Starting phenix.real_space_refine on Tue Mar 3 10:54:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uhb_26511/03_2026/7uhb_26511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhb_26511/03_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_26511/03_2026/7uhb_26511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhb_26511/03_2026/7uhb_26511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uhb_26511/03_2026/7uhb_26511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhb_26511/03_2026/7uhb_26511.map" } 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-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.69, per 1000 atoms: 0.32 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: 0.17 Conformation dependent library (CDL) restraints added in 77.2 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: 0.05 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: 0.28 Time building geometry restraints manager: 0.21 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: 1271 16.63 - 33.25: 52 33.25 - 49.88: 8 49.88 - 66.51: 1 66.51 - 83.14: 2 Dihedral angle restraints: 1334 sinusoidal: 542 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 1331 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: 2.110 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.240 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 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 : 9.643 83.136 814 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 covalent geometry : bond 0.01136 ( 2193) covalent geometry : angle 1.36429 ( 2984) SS BOND : bond 0.02642 ( 4) SS BOND : angle 3.25619 ( 8) hydrogen bonds : bond 0.20539 ( 94) hydrogen bonds : angle 7.17655 ( 243) link_BETA1-4 : bond 0.07207 ( 1) link_BETA1-4 : angle 2.70408 ( 3) link_BETA1-6 : bond 0.03473 ( 1) link_BETA1-6 : angle 0.48289 ( 3) link_NAG-ASN : bond 0.05175 ( 1) link_NAG-ASN : angle 2.96894 ( 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 : 0.066 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: 0.5922 time to fit residues: 33.1377 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 : 0.049 ------------------------------------------------------------------------------- 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: 0.6980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.149458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123686 restraints weight = 2406.886| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.04 r_work: 0.3312 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4689 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= 0.186 Angle : 0.664 6.902 3001 Z= 0.349 Chirality : 0.045 0.145 334 Planarity : 0.006 0.038 384 Dihedral : 4.702 16.405 356 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.37 % Allowed : 10.43 % Favored : 87.20 % 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: 0.20 (0.50), residues: 266 helix: -0.32 (0.56), residues: 92 sheet: 1.70 (0.75), residues: 46 loop : 0.03 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 74 TYR 0.024 0.002 TYR C 495 PHE 0.010 0.002 PHE C 338 TRP 0.014 0.002 TRP C 436 HIS 0.011 0.003 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 2193) covalent geometry : angle 0.66100 ( 2984) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.84220 ( 8) hydrogen bonds : bond 0.04657 ( 94) hydrogen bonds : angle 5.58520 ( 243) link_BETA1-4 : bond 0.00068 ( 1) link_BETA1-4 : angle 1.20472 ( 3) link_BETA1-6 : bond 0.00867 ( 1) link_BETA1-6 : angle 1.03303 ( 3) link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 1.47697 ( 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 51 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 356 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6991 (ptmt) REVERT: C 442 ASP cc_start: 0.6604 (m-30) cc_final: 0.6359 (m-30) REVERT: K 45 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5846 (mm-30) REVERT: K 70 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7369 (mt-10) REVERT: K 72 LEU cc_start: 0.5937 (mt) cc_final: 0.5718 (mt) outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.6809 time to fit residues: 32.4956 Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LYS 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: 0.0570 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.152227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124112 restraints weight = 2338.183| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.06 r_work: 0.3267 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2200 Z= 0.166 Angle : 0.583 6.991 3001 Z= 0.312 Chirality : 0.043 0.141 334 Planarity : 0.005 0.036 384 Dihedral : 4.261 17.086 356 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.27 % Allowed : 13.74 % 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: 0.50 (0.49), residues: 266 helix: 0.30 (0.56), residues: 94 sheet: 1.25 (0.72), residues: 48 loop : 0.14 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 357 TYR 0.026 0.002 TYR C 495 PHE 0.009 0.001 PHE C 515 TRP 0.016 0.002 TRP C 353 HIS 0.006 0.002 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2193) covalent geometry : angle 0.57891 ( 2984) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.79738 ( 8) hydrogen bonds : bond 0.04820 ( 94) hydrogen bonds : angle 4.87486 ( 243) link_BETA1-4 : bond 0.00806 ( 1) link_BETA1-4 : angle 1.28749 ( 3) link_BETA1-6 : bond 0.00818 ( 1) link_BETA1-6 : angle 1.09089 ( 3) link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 1.29204 ( 