Starting phenix.real_space_refine on Tue Mar 3 11:39:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wr8_32718/03_2026/7wr8_32718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr8_32718/03_2026/7wr8_32718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wr8_32718/03_2026/7wr8_32718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr8_32718/03_2026/7wr8_32718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wr8_32718/03_2026/7wr8_32718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr8_32718/03_2026/7wr8_32718.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 15 5.16 5 C 2086 2.51 5 N 555 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 3286 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 780 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.95, per 1000 atoms: 0.29 Number of scatterers: 3286 At special positions: 0 Unit cell: (100.88, 62.4, 69.68, 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 15 16.00 O 630 8.00 N 555 7.00 C 2086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 83.0 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 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: 8 helices and 8 sheets defined 9.6% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.925A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.319A pdb=" N VAL R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.912A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.804A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.668A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.631A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.353A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.522A pdb=" N SER A 17 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 83 " --> pdb=" O SER A 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.146A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.857A pdb=" N THR B 73 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.891A pdb=" N THR B 103 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 45 " --> pdb=" O GLN B 36 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 174 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: 0.45 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 813 1.33 - 1.45: 759 1.45 - 1.57: 1783 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3373 Sorted by residual: bond pdb=" CG LEU R 441 " pdb=" CD2 LEU R 441 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 bond pdb=" C GLU B 52 " pdb=" N ARG B 53 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.05e-02 9.07e+03 4.83e+00 bond pdb=" C ASP A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.72e+00 bond pdb=" C SER B 13 " pdb=" N PRO B 14 " ideal model delta sigma weight residual 1.332 1.357 -0.026 1.34e-02 5.57e+03 3.63e+00 bond pdb=" CB TRP A 47 " pdb=" CG TRP A 47 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 4546 4.43 - 8.86: 45 8.86 - 13.29: 1 13.29 - 17.72: 0 17.72 - 22.15: 1 Bond angle restraints: 4593 Sorted by residual: angle pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sigma weight residual 116.30 138.45 -22.15 3.50e+00 8.16e-02 4.00e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " ideal model delta sigma weight residual 116.20 120.25 -4.05 8.00e-01 1.56e+00 2.57e+01 angle pdb=" N ASN R 477 " pdb=" CA ASN R 477 " pdb=" C ASN R 477 " ideal model delta sigma weight residual 110.97 116.45 -5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 121.31 118.05 3.26 7.40e-01 1.83e+00 1.94e+01 angle pdb=" C LYS B 49 " pdb=" N ASP B 50 " pdb=" CA ASP B 50 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1763 15.93 - 31.86: 206 31.86 - 47.79: 45 47.79 - 63.72: 2 63.72 - 79.64: 4 Dihedral angle restraints: 2020 sinusoidal: 818 harmonic: 1202 Sorted by residual: dihedral pdb=" CA SER B 93 " pdb=" C SER B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 87 " pdb=" CB CYS B 87 " ideal model delta sinusoidal sigma weight residual 93.00 47.57 45.43 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ASP A 105 " pdb=" C ASP A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 2017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 342 0.052 - 0.105: 108 0.105 - 0.157: 42 0.157 - 0.210: 6 0.210 - 0.262: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.18e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.90e+01 chirality pdb=" CB ILE A 19 " pdb=" CA ILE A 19 " pdb=" CG1 ILE A 19 " pdb=" CG2 ILE A 19 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.136 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG C 1 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C VAL A 118 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 118 " -0.026 2.00e-02 2.50e+03 pdb=" N TRP A 119 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 27 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.49e+00 pdb=" N PRO B 28 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.042 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 597 2.76 - 3.30: 2775 3.30 - 3.83: 5395 3.83 - 4.37: 6177 4.37 - 4.90: 11042 Nonbonded interactions: 25986 Sorted