Starting phenix.real_space_refine on Wed Jul 1 22:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wr8_32718/07_2026/7wr8_32718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr8_32718/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2026/7wr8_32718.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2026/7wr8_32718.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2026/7wr8_32718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2026/7wr8_32718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2026/7wr8_32718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_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-6108/lib/python3.11/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 chiralities: 3 Time building chain proxies: 1.02, per 1000 atoms: 0.31 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: 0.30 Conformation dependent library (CDL) restraints added in 120.6 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: 0.10 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: 0.39 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: 1719 15.93 - 31.86: 193 31.86 - 47.79: 43 47.79 - 63.72: 2 63.72 - 79.64: 4 Dihedral angle restraints: 1961 sinusoidal: 759 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 1958 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: 3.420 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.190 Find NCS groups from input model: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 13.748 79.644 1186 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/Z covalent geometry : bond 0.00829 / 0.36 ( 3373) covalent geometry : angle 1.16026 / 0.63 ( 4593) SS BOND : bond 0.00462 / 0.25 ( 5) SS BOND : angle 0.87019 / 0.58 ( 10) hydrogen bonds : bond 0.27290 / 16.62 ( 74) hydrogen bonds : angle 11.40966 / 8.15 ( 174) link_BETA1-4 : bond 0.00141 / 0.07 ( 1) link_BETA1-4 : angle 2.52464 / 1.85 ( 3) link_BETA1-6 : bond 0.00991 / 0.52 ( 1) link_BETA1-6 : angle 2.88496 / 2.41 ( 3) link_NAG-ASN : bond 0.00681 / 0.36 ( 1) link_NAG-ASN : angle 2.80445 / 1.67 ( 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 : 0.116 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: 0.0622 time to fit residues: 5.6862 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 : 0.119 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.175340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.146710 restraints weight = 3708.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.150535 restraints weight = 2590.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.153230 restraints weight = 2019.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.155004 restraints weight = 1683.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.156146 restraints weight = 1480.477| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3381 Z= 0.144 Angle : 0.697 10.770 4612 Z= 0.358 Chirality : 0.046 0.140 502 Planarity : 0.006 0.066 591 Dihedral : 6.265 25.147 465 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.55 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: -3.19 (0.39), residues: 409 helix: -3.83 (0.69), residues: 27 sheet: -1.67 (0.42), residues: 144 loop : -2.23 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 346 TYR 0.017 0.001 TYR R 495 PHE 0.013 0.001 PHE A 101 TRP 0.012 0.001 TRP A 119 HIS 0.002 0.000 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 3373) covalent geometry : angle 0.69319 / 0.36 ( 4593) SS BOND : bond 0.00287 / 0.15 ( 5) SS BOND : angle 0.91553 / 0.86 ( 10) hydrogen bonds : bond 0.04820 / 2.87 ( 74) hydrogen bonds : angle 7.16512 / 4.91 ( 174) link_BETA1-4 : bond 0.00280 / 0.15 ( 1) link_BETA1-4 : angle 1.59250 / 1.17 ( 3) link_BETA1-6 : bond 0.00154 / 0.08 ( 1) link_BETA1-6 : angle 1.71049 / 1.24 ( 3) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 1.95217 / 1.73 ( 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 : 0.124 Fit side-chains REVERT: R 477 ASN cc_start: 0.7510 (t0) cc_final: 0.6914 (t0) REVERT: A 80 TYR cc_start: 0.7185 (m-10) cc_final: 0.6858 (m-80) REVERT: A 87 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6616 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.0626 time to fit residues: 5.8111 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3923 r_free = 0.3923 target = 0.176699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149835 restraints weight = 3749.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153583 restraints weight = 2606.