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 49 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: C 356 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8110 (ttpp) REVERT: C 391 CYS cc_start: 0.7700 (m) cc_final: 0.7407 (m) REVERT: C 406 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: C 415 THR cc_start: 0.8294 (p) cc_final: 0.8021 (m) REVERT: C 442 ASP cc_start: 0.7834 (m-30) cc_final: 0.7518 (m-30) REVERT: C 474 GLN cc_start: 0.8400 (tt0) cc_final: 0.8025 (tt0) REVERT: K 21 LEU cc_start: 0.8215 (mt) cc_final: 0.8014 (mp) REVERT: K 45 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6218 (mp0) REVERT: K 63 ARG cc_start: 0.7054 (tpp-160) cc_final: 0.6519 (mtt-85) outliers start: 9 outliers final: 2 residues processed: 44 average time/residue: 0.6677 time to fit residues: 29.8564 Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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 406 GLU 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: 0.3980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 12 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115516 restraints weight = 2346.908| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.99 r_work: 0.3101 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.8991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2200 Z= 0.164 Angle : 0.594 7.551 3001 Z= 0.307 Chirality : 0.042 0.185 334 Planarity : 0.005 0.049 384 Dihedral : 4.476 16.453 356 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.74 % Allowed : 13.74 % Favored : 81.52 % 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: 0.70 (0.49), residues: 266 helix: 0.86 (0.57), residues: 86 sheet: 1.17 (0.72), residues: 48 loop : 0.03 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 357 TYR 0.023 0.002 TYR C 495 PHE 0.020 0.001 PHE C 486 TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2193) covalent geometry : angle 0.58418 ( 2984) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.75462 ( 8) hydrogen bonds : bond 0.04005 ( 94) hydrogen bonds : angle 4.63184 ( 243) link_BETA1-4 : bond 0.00272 ( 1) link_BETA1-4 : angle 1.27597 ( 3) link_BETA1-6 : bond 0.00697 ( 1) link_BETA1-6 : angle 0.94150 ( 3) link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.57724 ( 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 54 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: C 472 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7560 (mm) REVERT: K 7 MET cc_start: 0.7871 (mmm) cc_final: 0.7603 (tpp) REVERT: K 45 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6408 (mp0) REVERT: K 63 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.6961 (mtt-85) REVERT: K 69 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7825 (mt) outliers start: 10 outliers final: 1 residues processed: 48 average time/residue: 0.5635 time to fit residues: 27.5519 Evaluate side-chains 43 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.055 ------------------------------------------------------------------------------- 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 69 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: 1.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112691 restraints weight = 2367.221| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.94 r_work: 0.3138 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.9676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2200 Z= 0.143 Angle : 0.528 6.113 3001 Z= 0.283 Chirality : 0.041 0.142 334 Planarity : 0.004 0.046 384 Dihedral : 4.140 16.557 356 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.74 % Allowed : 18.01 % 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: 0.69 (0.49), residues: 266 helix: 1.01 (0.56), residues: 86 sheet: 0.99 (0.73), residues: 48 loop : -0.02 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.016 0.001 TYR C 495 PHE 0.007 0.001 PHE C 377 TRP 0.006 0.001 TRP C 436 HIS 0.005 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2193) covalent geometry : angle 0.52404 ( 2984) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.84940 ( 8) hydrogen bonds : bond 0.04002 ( 94) hydrogen bonds : angle 4.57792 ( 243) link_BETA1-4 : bond 0.00554 ( 1) link_BETA1-4 : angle 1.01314 ( 3) link_BETA1-6 : bond 0.00465 ( 1) link_BETA1-6 : angle 1.06853 ( 3) link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 1.30563 ( 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 51 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: C 472 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7681 (mm) REVERT: K 45 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6415 (mp0) REVERT: K 63 ARG cc_start: 0.7517 (tpp-160) cc_final: 0.7124 (mtt-85) REVERT: K 70 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7634 (mt-10) outliers start: 10 outliers final: 3 residues processed: 47 average time/residue: 0.4724 time to fit residues: 22.5587 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 : 0.052 ------------------------------------------------------------------------------- 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 472 ILE 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: 0.