by model distance: nonbonded pdb=" NZ LYS R 440 " pdb=" N SER A 104 " model vdw 2.230 3.200 nonbonded pdb=" OG SER R 359 " pdb=" OD1 ASN R 394 " model vdw 2.295 3.040 nonbonded pdb=" O SER B 29 " pdb=" OG SER B 29 " model vdw 2.302 3.040 nonbonded pdb=" NE2 HIS A 35 " pdb=" OD1 ASP A 99 " model vdw 2.307 3.120 nonbonded pdb=" OH TYR B 35 " pdb=" OE1 GLN B 88 " model vdw 2.328 3.040 ... (remaining 25981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.470 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.008 0.084 3381 Z= 0.362 Angle : 1.165 22.149 4612 Z= 0.630 Chirality : 0.062 0.262 502 Planarity : 0.010 0.111 591 Dihedral : 13.718 79.644 1245 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -3.48 (0.38), residues: 409 helix: -3.53 (0.89), residues: 21 sheet: -1.93 (0.42), residues: 139 loop : -2.50 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 72 TYR 0.035 0.003 TYR R 501 PHE 0.050 0.004 PHE R 456 TRP 0.015 0.003 TRP A 47 HIS 0.004 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00829 ( 3373) covalent geometry : angle 1.16026 ( 4593) SS BOND : bond 0.00462 ( 5) SS BOND : angle 0.87019 ( 10) hydrogen bonds : bond 0.27290 ( 74) hydrogen bonds : angle 11.40966 ( 174) link_BETA1-4 : bond 0.00141 ( 1) link_BETA1-4 : angle 2.52464 ( 3) link_BETA1-6 : bond 0.00991 ( 1) link_BETA1-6 : angle 2.88496 ( 3) link_NAG-ASN : bond 0.00681 ( 1) link_NAG-ASN : angle 2.80445 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.163 Fit side-chains REVERT: A 80 TYR cc_start: 0.7233 (m-80) cc_final: 0.7012 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0600 time to fit residues: 5.5121 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136511 restraints weight = 3876.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137077 restraints weight = 3178.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138130 restraints weight = 2931.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138858 restraints weight = 2545.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140196 restraints weight = 2256.688| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3381 Z= 0.145 Angle : 0.682 10.646 4612 Z= 0.351 Chirality : 0.045 0.138 502 Planarity : 0.006 0.065 591 Dihedral : 6.621 26.200 524 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 1.14 % Allowed : 9.38 % Favored : 89.49 % 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: -3.17 (0.39), residues: 409 helix: -3.85 (0.68), residues: 27 sheet: -1.66 (0.42), residues: 144 loop : -2.21 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 346 TYR 0.016 0.001 TYR R 495 PHE 0.013 0.001 PHE A 101 TRP 0.013 0.002 TRP A 119 HIS 0.001 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3373) covalent geometry : angle 0.67727 ( 4593) SS BOND : bond 0.00726 ( 5) SS BOND : angle 0.95792 ( 10) hydrogen bonds : bond 0.04666 ( 74) hydrogen bonds : angle 7.06904 ( 174) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 1.77678 ( 3) link_BETA1-6 : bond 0.00002 ( 1) link_BETA1-6 : angle 2.11452 ( 3) link_NAG-ASN : bond 0.00434 ( 1) link_NAG-ASN : angle 1.61350 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.162 Fit side-chains REVERT: A 80 TYR cc_start: 0.7203 (m-10) cc_final: 0.6901 (m-80) REVERT: A 87 ARG cc_start: 0.6858 (mtm-85) cc_final: 0.6540 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.0641 time to fit residues: 5.9354 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 15 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 35 optimal weight: 0.4980 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.167358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137960 restraints weight = 3885.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141655 restraints weight = 2732.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144260 restraints weight = 2144.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.145696 restraints weight = 1807.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147134 restraints weight = 1613.854| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3381 Z= 0.114 Angle : 0.608 7.750 4612 Z= 0.312 Chirality : 0.045 0.145 502 Planarity : 0.005 0.052 591 Dihedral : 5.748 23.910 524 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 1.99 % Allowed : 11.93 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.41), residues: 409 helix: -4.12 (0.88), residues: 12 sheet: -1.44 (0.43), residues: 141 loop : -1.82 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 454 TYR 0.015 0.001 TYR R 495 PHE 0.010 0.001 PHE A 101 TRP 0.011 0.001 TRP A 119 HIS 0.001 0.000 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3373) covalent geometry : angle 0.60484 ( 4593) SS BOND : bond 0.00177 ( 5) SS BOND : angle 0.79365 ( 10) hydrogen bonds : bond 0.03672 ( 74) hydrogen bonds : angle 6.19760 ( 174) link_BETA1-4 : bond 0.00243 ( 1) link_BETA1-4 : angle 1.30980 ( 3) link_BETA1-6 : bond 0.00127 ( 1) link_BETA1-6 : angle 1.78864 ( 3) link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.01196 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.132 Fit side-chains REVERT: R 396 TYR cc_start: 0.7791 (m-80) cc_final: 0.7518 (m-80) REVERT: A 38 ARG cc_start: 0.8049 (ptm-80) cc_final: 0.7834 (ttp80) REVERT: A 80 TYR cc_start: 0.6882 (m-80) cc_final: 0.6548 (m-80) outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 0.0682 time to fit residues: 5.6238 Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133198 restraints weight = 3870.