) REVERT: K 45 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6491 (mp0) REVERT: K 46 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6939 (tt) REVERT: K 63 ARG cc_start: 0.7319 (tpp-160) cc_final: 0.6865 (mtt-85) outliers start: 10 outliers final: 1 residues processed: 49 average time/residue: 0.5979 time to fit residues: 29.8553 Evaluate side-chains 44 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113026 restraints weight = 2355.880| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.80 r_work: 0.3014 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 1.0023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2200 Z= 0.178 Angle : 0.592 6.593 3001 Z= 0.309 Chirality : 0.044 0.172 334 Planarity : 0.004 0.043 384 Dihedral : 4.301 15.959 297 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.21 % Allowed : 17.54 % Favored : 77.25 % 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: 0.46 (0.48), residues: 266 helix: 0.81 (0.54), residues: 86 sheet: 1.07 (0.75), residues: 49 loop : -0.26 (0.48), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 466 TYR 0.018 0.002 TYR C 495 PHE 0.010 0.001 PHE C 338 TRP 0.007 0.001 TRP C 353 HIS 0.002 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 2193) covalent geometry : angle 0.58477 / 0.31 ( 2984) SS BOND : bond 0.00195 / 0.09 ( 4) SS BOND : angle 0.91151 / 0.45 ( 8) hydrogen bonds : bond 0.04569 / 3.01 ( 94) hydrogen bonds : angle 4.75903 / 3.14 ( 243) link_BETA1-4 : bond 0.00585 / 0.31 ( 1) link_BETA1-4 : angle 1.50046 / 0.73 ( 3) link_BETA1-6 : bond 0.00411 / 0.22 ( 1) link_BETA1-6 : angle 1.07077 / 0.57 ( 3) link_NAG-ASN : bond 0.00011 / 0.01 ( 1) link_NAG-ASN : angle 2.28309 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: C 409 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8929 (mt0) REVERT: C 472 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7897 (mm) REVERT: K 7 MET cc_start: 0.8152 (mmm) cc_final: 0.7901 (tpp) REVERT: K 45 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6718 (mp0) REVERT: K 63 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.7455 (mtt-85) outliers start: 11 outliers final: 4 residues processed: 51 average time/residue: 0.6031 time to fit residues: 31.3233 Evaluate side-chains 48 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 22 optimal weight: 0.0980 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.0020 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110679 restraints weight = 2339.158| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.89 r_work: 0.3038 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 1.0166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2200 Z= 0.120 Angle : 0.511 5.849 3001 Z= 0.273 Chirality : 0.041 0.167 334 Planarity : 0.004 0.043 384 Dihedral : 4.097 16.211 297 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.32 % Allowed : 19.91 % Favored : 76.78 % 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: 0.91 (0.49), residues: 266 helix: 1.51 (0.57), residues: 80 sheet: 0.77 (0.74), residues: 49 loop : 0.09 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 466 TYR 0.012 0.001 TYR C 495 PHE 0.004 0.001 PHE C 338 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 2193) covalent geometry : angle 0.50140 / 0.27 ( 2984) SS BOND : bond 0.00318 / 0.15 ( 4) SS BOND : angle 1.58920 / 0.81 ( 8) hydrogen bonds : bond 0.03832 / 2.48 ( 94) hydrogen bonds : angle 4.64322 / 3.06 ( 243) link_BETA1-4 : bond 0.00474 / 0.25 ( 1) link_BETA1-4 : angle 0.81030 / 0.43 ( 3) link_BETA1-6 : bond 0.00373 / 0.20 ( 1) link_BETA1-6 : angle 1.14499 / 0.63 ( 3) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 1.41549 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: C 472 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (mm) REVERT: C 474 GLN cc_start: 0.8565 (tt0) cc_final: 0.8268 (tt0) REVERT: K 7 MET cc_start: 0.8189 (mmm) cc_final: 0.7972 (tpp) REVERT: K 45 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6518 (mp0) REVERT: K 63 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7429 (mtt-85) outliers start: 7 outliers final: 1 residues processed: 46 average time/residue: 0.6323 time to fit residues: 29.6134 Evaluate side-chains 42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 0 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN K 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106591 restraints weight = 2347.982| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.88 r_work: 0.2969 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 1.