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.156171 restraints weight = 2007.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157799 restraints weight = 1671.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.158514 restraints weight = 1471.586| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3381 Z= 0.124 Angle : 0.622 8.024 4612 Z= 0.319 Chirality : 0.045 0.142 502 Planarity : 0.005 0.053 591 Dihedral : 5.656 21.388 465 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 1.70 % Allowed : 12.50 % Favored : 85.80 % 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: -2.68 (0.41), residues: 409 helix: -4.12 (0.87), residues: 12 sheet: -1.54 (0.43), residues: 141 loop : -1.85 (0.40), residues: 256 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 0.011 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/Z covalent geometry : bond 0.00284 / 0.12 ( 3373) covalent geometry : angle 0.61847 / 0.32 ( 4593) SS BOND : bond 0.00458 / 0.23 ( 5) SS BOND : angle 0.86167 / 0.78 ( 10) hydrogen bonds : bond 0.03750 / 2.21 ( 74) hydrogen bonds : angle 6.22062 / 4.28 ( 174) link_BETA1-4 : bond 0.00411 / 0.22 ( 1) link_BETA1-4 : angle 1.28004 / 1.03 ( 3) link_BETA1-6 : bond 0.00337 / 0.18 ( 1) link_BETA1-6 : angle 1.56923 / 1.35 ( 3) link_NAG-ASN : bond 0.00089 / 0.05 ( 1) link_NAG-ASN : angle 1.47615 / 1.28 ( 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 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.140 Fit side-chains REVERT: R 396 TYR cc_start: 0.7822 (m-80) cc_final: 0.7544 (m-80) REVERT: A 80 TYR cc_start: 0.6905 (m-80) cc_final: 0.6431 (m-80) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.0593 time to fit residues: 4.8506 Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.160414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134577 restraints weight = 3901.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135839 restraints weight = 3094.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137271 restraints weight = 2713.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137692 restraints weight = 2329.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.138375 restraints weight = 2103.561| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3381 Z= 0.196 Angle : 0.680 13.151 4612 Z= 0.339 Chirality : 0.046 0.134 502 Planarity : 0.005 0.053 591 Dihedral : 5.568 22.102 465 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 2.56 % Allowed : 11.93 % Favored : 85.51 % 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: -2.85 (0.41), residues: 409 helix: -4.02 (0.68), residues: 20 sheet: -1.57 (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 R 498 TYR 0.019 0.002 TYR R 495 PHE 0.014 0.001 PHE A 101 TRP 0.010 0.002 TRP R 436 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 3373) covalent geometry : angle 0.67578 / 0.34 ( 4593) SS BOND : bond 0.00253 / 0.14 ( 5) SS BOND : angle 0.81469 / 0.66 ( 10) hydrogen bonds : bond 0.03553 / 2.09 ( 74) hydrogen bonds : angle 6.01672 / 4.20 ( 174) link_BETA1-4 : bond 0.00048 / 0.03 ( 1) link_BETA1-4 : angle 1.63909 / 1.34 ( 3) link_BETA1-6 : bond 0.00079 / 0.04 ( 1) link_BETA1-6 : angle 2.00729 / 1.67 ( 3) link_NAG-ASN : bond 0.00299 / 0.16 ( 1) link_NAG-ASN : angle 1.91106 / 1.65 ( 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 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.119 Fit side-chains REVERT: R 396 TYR cc_start: 0.7823 (m-80) cc_final: 0.7557 (m-80) REVERT: A 80 TYR cc_start: 0.7145 (m-80) cc_final: 0.6770 (m-80) REVERT: A 103 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.5015 (pp) REVERT: B 91 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6743 (t0) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.0598 time to fit residues: 5.3723 Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 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=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: 0.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.173677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.146561 restraints weight = 3696.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.149897 restraints weight = 2631.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152434 restraints weight = 2079.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154140 restraints weight = 1744.