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136886 restraints weight = 2681.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139313 restraints weight = 2085.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141174 restraints weight = 1747.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142050 restraints weight = 1529.312| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3381 Z= 0.152 Angle : 0.637 12.645 4612 Z= 0.317 Chirality : 0.045 0.141 502 Planarity : 0.005 0.044 591 Dihedral : 5.645 26.535 524 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 1.42 % Allowed : 12.50 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.41), residues: 409 helix: -4.00 (0.68), residues: 20 sheet: -1.41 (0.44), residues: 141 loop : -1.90 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 346 TYR 0.017 0.001 TYR R 495 PHE 0.011 0.001 PHE A 101 TRP 0.011 0.002 TRP A 36 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3373) covalent geometry : angle 0.63330 ( 4593) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.72198 ( 10) hydrogen bonds : bond 0.03266 ( 74) hydrogen bonds : angle 5.90012 ( 174) link_BETA1-4 : bond 0.00032 ( 1) link_BETA1-4 : angle 1.47577 ( 3) link_BETA1-6 : bond 0.00044 ( 1) link_BETA1-6 : angle 2.10213 ( 3) link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 1.29207 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.101 Fit side-chains REVERT: R 396 TYR cc_start: 0.7826 (m-80) cc_final: 0.7574 (m-80) REVERT: A 80 TYR cc_start: 0.7032 (m-80) cc_final: 0.6688 (m-80) REVERT: A 103 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4816 (pp) REVERT: A 109 TRP cc_start: 0.8994 (m-10) cc_final: 0.8582 (m-10) REVERT: B 91 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6665 (t0) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.0573 time to fit residues: 4.7525 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.158725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132550 restraints weight = 3919.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133711 restraints weight = 3133.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134809 restraints weight = 3262.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135426 restraints weight = 2488.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136171 restraints weight = 2196.129| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3381 Z= 0.227 Angle : 0.690 9.814 4612 Z= 0.351 Chirality : 0.046 0.131 502 Planarity : 0.005 0.049 591 Dihedral : 5.939 27.847 524 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 2.84 % Allowed : 14.20 % Favored : 82.95 % 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: -2.83 (0.41), residues: 409 helix: -4.07 (0.65), residues: 20 sheet: -1.53 (0.44), residues: 141 loop : -1.93 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 87 TYR 0.018 0.002 TYR R 495 PHE 0.017 0.002 PHE A 101 TRP 0.012 0.002 TRP A 36 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 3373) covalent geometry : angle 0.68401 ( 4593) SS BOND : bond 0.00337 ( 5) SS BOND : angle 0.91857 ( 10) hydrogen bonds : bond 0.03512 ( 74) hydrogen bonds : angle 6.03675 ( 174) link_BETA1-4 : bond 0.00153 ( 1) link_BETA1-4 : angle 1.81228 ( 3) link_BETA1-6 : bond 0.00337 ( 1) link_BETA1-6 : angle 2.50231 ( 3) link_NAG-ASN : bond 0.00333 ( 1) link_NAG-ASN : angle 1.69168 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.119 Fit side-chains REVERT: A 80 TYR cc_start: 0.7295 (m-80) cc_final: 0.6932 (m-80) REVERT: A 103 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.5054 (pp) REVERT: B 91 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6716 (t0) outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.0633 time to fit residues: 5.9370 Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.172797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146861 restraints weight = 3723.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146794 restraints weight = 3186.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148215 restraints weight = 2827.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149066 restraints weight = 2459.