Starting phenix.real_space_refine on Thu Jul 2 01:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8idn_35369/07_2026/8idn_35369.cif" } resolution = 3.35 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= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2169 atoms to isotropic. 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 14 5.16 5 C 2092 2.51 5 N 542 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3292 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.95, per 1000 atoms: 0.29 Number of scatterers: 3292 At special positions: 0 Unit cell: (68.34, 73.7, 87.77, 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 14 16.00 O 644 8.00 N 542 7.00 C 2092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN H 79 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 121.8 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 11.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.214A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 4.217A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.628A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.871A pdb=" N LYS H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.746A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 30 through 31 removed outlier: 7.117A pdb=" N VAL H 53 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N MET H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.515A pdb=" N THR L 126 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 106 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP L 56 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.515A pdb=" N THR L 126 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR L 113 " --> pdb=" O HIS L 116 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 0.53 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1043 1.35 - 1.47: 913 1.47 - 1.59: 1401 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3373 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.443 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 4459 1.33 - 2.65: 92 2.65 - 3.98: 29 3.98 - 5.31: 10 5.31 - 6.64: 5 Bond angle restraints: 4595 Sorted by residual: angle pdb=" C ALA L 71 " pdb=" N THR L 72 " pdb=" CA THR L 72 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 106.31 6.64 3.00e+00 1.11e-01 4.89e+00 angle pdb=" CG1 ILE H 49 " pdb=" CB ILE H 49 " pdb=" CG2 ILE H 49 " ideal model delta sigma weight residual 110.70 104.21 6.49 3.00e+00 1.11e-01 4.69e+00 angle pdb=" C3 MAN B 4 " pdb=" C2 MAN B 4 " pdb=" O2 MAN B 4 " ideal model delta sigma weight residual 111.77 105.60 6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 113.24 107.33 5.91 3.00e+00 1.11e-01 3.88e+00 ... (remaining 4590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 1744 15.96 - 31.92: 157 31.92 - 47.87: 34 47.87 - 63.83: 3 63.83 - 79.79: 3 Dihedral angle restraints: 1941 sinusoidal: 741 harmonic: 1200 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 49.97 43.03 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 122.07 -29.07 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CB CYS L 41 " pdb=" SG CYS L 41 " pdb=" SG CYS L 109 " pdb=" CB CYS L 109 " ideal model delta sinusoidal sigma weight residual 93.00 66.41 26.59 1 1.00e+01 1.00e-02 1.02e+01 ... (remaining 1938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 421 0.053 - 0.106: 80 0.106 - 0.159: 15 0.159 - 0.212: 0 0.212 - 0.265: 3 Chirality restraints: 519 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE H 49 " pdb=" CA ILE H 49 " pdb=" CG1 ILE H 49 " pdb=" CG2 ILE H 49 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 79 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 516 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 463 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 60 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.55e-01 pdb=" N PRO L 61 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.006 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE A 347 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 55 2.68 - 3.23: 2959 3.23 - 3.79: 4611 3.79 - 4.34: 6491 4.34 - 4.90: 10839 Nonbonded interactions: 24955 Sorted by model distance: nonbonded pdb=" O TYR H 120 " pdb=" OG SER L 74 " model vdw 2.120 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.153 3.040 nonbonded pdb=" O ALA L 71 " pdb=" OG1 THR L 72 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.262 3.040 nonbonded pdb=" O