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2200 Z= 0.195 Angle : 0.580 6.262 3001 Z= 0.307 Chirality : 0.044 0.184 334 Planarity : 0.004 0.043 384 Dihedral : 4.288 16.111 297 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.27 % Allowed : 19.43 % Favored : 76.30 % 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: 0.60 (0.48), residues: 266 helix: 1.12 (0.54), residues: 86 sheet: 0.65 (0.74), residues: 49 loop : -0.10 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 466 TYR 0.017 0.002 TYR C 495 PHE 0.006 0.001 PHE C 338 TRP 0.006 0.001 TRP C 353 HIS 0.002 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 ( 2193) covalent geometry : angle 0.56856 / 0.30 ( 2984) SS BOND : bond 0.00528 / 0.25 ( 4) SS BOND : angle 1.98055 / 1.01 ( 8) hydrogen bonds : bond 0.04387 / 2.94 ( 94) hydrogen bonds : angle 4.76070 / 3.15 ( 243) link_BETA1-4 : bond 0.00633 / 0.33 ( 1) link_BETA1-4 : angle 1.01760 / 0.52 ( 3) link_BETA1-6 : bond 0.00308 / 0.16 ( 1) link_BETA1-6 : angle 1.17065 / 0.63 ( 3) link_NAG-ASN : bond 0.00080 / 0.04 ( 1) link_NAG-ASN : angle 1.58672 / 0.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: C 357 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7784 (ttt-90) REVERT: C 406 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: C 472 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8053 (mm) REVERT: C 474 GLN cc_start: 0.8637 (tt0) cc_final: 0.8309 (tt0) REVERT: K 15 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7112 (mt-10) REVERT: K 45 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6735 (mp0) REVERT: K 63 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7504 (mtt-85) outliers start: 9 outliers final: 4 residues processed: 44 average time/residue: 0.6371 time to fit residues: 28.5447 Evaluate side-chains 47 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110363 restraints weight = 2350.407| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.91 r_work: 0.3076 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 1.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2200 Z= 0.114 Angle : 0.487 5.642 3001 Z= 0.266 Chirality : 0.041 0.163 334 Planarity : 0.004 0.043 384 Dihedral : 3.992 15.396 297 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.90 % Allowed : 21.33 % Favored : 76.78 % 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 (0.49), residues: 266 helix: 1.58 (0.56), residues: 80 sheet: 0.66 (0.74), residues: 49 loop : 0.10 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 466 TYR 0.010 0.001 TYR C 495 PHE 0.005 0.001 PHE C 347 TRP 0.008 0.001 TRP C 353 HIS 0.001 0.000 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 2193) covalent geometry : angle 0.47876 / 0.26 ( 2984) SS BOND : bond 0.00344 / 0.16 ( 4) SS BOND : angle 1.35890 / 0.69 ( 8) hydrogen bonds : bond 0.03665 / 2.38 ( 94) hydrogen bonds : angle 4.65220 / 3.08 ( 243) link_BETA1-4 : bond 0.00560 / 0.29 ( 1) link_BETA1-4 : angle 0.88343 / 0.48 ( 3) link_BETA1-6 : bond 0.00307 / 0.16 ( 1) link_BETA1-6 : angle 1.18389 / 0.65 ( 3) link_NAG-ASN : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : angle 1.33559 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: C 472 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7923 (mm) REVERT: C 474 GLN cc_start: 0.8655 (tt0) cc_final: 0.8292 (tt0) REVERT: K 15 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6990 (mt-10) REVERT: K 45 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6486 (mp0) REVERT: K 63 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.7458 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 42 average time/residue: 0.6335 time to fit residues: 27.0660 Evaluate side-chains 42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108213 restraints weight = 2376.945| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.93 r_work: 0.2983 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 1.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2200 Z= 0.140 Angle : 0.517 5.670 3001 Z= 0.279 Chirality : 0.042 0.169 334 Planarity : 0.004 0.042 384 Dihedral : 4.026 15.457 297 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.27 % Allowed : 18.96 % Favored : 76.78 % 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 (0.49), residues: 266 helix: 1.70 (0.57), residues: 80 sheet: 0.49 (0.72), residues: 49 loop : 0.16 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.013 0.001 TYR C 495 PHE 0.004 0.001 PHE C 490 TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 2193) covalent geometry : angle 0.50754 / 0.28 ( 2984) SS BOND : bond 0.00379 / 0.18 ( 4) SS BOND : angle 1.54931 / 0.79 ( 8) hydrogen bonds : bond 0.03899 / 2.60 ( 94) hydrogen bonds : angle 4.65376 / 3.08 ( 243) link_BETA1-4 : bond 0.00533 / 0.28 ( 1) link_BETA1-4 : angle 0.96831 / 0.51 ( 3) link_BETA1-6 : bond 0.00315 / 0.17 ( 1) link_BETA1-6 : angle 1.19967 / 0.65 ( 3) link_NAG-ASN : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : angle 1.36659 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: C 357 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7821 (ttt-90) REVERT: C 406 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: C 472 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8026 (mm) REVERT: C 474 GLN cc_start: 0.8661 (tt0) cc_final: 0.8288 (tt0) REVERT: K 15 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7047 (mt-10) REVERT: K 45 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6512 (mp0) REVERT: K 63 ARG cc_start: 0.7719 (tpp-160) cc_final: 0.7504 (mtt-85) outliers start: 9 outliers final: 4 residues processed: 43 average time/residue: 0.6117 time to fit residues: 26.7944 Evaluate side-chains 46 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107484 restraints weight = 2399.312| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.92 r_work: 0.2979 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 1.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2200 Z= 0.211 Angle : 0.601 6.183 3001 Z= 0.319 Chirality : 0.046 0.202 334 Planarity : 0.004 0.044 384 Dihedral : 4.312 15.873 297 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.79 % Allowed : 18.96 % Favored : 77.25 % 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: 0.64 (0.49), residues: 266 helix: 1.35 (0.55), residues: 86 sheet: 0.37 (0.72), residues: 49 loop : -0.08 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 466 TYR 0.017 0.002 TYR C 495 PHE 0.006 0.001 PHE C 429 TRP 0.006 0.002 TRP C 353 HIS 0.003 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 ( 2193) covalent geometry : angle 0.59065 / 0.32 ( 2984) SS BOND : bond 0.00423 / 0.20 ( 4) SS BOND : angle 1.92186 / 1.00 ( 8) hydrogen bonds : bond 0.04547 / 3.05 ( 94) hydrogen bonds : angle 4.79097 / 3.17 ( 243) link_BETA1-4 : bond 0.00608 / 0.32 ( 1) link_BETA1-4 : angle 1.02956 / 0.53 ( 3) link_BETA1-6 : bond 0.00326 / 0.17 ( 1) link_BETA1-6 : angle 1.24964 / 0.68 ( 3) link_NAG-ASN : bond 0.00092 / 0.05 ( 1) link_NAG-ASN : angle 1.50493 / 0.88 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 357 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7846 (ttt-90) REVERT: C 406 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8227 (mm-30) REVERT: C 472 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8118 (mm) REVERT: C 474 GLN cc_start: 0.8718 (tt0) cc_final: 0.8349 (tt0) REVERT: K 15 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7101 (mt-10) REVERT: K 45 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6645 (mp0) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.5603 time to fit residues: 25.6895 Evaluate side-chains 48 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 20 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 23 optimal weight: 0.3980 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN K 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.136972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109057 restraints weight = 2434.672| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.94 r_work: 0.3031 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 1.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2200 Z= 0.102 Angle : 0.482 5.192 3001 Z= 0.266 Chirality : 0.041 0.145 334 Planarity : 0.004 0.042 384 Dihedral : 3.966 15.312 297 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.84 % Allowed : 20.38 % Favored : 76.78 % 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: 0.96 (0.50), residues: 266 helix: 1.70 (0.57), residues: 80 sheet: 0.55 (0.75), residues: 49 loop : 0.12 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.009 0.001 TYR C 505 PHE 0.004 0.001 PHE C 347 TRP 0.009 0.001 TRP C 353 HIS 0.001 0.000 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 2193) covalent geometry : angle 0.47449 / 0.26 ( 2984) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 1.22415 / 0.62 ( 8) hydrogen bonds : bond 0.03625 / 2.37 ( 94) hydrogen bonds : angle 4.69500 / 3.11 ( 243) link_BETA1-4 : bond 0.00494 / 0.26 ( 1) link_BETA1-4 : angle 0.97280 / 0.53 ( 3) link_BETA1-6 : bond 0.00288 / 0.15 ( 1) link_BETA1-6 : angle 1.18543 / 0.65 ( 3) link_NAG-ASN : bond 0.00026 / 0.01 ( 1) link_NAG-ASN : angle 1.36481 / 0.78 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1086.99 seconds wall clock time: 19 minutes 14.08 seconds (1154.08 seconds total)