Starting phenix.real_space_refine on Wed Jul 1 22:22:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdw_23782/07_2026/7mdw_23782.map" } resolution = 3.58 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= 0.011 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 2138 2.51 5 N 587 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3392 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.89, per 1000 atoms: 0.26 Number of scatterers: 3392 At special positions: 0 Unit cell: (57.5916, 79.4066, 107.33, 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 652 8.00 N 587 7.00 C 2138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 NAG-ASN " NAG R 601 " - " ASN R 343 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 126.8 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 8.5% alpha, 17.9% 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 337 through 343 Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.685A pdb=" N ASN R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 390 Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'B' and resid 27 through 32 removed outlier: 4.388A pdb=" N SER B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.199A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 361 through 362 removed outlier: 7.585A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 448 through 454 removed outlier: 4.340A pdb=" N ASN R 450 " --> pdb=" O TYR R 495 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR R 495 " --> pdb=" O ASN R 450 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU R 452 " --> pdb=" O GLN R 493 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN R 493 " --> pdb=" O LEU R 452 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.977A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.510A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 141 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: 0.41 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1112 1.34 - 1.46: 899 1.46 - 1.58: 1440 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3469 Sorted by residual: bond pdb=" C1 NAG R 601 " pdb=" O5 NAG R 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C5 NAG R 601 " pdb=" O5 NAG R 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3 NAG R 601 " pdb=" O3 NAG R 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA ILE R 410 " pdb=" CB ILE R 410 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.96e-01 bond pdb=" C2 NAG R 601 " pdb=" N2 NAG R 601 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.29e-01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 4561 1.32 - 2.64: 117 2.64 - 3.96: 22 3.96 - 5.28: 6 5.28 - 6.60: 2 Bond angle restraints: 4708 Sorted by residual: angle pdb=" N GLY R 496 " pdb=" CA GLY R 496 " pdb=" C GLY R 496 " ideal model delta sigma weight residual 111.19 117.79 -6.60 1.75e+00 3.27e-01 1.42e+01 angle pdb=" C ASN A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" CA THR A 105 " pdb=" CB THR A 105 " pdb=" CG2 THR A 105 " ideal model delta sigma weight residual 110.50 114.38 -3.88 1.70e+00 3.46e-01 5.22e+00 angle pdb=" N VAL A 2 " pdb=" CA VAL A 2 " pdb=" C VAL A 2 " ideal model delta sigma weight residual 111.48 109.38 2.10 9.40e-01 1.13e+00 5.00e+00 angle pdb=" C PHE A 66 " pdb=" CA PHE A 66 " pdb=" CB PHE A 66 " ideal model delta sigma weight residual 110.42 114.77 -4.35 1.99e+00 2.53e-01 4.79e+00 ... (remaining 4703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1853 17.94 - 35.88: 141 35.88 - 53.82: 20 53.82 - 71.77: 3 71.77 - 89.71: 2 Dihedral angle restraints: 2019 sinusoidal: 774 harmonic: 1245 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -140.97 54.97 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA THR A 105 " pdb=" C THR A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ASP B 46 " pdb=" CB ASP B 46 " pdb=" CG ASP B 46 " pdb=" OD1 ASP B 46 " ideal model delta sinusoidal sigma weight residual -30.00 -88.19 58.19 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 372 0.039 - 0.079: 90 0.079 - 0.118: 43 0.118 - 0.157: 0 0.157 - 0.196: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB THR A 105 " pdb=" CA THR A 105 " pdb=" OG1 THR A 105 " pdb=" CG2 THR A 105 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE R 468 " pdb=" N ILE R 468 " pdb=" C ILE R 468 " pdb=" CB ILE R 468 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 503 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO R 491 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 104 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C TYR A 104 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A 104 " 0.009 2.00e-02 2.50e+03 pdb=" N THR A 105 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 34 " -0.002 2.00e-02 2.50e+03 7.83e-03 1.53e+00 pdb=" CG TRP