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 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 = 0.3535 r_free = 0.3535 target = 0.139946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112348 restraints weight = 2342.376| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.90 r_work: 0.3036 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 1.0094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2200 Z= 0.134 Angle : 0.531 5.928 3001 Z= 0.282 Chirality : 0.042 0.170 334 Planarity : 0.004 0.048 384 Dihedral : 4.444 23.213 356 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.32 % Allowed : 18.96 % Favored : 77.73 % 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: 0.85 (0.49), residues: 266 helix: 1.47 (0.57), residues: 80 sheet: 0.80 (0.74), residues: 49 loop : 0.02 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.014 0.001 TYR C 495 PHE 0.006 0.001 PHE C 377 TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2193) covalent geometry : angle 0.52066 ( 2984) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.14725 ( 8) hydrogen bonds : bond 0.03799 ( 94) hydrogen bonds : angle 4.59910 ( 243) link_BETA1-4 : bond 0.00825 ( 1) link_BETA1-4 : angle 1.03384 ( 3) link_BETA1-6 : bond 0.01006 ( 1) link_BETA1-6 : angle 0.79829 ( 3) link_NAG-ASN : bond 0.00608 ( 1) link_NAG-ASN : angle 2.62724 ( 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 46 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: C 472 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7849 (mm) REVERT: C 474 GLN cc_start: 0.8599 (tt0) cc_final: 0.8295 (tt0) REVERT: K 45 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6487 (mp0) REVERT: K 63 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7461 (mtt-85) REVERT: K 70 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7706 (mt-10) outliers start: 7 outliers final: 3 residues processed: 44 average time/residue: 0.4494 time to fit residues: 20.1472 Evaluate side-chains 43 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 C residue 514 SER 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: 0.0770 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 14 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 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 = 0.3538 r_free = 0.3538 target = 0.140400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112591 restraints weight = 2361.412| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.92 r_work: 0.3023 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 1.0375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2200 Z= 0.128 Angle : 0.513 5.340 3001 Z= 0.275 Chirality : 0.041 0.145 334 Planarity : 0.004 0.050 384 Dihedral : 4.276 21.826 356 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.90 % Allowed : 21.80 % 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: 0.83 (0.49), residues: 266 helix: 1.52 (0.58), residues: 80 sheet: 0.72 (0.75), residues: 49 loop : -0.02 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 357 TYR 0.013 0.001 TYR C 495 PHE 0.006 0.001 PHE C 377 TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2193) covalent geometry : angle 0.50157 ( 2984) SS BOND : bond 0.00126 ( 4) SS BOND : angle 1.16520 ( 8) hydrogen bonds : bond 0.03743 ( 94) hydrogen bonds : angle 4.60135 ( 243) link_BETA1-4 : bond 0.00382 ( 1) link_BETA1-4 : angle 1.07125 ( 3) link_BETA1-6 : bond 0.00323 ( 1) link_BETA1-6 : angle 1.21964 ( 3) link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 2.60049 ( 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 43 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: C 472 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7847 (mm) REVERT: C 474 GLN cc_start: 0.8640 (tt0) cc_final: 0.8321 (tt0) REVERT: K 45 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6396 (mp0) REVERT: K 63 ARG cc_start: 0.7784 (tpp-160) cc_final: 0.7458 (mtt-85) REVERT: K 70 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7753 (mm-30) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.6463 time to fit residues: 27.5836 Evaluate side-chains 43 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 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 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: 0.9990 chunk 15 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 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 = 0.3508 r_free = 0.3508 target = 0.137949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109526 restraints weight = 2399.320| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.96 r_work: 0.3029 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 1.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2200 Z= 0.119 Angle : 0.505 5.067 3001 Z= 0.271 Chirality : 0.042 0.162 334 Planarity : 0.004 0.048 384 Dihedral : 4.229 21.850 356 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.84 % Allowed : 20.85 % 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: 0.92 (0.50), residues: 266 helix: 1.58 (0.59), residues: 80 sheet: 0.72 (0.76), residues: 49 loop : 0.06 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 408 TYR 0.012 0.001 TYR C 495 PHE 0.005 0.001 PHE C 347 TRP 0.006 0.001 TRP C 436 HIS 0.001 0.000 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2193) covalent geometry : angle 0.49617 ( 2984) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.98350 ( 8) hydrogen bonds : bond 0.03580 ( 94) hydrogen bonds : angle 4.56322 ( 243) link_BETA1-4 : bond 0.00452 ( 1) link_BETA1-4 : angle 1.04296 ( 3) link_BETA1-6 : bond 0.00304 ( 1) link_BETA1-6 : angle 1.26188 ( 3) link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 2.21816 ( 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: 6 poor density : 39 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: C 474 GLN cc_start: 0.8587 (tt0) cc_final: 0.8245 (tt0) REVERT: K 43 MET cc_start: 0.8090 (mtt) cc_final: 0.7827 (mtt) REVERT: K 45 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6425 (mp0) REVERT: K 63 ARG cc_start: 0.7727 (tpp-160) cc_final: 0.7418 (mtt-85) REVERT: K 70 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7796 (mm-30) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.5966 time to fit residues: 26.7151 Evaluate side-chains 43 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109587 restraints weight = 2436.281| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.93 r_work: 0.3017 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 1.