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150907 restraints weight = 2100.727| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3381 Z= 0.168 Angle : 0.636 8.948 4612 Z= 0.323 Chirality : 0.045 0.129 502 Planarity : 0.005 0.054 591 Dihedral : 5.798 27.966 524 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.84 % Allowed : 15.62 % Favored : 81.53 % 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: -2.85 (0.40), residues: 409 helix: -4.01 (0.67), residues: 20 sheet: -1.54 (0.44), residues: 141 loop : -1.95 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 87 TYR 0.017 0.001 TYR R 495 PHE 0.018 0.001 PHE R 456 TRP 0.010 0.002 TRP R 436 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 3373) covalent geometry : angle 0.63217 ( 4593) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.81530 ( 10) hydrogen bonds : bond 0.03103 ( 74) hydrogen bonds : angle 5.93824 ( 174) link_BETA1-4 : bond 0.00069 ( 1) link_BETA1-4 : angle 1.41377 ( 3) link_BETA1-6 : bond 0.00205 ( 1) link_BETA1-6 : angle 2.11030 ( 3) link_NAG-ASN : bond 0.00099 ( 1) link_NAG-ASN : angle 1.05127 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.121 Fit side-chains REVERT: R 396 TYR cc_start: 0.7776 (m-80) cc_final: 0.7532 (m-80) REVERT: R 490 PHE cc_start: 0.7347 (t80) cc_final: 0.7135 (t80) REVERT: A 103 LEU cc_start: 0.5379 (OUTLIER) cc_final: 0.4999 (pp) REVERT: A 109 TRP cc_start: 0.8995 (m-10) cc_final: 0.8711 (m-10) REVERT: B 91 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6786 (t0) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.0612 time to fit residues: 5.3160 Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.0030 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139265 restraints weight = 3828.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142703 restraints weight = 2696.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145404 restraints weight = 2123.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147043 restraints weight = 1794.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148385 restraints weight = 1591.161| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3381 Z= 0.137 Angle : 0.622 8.070 4612 Z= 0.315 Chirality : 0.044 0.138 502 Planarity : 0.005 0.049 591 Dihedral : 5.563 27.420 524 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.69 % Allowed : 15.91 % Favored : 80.40 % 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: -2.69 (0.41), residues: 409 helix: -3.57 (0.96), residues: 14 sheet: -1.48 (0.44), residues: 141 loop : -1.91 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 87 TYR 0.015 0.001 TYR R 495 PHE 0.018 0.001 PHE R 456 TRP 0.009 0.001 TRP A 119 HIS 0.001 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3373) covalent geometry : angle 0.61926 ( 4593) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.73147 ( 10) hydrogen bonds : bond 0.02873 ( 74) hydrogen bonds : angle 5.85460 ( 174) link_BETA1-4 : bond 0.00164 ( 1) link_BETA1-4 : angle 1.25724 ( 3) link_BETA1-6 : bond 0.00102 ( 1) link_BETA1-6 : angle 1.94047 ( 3) link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 0.95942 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.127 Fit side-chains REVERT: R 396 TYR cc_start: 0.7791 (m-80) cc_final: 0.7528 (m-80) REVERT: A 103 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4989 (pp) REVERT: B 91 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6784 (t0) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 0.0560 time to fit residues: 5.1232 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.170388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142050 restraints weight = 3853.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145590 restraints weight = 2750.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148012 restraints weight = 2171.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149828 restraints weight = 1836.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150466 restraints weight = 1629.972| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3381 Z= 0.130 Angle : 0.643 8.336 4612 Z= 0.323 Chirality : 0.045 0.207 502 Planarity : 0.005 0.049 591 Dihedral : 5.424 25.927 524 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.84 % Allowed : 17.05 % Favored : 80.11 % 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: -2.61 (0.41), residues: 409 helix: -3.59 (0.92), residues: 14 sheet: -1.34 (0.45), residues: 135 loop : -1.90 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 87 TYR 0.014 0.001 TYR A 94 PHE 0.018 0.001 PHE R 456 TRP 0.009 0.001 TRP A 119 HIS 0.001 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3373) covalent geometry : angle 0.63551 ( 4593) SS BOND : bond 0.00769 ( 5) SS BOND : angle 1.89876 ( 10) hydrogen bonds : bond 0.02889 ( 74) hydrogen bonds : angle 5.89866 ( 174) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 1.15404 ( 3) link_BETA1-6 : bond 0.00069 ( 1) link_BETA1-6 : angle 1.74331 ( 3) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 0.75319 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.129 Fit side-chains REVERT: R 340 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8111 (tp30) REVERT: R 396 TYR cc_start: 0.7769 (m-80) cc_final: 0.7517 (m-80) REVERT: A 103 LEU cc_start: 0.5266 (OUTLIER) cc_final: 0.4988 (pp) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.0548 time to fit residues: 5.1053 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.147216 restraints weight = 3777.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147254 restraints weight = 3305.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148803 restraints weight = 2839.