A 34 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 34 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 34 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 34 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 34 " 0.000 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1006 2.81 - 3.34: 2901 3.34 - 3.86: 5326 3.86 - 4.38: 6065 4.38 - 4.90: 10459 Nonbonded interactions: 25757 Sorted by model distance: nonbonded pdb=" ND2 ASN A 52 " pdb=" O TYR R 449 " model vdw 2.293 3.120 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.359 3.040 nonbonded pdb=" OG SER R 477 " pdb=" OD1 ASN R 487 " model vdw 2.367 3.040 nonbonded pdb=" OH TYR R 365 " pdb=" O PRO R 384 " model vdw 2.372 3.040 nonbonded pdb=" NH2 ARG R 357 " pdb=" OD1 ASN R 394 " model vdw 2.380 3.120 ... (remaining 25752 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=0.50 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.360 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4436 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 : 0.002 0.031 3476 Z= 0.117 Angle : 0.547 6.596 4723 Z= 0.311 Chirality : 0.041 0.196 506 Planarity : 0.003 0.043 614 Dihedral : 12.653 89.707 1217 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.58 (0.38), residues: 429 helix: -1.98 (0.79), residues: 39 sheet: -0.34 (0.53), residues: 98 loop : -1.21 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.015 0.001 TYR R 495 PHE 0.006 0.001 PHE A 45 TRP 0.018 0.001 TRP A 34 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 ( 3469) covalent geometry : angle 0.54594 / 0.31 ( 4708) SS BOND : bond 0.00077 / 0.04 ( 6) SS BOND : angle 0.70305 / 0.41 ( 12) hydrogen bonds : bond 0.32263 / 20.27 ( 63) hydrogen bonds : angle 11.12819 / 8.34 ( 141) link_NAG-ASN : bond 0.00151 / 0.08 ( 1) link_NAG-ASN : angle 0.75320 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.118 Fit side-chains REVERT: B 80 TYR cc_start: 0.4771 (m-80) cc_final: 0.4339 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0616 time to fit residues: 1.6149 Evaluate side-chains 20 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4842 r_free = 0.4842 target = 0.235389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.227914 restraints weight = 5697.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.229059 restraints weight = 4524.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.229770 restraints weight = 3738.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.230616 restraints weight = 3201.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.230965 restraints weight = 2760.327| |-----------------------------------------------------------------------------| r_work (final): 0.4758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4791 r_free = 0.4791 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4789 r_free = 0.4789 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.4789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4720 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3476 Z= 0.205 Angle : 0.660 7.479 4723 Z= 0.356 Chirality : 0.046 0.175 506 Planarity : 0.005 0.044 614 Dihedral : 6.732 89.295 490 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.11 (0.38), residues: 429 helix: -2.29 (0.66), residues: 45 sheet: -1.05 (0.51), residues: 96 loop : -1.42 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.015 0.002 TYR A 78 PHE 0.019 0.002 PHE R 400 TRP 0.017 0.003 TRP A 34 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 3469) covalent geometry : angle 0.65539 / 0.35 ( 4708) SS BOND : bond 0.00324 / 0.16 ( 6) SS BOND : angle 1.20494 / 0.70 ( 12) hydrogen bonds : bond 0.05402 / 3.47 ( 63) hydrogen bonds : angle 8.32171 / 6.25 ( 141) link_NAG-ASN : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : angle 2.25002 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.122 Fit side-chains REVERT: R 493 GLN cc_start: 0.6505 (mp10) cc_final: 0.5850 (mp10) REVERT: B 80 TYR cc_start: 0.4590 (m-80) cc_final: 0.4271 (m-10) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0500 time to fit residues: 1.5019 Evaluate side-chains 20 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.229338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.214950 restraints weight = 5382.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.218057 restraints weight = 3618.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.220410 restraints weight = 2605.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.222097 restraints weight = 1957.