TRP A 353 " pdb=" NH2 ARG A 466 " model vdw 2.321 3.120 ... (remaining 24950 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3383 Z= 0.134 Angle : 0.590 6.637 4619 Z= 0.281 Chirality : 0.046 0.265 519 Planarity : 0.003 0.036 584 Dihedral : 12.548 79.789 1163 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.36 % Favored : 95.40 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.87 % 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: -0.05 (0.42), residues: 413 helix: -1.63 (1.06), residues: 27 sheet: 1.39 (0.44), residues: 146 loop : -0.79 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.010 0.001 TYR A 505 PHE 0.016 0.001 PHE A 347 TRP 0.006 0.001 TRP H 127 HIS 0.000 0.000 HIS L 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 3373) covalent geometry : angle 0.57889 / 0.28 ( 4595) SS BOND : bond 0.00259 / 0.13 ( 6) SS BOND : angle 1.21775 / 0.79 ( 12) hydrogen bonds : bond 0.27898 / 17.15 ( 108) hydrogen bonds : angle 10.09339 / 7.02 ( 264) link_ALPHA1-3 : bond 0.00321 / 0.17 ( 1) link_ALPHA1-3 : angle 1.70239 / 0.91 ( 3) link_BETA1-4 : bond 0.00329 / 0.16 ( 2) link_BETA1-4 : angle 2.11182 / 1.03 ( 6) link_NAG-ASN : bond 0.00302 / 0.16 ( 1) link_NAG-ASN : angle 2.08253 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.125 Fit side-chains REVERT: A 509 ARG cc_start: 0.6952 (mtt90) cc_final: 0.6531 (mtt90) outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.0598 time to fit residues: 5.7563 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.191688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.149201 restraints weight = 4190.201| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.47 r_work: 0.3714 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3383 Z= 0.125 Angle : 0.594 6.701 4619 Z= 0.319 Chirality : 0.045 0.182 519 Planarity : 0.004 0.036 584 Dihedral : 4.564 50.141 460 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.37 % Rotamer: Outliers : 1.13 % Allowed : 10.73 % Favored : 88.14 % 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: 0.03 (0.42), residues: 413 helix: -1.65 (1.04), residues: 27 sheet: 1.38 (0.43), residues: 145 loop : -0.66 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.010 0.001 TYR A 380 PHE 0.011 0.001 PHE L 65 TRP 0.012 0.001 TRP H 66 HIS 0.001 0.000 HIS L 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 3373) covalent geometry : angle 0.58422 / 0.32 ( 4595) SS BOND : bond 0.00346 / 0.19 ( 6) SS BOND : angle 0.96465 / 0.61 ( 12) hydrogen bonds : bond 0.05075 / 3.27 ( 108) hydrogen bonds : angle 7.00019 / 4.81 ( 264) link_ALPHA1-3 : bond 0.00282 / 0.15 ( 1) link_ALPHA1-3 : angle 1.67089 / 0.90 ( 3) link_BETA1-4 : bond 0.00304 / 0.15 ( 2) link_BETA1-4 : angle 1.97281 / 1.01 ( 6) link_NAG-ASN : bond 0.00393 / 0.21 ( 1) link_NAG-ASN : angle 2.31270 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7751 (m-30) cc_final: 0.7531 (m-30) REVERT: L 75 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7851 (mtp-110) outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.0618 time to fit residues: 5.7218 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN L 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.192913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149649 restraints weight = 4180.487| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.76 r_work: 0.3732 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3383 Z= 0.100 Angle : 0.555 6.999 4619 Z= 0.291 Chirality : 0.043 0.154 519 Planarity : 0.004 0.050 584 Dihedral : 4.229 39.604 458 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 13.84 % Favored : 84.46 % 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: 0.03 (0.42), residues: 413 helix: -1.77 (1.01), residues: 27 sheet: 1.47 (0.43), residues: 146 loop : -0.71 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.012 0.001 TYR L 53 PHE 0.011 0.001 PHE L 65 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS L 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 3373) covalent geometry : angle 0.54692 / 0.29 ( 4595) SS BOND : bond 0.00340 / 0.19 ( 6) SS BOND : angle 0.78956 / 0.51 ( 12) hydrogen bonds : bond 0.04173 / 2.70 ( 108) hydrogen bonds : angle 6.44489 / 4.44 ( 264) link_ALPHA1-3 : bond 0.00461 / 0.24 ( 1) link_ALPHA1-3 : angle 1.36462 / 0.76 ( 3) link_BETA1-4 : bond 0.00374 / 0.18 ( 2) link_BETA1-4 : angle 1.79856 / 0.94 ( 6) link_NAG-ASN : bond 0.00357 / 0.19 ( 1) link_NAG-ASN : angle 