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.155343 restraints weight = 1538.386| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2019 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 : 0.645 10.282 4612 Z= 0.324 Chirality : 0.045 0.128 502 Planarity : 0.005 0.055 591 Dihedral : 5.485 20.405 465 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 2.27 % Allowed : 15.62 % Favored : 82.10 % 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: -2.81 (0.41), residues: 409 helix: -4.01 (0.67), residues: 20 sheet: -1.54 (0.44), residues: 141 loop : -1.90 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 87 TYR 0.016 0.001 TYR R 495 PHE 0.013 0.001 PHE A 101 TRP 0.010 0.002 TRP R 436 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 3373) covalent geometry : angle 0.64108 / 0.32 ( 4593) SS BOND : bond 0.00287 / 0.15 ( 5) SS BOND : angle 0.89299 / 0.79 ( 10) hydrogen bonds : bond 0.03301 / 1.94 ( 74) hydrogen bonds : angle 5.90712 / 4.15 ( 174) link_BETA1-4 : bond 0.00038 / 0.02 ( 1) link_BETA1-4 : angle 1.39817 / 1.12 ( 3) link_BETA1-6 : bond 0.00075 / 0.04 ( 1) link_BETA1-6 : angle 1.75376 / 1.46 ( 3) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 1.57415 / 1.38 ( 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 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.136 Fit side-chains REVERT: R 396 TYR cc_start: 0.7809 (m-80) cc_final: 0.7549 (m-80) REVERT: A 80 TYR cc_start: 0.7056 (m-80) cc_final: 0.6775 (m-80) REVERT: A 103 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.4978 (pp) REVERT: B 91 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6922 (t0) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.0669 time to fit residues: 5.4177 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.165704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136315 restraints weight = 3821.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139849 restraints weight = 2723.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142374 restraints weight = 2158.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143679 restraints weight = 1822.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144918 restraints weight = 1642.388| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3381 Z= 0.136 Angle : 0.621 9.161 4612 Z= 0.313 Chirality : 0.045 0.130 502 Planarity : 0.005 0.049 591 Dihedral : 5.361 20.704 465 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 1.99 % Allowed : 16.48 % 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: -2.75 (0.41), residues: 409 helix: -3.99 (0.67), residues: 20 sheet: -1.50 (0.44), residues: 141 loop : -1.86 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 87 TYR 0.015 0.001 TYR R 495 PHE 0.017 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.001 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 3373) covalent geometry : angle 0.61772 / 0.31 ( 4593) SS BOND : bond 0.00180 / 0.10 ( 5) SS BOND : angle 0.81403 / 0.73 ( 10) hydrogen bonds : bond 0.03068 / 1.81 ( 74) hydrogen bonds : angle 5.81919 / 4.12 ( 174) link_BETA1-4 : bond 0.00185 / 0.10 ( 1) link_BETA1-4 : angle 1.21522 / 0.96 ( 3) link_BETA1-6 : bond 0.00017 / 0.01 ( 1) link_BETA1-6 : angle 1.61661 / 1.35 ( 3) link_NAG-ASN : bond 0.00085 / 0.04 ( 1) link_NAG-ASN : angle 1.30439 / 1.10 ( 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 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.124 Fit side-chains REVERT: R 396 TYR cc_start: 0.7776 (m-80) cc_final: 0.7511 (m-80) REVERT: A 80 TYR cc_start: 0.7039 (m-80) cc_final: 0.6830 (m-80) REVERT: A 103 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4905 (pp) outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 0.0620 time to fit residues: 5.2170 Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133933 restraints weight = 3912.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137367 restraints weight = 2814.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139825 restraints weight = 2247.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141570 restraints weight = 1912.