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2200 Z= 0.126 Angle : 0.518 5.429 3001 Z= 0.278 Chirality : 0.041 0.133 334 Planarity : 0.004 0.054 384 Dihedral : 4.230 21.103 356 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.42 % Allowed : 22.27 % 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: 0.90 (0.50), residues: 266 helix: 1.63 (0.58), residues: 80 sheet: 0.61 (0.75), residues: 49 loop : 0.06 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 357 TYR 0.013 0.001 TYR C 495 PHE 0.006 0.001 PHE C 377 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2193) covalent geometry : angle 0.50838 ( 2984) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.20721 ( 8) hydrogen bonds : bond 0.03639 ( 94) hydrogen bonds : angle 4.60075 ( 243) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 1.05031 ( 3) link_BETA1-6 : bond 0.00246 ( 1) link_BETA1-6 : angle 1.28137 ( 3) link_NAG-ASN : bond 0.00000 ( 1) link_NAG-ASN : angle 2.22730 ( 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 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: C 474 GLN cc_start: 0.8606 (tt0) cc_final: 0.8278 (tt0) REVERT: K 45 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6503 (mp0) REVERT: K 63 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7458 (mtt-85) REVERT: K 70 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7809 (mm-30) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.6379 time to fit residues: 25.3379 Evaluate side-chains 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 406 GLU 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: 0.0010 chunk 24 optimal weight: 0.0370 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3494 r_free = 0.3494 target = 0.136748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108242 restraints weight = 2464.385| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.97 r_work: 0.3074 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 1.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2200 Z= 0.140 Angle : 0.535 5.630 3001 Z= 0.285 Chirality : 0.042 0.167 334 Planarity : 0.004 0.048 384 Dihedral : 4.285 21.054 356 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.37 % Allowed : 21.33 % 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: 0.91 (0.50), residues: 266 helix: 1.64 (0.58), residues: 80 sheet: 0.55 (0.75), residues: 49 loop : 0.09 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 357 TYR 0.014 0.001 TYR C 495 PHE 0.006 0.001 PHE C 347 TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2193) covalent geometry : angle 0.52518 ( 2984) SS BOND : bond 0.00236 ( 4) SS BOND : angle 1.23115 ( 8) hydrogen bonds : bond 0.03749 ( 94) hydrogen bonds : angle 4.59240 ( 243) link_BETA1-4 : bond 0.00474 ( 1) link_BETA1-4 : angle 1.06413 ( 3) link_BETA1-6 : bond 0.00321 ( 1) link_BETA1-6 : angle 1.32986 ( 3) link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 2.18781 ( 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 43 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8189 (mm-30) REVERT: C 474 GLN cc_start: 0.8607 (tt0) cc_final: 0.8232 (tt0) REVERT: K 43 MET cc_start: 0.8081 (mtt) cc_final: 0.7844 (mtt) REVERT: K 45 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6503 (mp0) REVERT: K 63 ARG cc_start: 0.7673 (tpp-160) cc_final: 0.7454 (mtt-85) REVERT: K 70 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7743 (mm-30) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.6734 time to fit residues: 27.3599 Evaluate side-chains 42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3507 r_free = 0.3507 target = 0.137186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109304 restraints weight = 2442.901| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.88 r_work: 0.3003 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 1.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2200 Z= 0.180 Angle : 0.585 5.437 3001 Z= 0.307 Chirality : 0.044 0.161 334 Planarity : 0.004 0.054 384 Dihedral : 4.495 20.934 356 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.32 % Allowed : 20.38 % 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: 0.83 (0.50), residues: 266 helix: 1.61 (0.57), residues: 80 sheet: 0.42 (0.74), residues: 49 loop : 0.05 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.017 0.002 TYR C 495 PHE 0.007 0.001 PHE C 347 TRP 0.005 0.001 TRP C 436 HIS 0.004 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 2193) covalent geometry : angle 0.56979 ( 2984) SS BOND : bond 0.00336 ( 4) SS BOND : angle 2.02967 ( 8) hydrogen bonds : bond 0.04118 ( 94) hydrogen bonds : angle 4.66973 ( 243) link_BETA1-4 : bond 0.00497 ( 1) link_BETA1-4 : angle 1.11013 ( 3) link_BETA1-6 : bond 0.00292 ( 1) link_BETA1-6 : angle 1.35604 ( 3) link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 2.24323 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.95 seconds wall clock time: 19 minutes 26.21 seconds (1166.21 seconds total)