2.12121 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.154 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 74 average time/residue: 0.0720 time to fit residues: 6.5244 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 54 ASN H 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.185057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137395 restraints weight = 4195.766| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.50 r_work: 0.3617 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3383 Z= 0.234 Angle : 0.672 7.535 4619 Z= 0.344 Chirality : 0.046 0.161 519 Planarity : 0.005 0.044 584 Dihedral : 4.336 14.986 456 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.08 % Favored : 94.67 % Rotamer: Outliers : 1.98 % Allowed : 13.84 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.42), residues: 413 helix: -1.83 (1.01), residues: 27 sheet: 1.19 (0.43), residues: 143 loop : -0.96 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 75 TYR 0.027 0.002 TYR L 53 PHE 0.021 0.002 PHE L 83 TRP 0.012 0.003 TRP L 112 HIS 0.002 0.001 HIS L 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 3373) covalent geometry : angle 0.66384 / 0.34 ( 4595) SS BOND : bond 0.00360 / 0.19 ( 6) SS BOND : angle 0.95613 / 0.62 ( 12) hydrogen bonds : bond 0.04422 / 2.87 ( 108) hydrogen bonds : angle 6.39135 / 4.40 ( 264) link_ALPHA1-3 : bond 0.00464 / 0.24 ( 1) link_ALPHA1-3 : angle 1.07517 / 0.58 ( 3) link_BETA1-4 : bond 0.00100 / 0.05 ( 2) link_BETA1-4 : angle 2.21453 / 1.10 ( 6) link_NAG-ASN : bond 0.00079 / 0.04 ( 1) link_NAG-ASN : angle 2.55429 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.123 Fit side-chains REVERT: A 398 ASP cc_start: 0.7747 (m-30) cc_final: 0.7334 (m-30) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.0545 time to fit residues: 5.1111 Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.188083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145105 restraints weight = 4214.714| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.23 r_work: 0.3670 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3383 Z= 0.122 Angle : 0.576 6.161 4619 Z= 0.302 Chirality : 0.044 0.155 519 Planarity : 0.004 0.041 584 Dihedral : 4.009 13.456 456 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.37 % Rotamer: Outliers : 3.11 % Allowed : 14.97 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.42), residues: 413 helix: -1.94 (0.98), residues: 27 sheet: 1.13 (0.43), residues: 145 loop : -0.91 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.018 0.001 TYR A 421 PHE 0.008 0.001 PHE L 65 TRP 0.009 0.001 TRP H 127 HIS 0.001 0.001 HIS L 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 3373) covalent geometry : angle 0.56832 / 0.30 ( 4595) SS BOND : bond 0.00532 / 0.26 ( 6) SS BOND : angle 0.64394 / 0.42 ( 12) hydrogen bonds : bond 0.03526 / 2.29 ( 108) hydrogen bonds : angle 6.03193 / 4.15 ( 264) link_ALPHA1-3 : bond 0.00354 / 0.19 ( 1) link_ALPHA1-3 : angle 1.26087 / 0.69 ( 3) link_BETA1-4 : bond 0.00299 / 0.15 ( 2) link_BETA1-4 : angle 1.81873 / 0.93 ( 6) link_NAG-ASN : bond 0.00321 / 0.17 ( 1) link_NAG-ASN : angle 2.47227 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7604 (p-90) REVERT: A 471 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 489 TYR cc_start: 0.7961 (m-10) cc_final: 0.7634 (m-10) REVERT: L 84 SER cc_start: 0.8079 (t) cc_final: 0.7769 (t) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.0611 time to fit residues: 5.7279 Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.3980 chunk 1 optimal weight: 0.0870 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147468 restraints weight = 4212.322| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.45 r_work: 0.3665 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3383 Z= 0.109 Angle : 0.575 8.315 4619 Z= 0.298 Chirality : 0.043 0.150 519 Planarity : 0.004 0.039 584 Dihedral : 3.924 12.674 456 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 3.11 % Allowed : 16.10 % Favored : 80.79 % 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: -0.34 (0.42), residues: 413 helix: -1.93 (0.97), residues: 27 sheet: 0.98 (0.43), residues: 150 loop : -0.85 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.016 0.001 TYR L 53 PHE 0.010 0.001 PHE L 65 TRP 0.007 0.001 TRP H 127 HIS 0.001 0.000 HIS L 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 3373) covalent geometry : angle 0.56766 / 0.30 ( 4595) SS BOND : bond 0.00376 / 0.19 ( 6) SS BOND : angle 0.61534 / 0.40 ( 12) hydrogen bonds : bond 0.03397 / 2.20 ( 108) hydrogen bonds : angle 5.95428 / 4.10 ( 264) link_ALPHA1-3 : bond 0.00411 / 0.22 ( 1) link_ALPHA1-3 : angle 1.30170 / 0.71 ( 3) link_BETA1-4 : bond 0.00249 / 0.12 ( 2) link_BETA1-4 : angle 1.80309 / 0.91 ( 6) link_NAG-ASN : bond 0.00244 / 0.13 ( 1) link_NAG-ASN : angle 2.28306 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.155 Fit side-chains REVERT: A 471 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7340 (tm-30) REVERT: A 489 TYR cc_start: 0.7977 (m-10) cc_final: 0.7572 (m-10) REVERT: L 84 SER cc_start: 0.8069 (t) cc_final: 0.7774 (t) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.0657 time to fit residues: 6.0857 Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.0070 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.189391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.146309 restraints weight = 4238.340| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.26 r_work: 0.3674 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3383 Z= 0.100 Angle : 0.565 8.173 4619 Z= 0.292 Chirality : 0.043 0.150 519 Planarity : 0.004 0.039 584 Dihedral : 3.889 12.345 456 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 2.82 % Allowed : 16.95 % Favored : 80.23 % 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: -0.31 (0.42), residues: 413 helix: -1.90 (0.98), residues: 27 sheet: 1.01 (0.43), residues: 150 loop : -0.83 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.014 0.001 TYR A 421 PHE 0.011 0.001 PHE L 65 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS L 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 3373) covalent geometry : angle 0.55753 / 0.29 ( 4595) SS BOND : bond 0.00552 / 0.27 ( 6) SS BOND : angle 0.60675 / 0.39 ( 12) hydrogen bonds : bond 0.03213 / 2.08 ( 108) hydrogen bonds : angle 5.84200 / 4.01 ( 264) link_ALPHA1-3 : bond 0.00388 / 0.20 ( 1) link_ALPHA1-3 : angle 1.32458 / 0.72 ( 3) link_BETA1-4 : bond 0.00138 / 0.07 ( 2) link_BETA1-4 : angle 2.01985 / 0.98 ( 6) link_NAG-ASN : bond 0.00209 / 0.11 ( 1) link_NAG-ASN : angle 2.17588 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 489 TYR cc_start: 0.8004 (m-10) cc_final: 0.7561 (m-10) REVERT: H 69 MET cc_start: 0.8201 (tpp) cc_final: 0.7960 (ttm) REVERT: L 84 SER cc_start: 0.8061 (t) cc_final: 0.7800 (t) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.0580 time to fit residues: 5.3077 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.189137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146534 restraints weight = 4248.496| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.20 r_work: 0.3663 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3383 Z= 0.111 Angle : 0.582 8.007 4619 Z= 0.299 Chirality : 0.043 0.148 519 Planarity : 0.004 0.037 584 Dihedral : 3.898 12.191 456 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 2.82 % Allowed : 16.38 % Favored : 80.79 % 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: -0.29 (0.42), residues: 413 helix: -1.90 (0.98), residues: 27 sheet: 1.02 (0.43), residues: 150 loop : -0.81 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.015 0.001 TYR L 53 PHE 0.015 0.001 PHE L 65 TRP 0.008 0.001 TRP H 127 HIS 0.001 0.000 HIS L 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 3373) covalent geometry : angle 0.57438 / 0.30 ( 4595) SS BOND : bond 0.00386 / 0.19 ( 6) SS BOND : angle 0.53469 / 0.34 ( 12) hydrogen bonds : bond 0.03215 / 2.08 ( 108) hydrogen bonds : angle 5.81173 / 3.98 ( 264) link_ALPHA1-3 : bond 0.00389 / 0.20 ( 1) link_ALPHA1-3 : angle 1.25378 / 0.69 ( 3) link_BETA1-4 : bond 0.00152 / 0.07 ( 2) link_BETA1-4 : angle 2.00721 / 1.00 ( 6) link_NAG-ASN : bond 0.00119 / 0.06 ( 1) link_NAG-ASN : angle 2.21837 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 489 TYR cc_start: 0.8049 (m-10) cc_final: 0.7601 (m-10) REVERT: H 69 MET cc_start: 0.8221 (tpp) cc_final: 0.8015 (ttm) REVERT: L 84 SER cc_start: 0.8030 (t) cc_final: 0.7791 (t) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.0540 time to fit residues: 4.7989 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.1980 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.189109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.147019 restraints weight = 4210.511| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.15 r_work: 0.3672 