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142251 restraints weight = 1701.403| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3381 Z= 0.146 Angle : 0.623 8.191 4612 Z= 0.315 Chirality : 0.045 0.129 502 Planarity : 0.005 0.049 591 Dihedral : 5.303 20.504 465 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 2.56 % Allowed : 16.48 % Favored : 80.97 % 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: -2.70 (0.41), residues: 409 helix: -3.64 (0.91), residues: 14 sheet: -1.49 (0.44), residues: 141 loop : -1.91 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 87 TYR 0.014 0.001 TYR R 495 PHE 0.019 0.001 PHE R 456 TRP 0.008 0.002 TRP R 436 HIS 0.001 0.000 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3373) covalent geometry : angle 0.61971 / 0.31 ( 4593) SS BOND : bond 0.00210 / 0.12 ( 5) SS BOND : angle 0.73411 / 0.61 ( 10) hydrogen bonds : bond 0.03052 / 1.79 ( 74) hydrogen bonds : angle 5.82131 / 4.12 ( 174) link_BETA1-4 : bond 0.00063 / 0.03 ( 1) link_BETA1-4 : angle 1.28073 / 1.02 ( 3) link_BETA1-6 : bond 0.00004 / 0.00 ( 1) link_BETA1-6 : angle 1.66108 / 1.39 ( 3) link_NAG-ASN : bond 0.00145 / 0.08 ( 1) link_NAG-ASN : angle 1.40811 / 1.19 ( 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 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.119 Fit side-chains REVERT: R 396 TYR cc_start: 0.7751 (m-80) cc_final: 0.7497 (m-80) REVERT: A 103 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4922 (pp) outliers start: 9 outliers final: 8 residues processed: 66 average time/residue: 0.0640 time to fit residues: 5.2712 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 64 SER Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.0040 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134206 restraints weight = 3958.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137781 restraints weight = 2866.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139978 restraints weight = 2293.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141509 restraints weight = 1982.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143179 restraints weight = 1777.504| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2400 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= 0.142 Angle : 0.615 7.789 4612 Z= 0.311 Chirality : 0.044 0.132 502 Planarity : 0.005 0.047 591 Dihedral : 5.198 19.879 465 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 3.69 % Allowed : 16.48 % Favored : 79.83 % 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: -2.65 (0.41), residues: 409 helix: -3.64 (0.91), residues: 14 sheet: -1.42 (0.44), residues: 141 loop : -1.90 (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 0.021 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/Z covalent geometry : bond 0.00333 / 0.14 ( 3373) covalent geometry : angle 0.61247 / 0.31 ( 4593) SS BOND : bond 0.00185 / 0.11 ( 5) SS BOND : angle 0.71833 / 0.59 ( 10) hydrogen bonds : bond 0.03052 / 1.79 ( 74) hydrogen bonds : angle 5.79241 / 4.13 ( 174) link_BETA1-4 : bond 0.00135 / 0.07 ( 1) link_BETA1-4 : angle 1.25240 / 1.01 ( 3) link_BETA1-6 : bond 0.00032 / 0.02 ( 1) link_BETA1-6 : angle 1.59517 / 1.34 ( 3) link_NAG-ASN : bond 0.00132 / 0.07 ( 1) link_NAG-ASN : angle 1.30910 / 1.08 ( 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: 13 poor density : 63 time to evaluate : 0.073 Fit side-chains REVERT: R 396 TYR cc_start: 0.7787 (m-80) cc_final: 0.7525 (m-80) REVERT: A 103 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4961 (pp) REVERT: A 109 TRP cc_start: 0.8981 (m-10) cc_final: 0.8729 (m-10) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.0467 time to fit residues: 4.2357 Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 74 THR 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 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: 0.0040 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.168387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136674 restraints weight = 3933.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140205 restraints weight = 2870.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142459 restraints weight = 2327.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143211 restraints weight = 2005.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143211 restraints weight = 1883.282| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3381 Z= 0.129 Angle : 0.650 10.811 4612 Z= 0.326 Chirality : 0.046 0.233 502 Planarity : 0.005 0.048 591 Dihedral : 5.164 19.857 465 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.84 % Allowed : 17.61 % 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 (0.41), residues: 409 helix: -3.55 (0.94), residues: 14 sheet: -1.39 (0.44), residues: 143 loop : -1.93 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 87 TYR 0.013 0.001 TYR R 495 PHE 0.022 0.001 PHE R 456 TRP 0.010 0.001 TRP R 436 HIS 0.001 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 3373) covalent geometry : angle 0.64414 / 0.32 ( 4593) SS BOND : bond 0.00918 / 0.44 ( 5) SS BOND : angle 1.78925 / 1.75 ( 10) hydrogen bonds : bond 0.03070 / 1.86 ( 74) hydrogen bonds : angle 