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150065 restraints weight = 2467.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150714 restraints weight = 2083.235| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3381 Z= 0.198 Angle : 0.734 11.753 4612 Z= 0.361 Chirality : 0.047 0.241 502 Planarity : 0.005 0.041 591 Dihedral : 5.649 27.757 524 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.27 % Allowed : 18.18 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.40), residues: 409 helix: -3.68 (0.90), residues: 14 sheet: -1.26 (0.45), residues: 130 loop : -2.01 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 38 TYR 0.016 0.001 TYR R 495 PHE 0.021 0.002 PHE R 456 TRP 0.008 0.002 TRP A 109 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 3373) covalent geometry : angle 0.72476 ( 4593) SS BOND : bond 0.00763 ( 5) SS BOND : angle 2.07933 ( 10) hydrogen bonds : bond 0.03024 ( 74) hydrogen bonds : angle 5.90426 ( 174) link_BETA1-4 : bond 0.00058 ( 1) link_BETA1-4 : angle 1.57976 ( 3) link_BETA1-6 : bond 0.00294 ( 1) link_BETA1-6 : angle 2.20514 ( 3) link_NAG-ASN : bond 0.00305 ( 1) link_NAG-ASN : angle 1.42902 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.124 Fit side-chains REVERT: R 396 TYR cc_start: 0.7823 (m-80) cc_final: 0.7567 (m-80) REVERT: A 103 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5110 (pp) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.0580 time to fit residues: 5.2627 Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 37 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.168412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138953 restraints weight = 3827.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142406 restraints weight = 2721.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145047 restraints weight = 2162.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146595 restraints weight = 1835.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147072 restraints weight = 1634.849| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3381 Z= 0.155 Angle : 0.683 10.625 4612 Z= 0.340 Chirality : 0.046 0.203 502 Planarity : 0.005 0.052 591 Dihedral : 5.524 27.012 524 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.27 % Allowed : 18.18 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.41), residues: 409 helix: -3.61 (0.91), residues: 14 sheet: -1.20 (0.46), residues: 130 loop : -1.97 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.015 0.001 TYR R 495 PHE 0.024 0.001 PHE R 456 TRP 0.010 0.001 TRP A 119 HIS 0.002 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3373) covalent geometry : angle 0.67711 ( 4593) SS BOND : bond 0.00687 ( 5) SS BOND : angle 1.66561 ( 10) hydrogen bonds : bond 0.02964 ( 74) hydrogen bonds : angle 5.83414 ( 174) link_BETA1-4 : bond 0.00121 ( 1) link_BETA1-4 : angle 1.27404 ( 3) link_BETA1-6 : bond 0.00124 ( 1) link_BETA1-6 : angle 1.91636 ( 3) link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 0.97716 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.081 Fit side-chains REVERT: R 396 TYR cc_start: 0.7783 (m-80) cc_final: 0.7541 (m-80) REVERT: A 103 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.4970 (pp) REVERT: A 109 TRP cc_start: 0.9005 (m-10) cc_final: 0.8725 (m-10) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.0529 time to fit residues: 4.7575 Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 0.0050 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.165326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135701 restraints weight = 3949.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139239 restraints weight = 2809.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141550 restraints weight = 2231.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143571 restraints weight = 1897.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144607 restraints weight = 1678.481| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3381 Z= 0.163 Angle : 0.671 11.311 4612 Z= 0.337 Chirality : 0.046 0.190 502 Planarity : 0.005 0.042 591 Dihedral : 5.516 27.313 524 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.56 % Allowed : 17.90 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.41), residues: 409 helix: -3.62 (0.91), residues: 14 sheet: -1.18 (0.45), residues: 130 loop : -2.00 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.015 0.001 TYR R 495 PHE 0.023 0.002 PHE R 456 TRP 0.015 0.002 TRP A 36 HIS 0.002 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3373) covalent geometry : angle 0.66459 ( 4593) SS BOND : bond 0.00664 ( 5) SS BOND : angle 1.57305 ( 10) hydrogen bonds : bond 0.03018 ( 74) hydrogen bonds : angle 5.78538 ( 174) link_BETA1-4 : bond 0.00055 ( 1) link_BETA1-4 : angle 1.39897 ( 3) link_BETA1-6 : bond 0.00149 ( 1) link_BETA1-6 : angle 2.00099 ( 3) link_NAG-ASN : bond 0.00209 ( 1) link_NAG-ASN : angle 1.16642 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 817.01 seconds wall clock time: 14 minutes 44.91 seconds (884.91 seconds total)