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3383 Z= 0.114 Angle : 0.587 8.219 4619 Z= 0.302 Chirality : 0.043 0.147 519 Planarity : 0.004 0.037 584 Dihedral : 3.882 11.767 456 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 2.82 % Allowed : 16.95 % Favored : 80.23 % 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: -0.28 (0.42), residues: 413 helix: -1.90 (0.98), residues: 27 sheet: 1.02 (0.43), residues: 150 loop : -0.79 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.016 0.001 TYR L 53 PHE 0.014 0.001 PHE L 65 TRP 0.008 0.001 TRP H 127 HIS 0.001 0.000 HIS L 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 3373) covalent geometry : angle 0.58034 / 0.30 ( 4595) SS BOND : bond 0.00336 / 0.17 ( 6) SS BOND : angle 0.53572 / 0.34 ( 12) hydrogen bonds : bond 0.03188 / 2.06 ( 108) hydrogen bonds : angle 5.78510 / 3.95 ( 264) link_ALPHA1-3 : bond 0.00392 / 0.21 ( 1) link_ALPHA1-3 : angle 1.25919 / 0.69 ( 3) link_BETA1-4 : bond 0.00197 / 0.09 ( 2) link_BETA1-4 : angle 1.99631 / 1.00 ( 6) link_NAG-ASN : bond 0.00127 / 0.07 ( 1) link_NAG-ASN : angle 2.20405 / 1.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 489 TYR cc_start: 0.8082 (m-10) cc_final: 0.7648 (m-10) REVERT: L 84 SER cc_start: 0.8014 (t) cc_final: 0.7797 (t) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.0510 time to fit residues: 4.4977 Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.188400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146936 restraints weight = 4215.022| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.16 r_work: 0.3670 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3383 Z= 0.124 Angle : 0.598 8.267 4619 Z= 0.308 Chirality : 0.044 0.150 519 Planarity : 0.004 0.036 584 Dihedral : 3.940 11.523 456 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 2.82 % Allowed : 16.67 % Favored : 80.51 % 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: -0.33 (0.42), residues: 413 helix: -1.87 (1.00), residues: 27 sheet: 0.96 (0.43), residues: 150 loop : -0.82 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.016 0.001 TYR L 53 PHE 0.013 0.001 PHE A 342 TRP 0.008 0.001 TRP H 127 HIS 0.001 0.000 HIS L 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 3373) covalent geometry : angle 0.59095 / 0.31 ( 4595) SS BOND : bond 0.00317 / 0.16 ( 6) SS BOND : angle 0.54264 / 0.35 ( 12) hydrogen bonds : bond 0.03212 / 2.09 ( 108) hydrogen bonds : angle 5.76074 / 3.93 ( 264) link_ALPHA1-3 : bond 0.00423 / 0.22 ( 1) link_ALPHA1-3 : angle 1.24904 / 0.68 ( 3) link_BETA1-4 : bond 0.00196 / 0.09 ( 2) link_BETA1-4 : angle 1.99483 / 0.99 ( 6) link_NAG-ASN : bond 0.00104 / 0.05 ( 1) link_NAG-ASN : angle 2.20351 / 1.17 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 489 TYR cc_start: 0.8082 (m-10) cc_final: 0.7613 (m-10) REVERT: L 84 SER cc_start: 0.8029 (t) cc_final: 0.7810 (t) outliers start: 10 outliers final: 10 residues processed: 67 average time/residue: 0.0590 time to fit residues: 4.9939 Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.188695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147180 restraints weight = 4281.755| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.16 r_work: 0.3688 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3383 Z= 0.118 Angle : 0.592 8.279 4619 Z= 0.307 Chirality : 0.044 0.149 519 Planarity : 0.004 0.037 584 Dihedral : 3.951 11.370 456 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 2.82 % Allowed : 16.38 % Favored : 80.79 % 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: -0.34 (0.42), residues: 413 helix: -1.85 (1.01), residues: 27 sheet: 0.96 (0.43), residues: 150 loop : -0.83 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.015 0.001 TYR L 53 PHE 0.014 0.001 PHE L 65 TRP 0.008 0.001 TRP H 127 HIS 0.001 0.000 HIS L 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 3373) covalent geometry : angle 0.58489 / 0.31 ( 4595) SS BOND : bond 0.00316 / 0.16 ( 6) SS BOND : angle 0.53163 / 0.34 ( 12) hydrogen bonds : bond 0.03147 / 2.04 ( 108) hydrogen bonds : angle 5.72818 / 3.92 ( 264) link_ALPHA1-3 : bond 0.00412 / 0.22 ( 1) link_ALPHA1-3 : angle 1.28296 / 0.70 ( 3) link_BETA1-4 : bond 0.00233 / 0.11 ( 2) link_BETA1-4 : angle 1.96798 / 0.98 ( 6) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 2.19981 / 1.17 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.69 seconds wall clock time: 18 minutes 54.86 seconds (1134.86 seconds total)