5.85164 / 4.10 ( 174) link_BETA1-4 : bond 0.00155 / 0.08 ( 1) link_BETA1-4 : angle 1.06492 / 0.83 ( 3) link_BETA1-6 : bond 0.00126 / 0.07 ( 1) link_BETA1-6 : angle 1.40134 / 1.21 ( 3) link_NAG-ASN : bond 0.00033 / 0.02 ( 1) link_NAG-ASN : angle 1.04174 / 0.85 ( 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 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.124 Fit side-chains REVERT: R 396 TYR cc_start: 0.7766 (m-80) cc_final: 0.7519 (m-80) REVERT: A 103 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4845 (pp) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.0421 time to fit residues: 3.8102 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 THR 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: 0.0070 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.177861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147396 restraints weight = 3795.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.151464 restraints weight = 2624.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.154492 restraints weight = 2036.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.156355 restraints weight = 1700.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.156937 restraints weight = 1495.310| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3381 Z= 0.112 Angle : 0.618 10.254 4612 Z= 0.313 Chirality : 0.045 0.194 502 Planarity : 0.005 0.045 591 Dihedral : 5.042 21.131 465 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.56 % Allowed : 17.33 % 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: -2.14 (0.42), residues: 409 helix: -2.88 (1.78), residues: 6 sheet: -0.78 (0.47), residues: 131 loop : -1.81 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.010 0.001 TYR R 495 PHE 0.023 0.001 PHE R 456 TRP 0.012 0.001 TRP R 436 HIS 0.001 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 3373) covalent geometry : angle 0.61395 / 0.31 ( 4593) SS BOND : bond 0.00716 / 0.35 ( 5) SS BOND : angle 1.55317 / 1.52 ( 10) hydrogen bonds : bond 0.03004 / 1.85 ( 74) hydrogen bonds : angle 5.63396 / 3.90 ( 174) link_BETA1-4 : bond 0.00362 / 0.19 ( 1) link_BETA1-4 : angle 0.88486 / 0.68 ( 3) link_BETA1-6 : bond 0.00259 / 0.14 ( 1) link_BETA1-6 : angle 1.14251 / 1.02 ( 3) link_NAG-ASN : bond 0.00249 / 0.13 ( 1) link_NAG-ASN : angle 0.47147 / 0.36 ( 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 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.124 Fit side-chains REVERT: A 103 LEU cc_start: 0.4841 (OUTLIER) cc_final: 0.4638 (pp) outliers start: 9 outliers final: 8 residues processed: 76 average time/residue: 0.0469 time to fit residues: 4.6449 Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 THR Chi-restraints excluded: chain A residue 76 THR 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: 9.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.177659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146886 restraints weight = 3866.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151174 restraints weight = 2644.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153791 restraints weight = 2051.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156107 restraints weight = 1725.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157564 restraints weight = 1507.023| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3381 Z= 0.174 Angle : 0.693 10.494 4612 Z= 0.347 Chirality : 0.047 0.189 502 Planarity : 0.005 0.039 591 Dihedral : 5.188 22.191 465 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.12 % Allowed : 18.47 % Favored : 78.41 % 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: -2.38 (0.41), residues: 409 helix: -2.77 (0.82), residues: 21 sheet: -0.84 (0.47), residues: 131 loop : -1.96 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.014 0.001 TYR R 495 PHE 0.026 0.002 PHE R 456 TRP 0.008 0.001 TRP R 436 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 ( 3373) covalent geometry : angle 0.67657 / 0.34 ( 4593) SS BOND : bond 0.00744 / 0.38 ( 5) SS BOND : angle 3.09200 / 2.18 ( 10) hydrogen bonds : bond 0.03224 / 2.00 ( 74) hydrogen bonds : angle 5.66868 / 3.91 ( 174) link_BETA1-4 : bond 0.00015 / 0.01 ( 1) link_BETA1-4 : angle 1.35974 / 1.15 ( 3) link_BETA1-6 : bond 0.00014 / 0.01 ( 1) link_BETA1-6 : angle 1.62536 / 1.36 ( 3) link_NAG-ASN : bond 0.00182 / 0.10 ( 1) link_NAG-ASN : angle 1.37620 / 1.14 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 870.57 seconds wall clock time: 15 minutes 40.06 seconds (940.06 seconds total)