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.223103 restraints weight = 1534.188| |-----------------------------------------------------------------------------| r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4807 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3476 Z= 0.183 Angle : 0.631 6.836 4723 Z= 0.340 Chirality : 0.045 0.161 506 Planarity : 0.004 0.037 614 Dihedral : 6.891 87.586 490 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.69 % Allowed : 12.39 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.47 (0.37), residues: 429 helix: -2.93 (0.64), residues: 40 sheet: -1.45 (0.49), residues: 98 loop : -1.57 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.020 0.002 TYR R 495 PHE 0.016 0.002 PHE B 47 TRP 0.018 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 3469) covalent geometry : angle 0.62737 / 0.34 ( 4708) SS BOND : bond 0.00255 / 0.12 ( 6) SS BOND : angle 1.06018 / 0.62 ( 12) hydrogen bonds : bond 0.05096 / 3.18 ( 63) hydrogen bonds : angle 7.71638 / 5.80 ( 141) link_NAG-ASN : bond 0.00037 / 0.02 ( 1) link_NAG-ASN : angle 2.01852 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.121 Fit side-chains REVERT: A 93 TYR cc_start: 0.4312 (OUTLIER) cc_final: 0.3015 (p90) REVERT: R 493 GLN cc_start: 0.6415 (mp10) cc_final: 0.5830 (mp10) REVERT: B 80 TYR cc_start: 0.4631 (m-80) cc_final: 0.4312 (m-10) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.0520 time to fit residues: 1.7598 Evaluate side-chains 24 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 400 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 0.0770 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 29 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.0632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.234679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.220074 restraints weight = 5282.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.223488 restraints weight = 3568.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.225895 restraints weight = 2522.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.227657 restraints weight = 1865.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.228930 restraints weight = 1438.489| |-----------------------------------------------------------------------------| r_work (final): 0.4764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4630 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3476 Z= 0.084 Angle : 0.503 5.711 4723 Z= 0.265 Chirality : 0.042 0.145 506 Planarity : 0.003 0.032 614 Dihedral : 6.038 88.762 490 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.56 % Allowed : 13.24 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.37), residues: 429 helix: -2.56 (0.62), residues: 46 sheet: -1.39 (0.50), residues: 94 loop : -1.48 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 457 TYR 0.015 0.001 TYR R 495 PHE 0.010 0.001 PHE B 47 TRP 0.009 0.001 TRP B 104 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 ( 3469) covalent geometry : angle 0.50243 / 0.27 ( 4708) SS BOND : bond 0.00145 / 0.06 ( 6) SS BOND : angle 0.48467 / 0.28 ( 12) hydrogen bonds : bond 0.03300 / 2.09 ( 63) hydrogen bonds : angle 6.76951 / 5.30 ( 141) link_NAG-ASN : bond 0.00305 / 0.16 ( 1) link_NAG-ASN : angle 1.03805 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.115 Fit side-chains REVERT: A 93 TYR cc_start: 0.4177 (OUTLIER) cc_final: 0.3081 (p90) REVERT: R 493 GLN cc_start: 0.6139 (mp10) cc_final: 0.5574 (mp10) outliers start: 2 outliers final: 0 residues processed: 21 average time/residue: 0.0537 time to fit residues: 1.6219 Evaluate side-chains 19 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0050 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.3808 ------------------------------------------------------------------------------- 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 = 0.4773 r_free = 0.4773 target = 0.229648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.215239 restraints weight = 5358.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.218472 restraints weight = 3607.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.220824 restraints weight = 2595.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.222219 restraints weight = 1953.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.223642 restraints weight = 1563.809| |-----------------------------------------------------------------------------| r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4786 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3476 Z= 0.144 Angle : 0.579 6.762 4723 Z= 0.305 Chirality : 0.044 0.202 506 Planarity : 0.003 0.032 614 Dihedral : 6.504 87.721 490 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.13 % Allowed : 13.80 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.42 (0.38), residues: 429 helix: -2.87 (0.65), residues: 40 sheet: -1.59 (0.49), residues: 98 loop : -1.47 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.017 0.002 TYR R 495 PHE 0.012 0.001 PHE R 400 TRP 0.013 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 3469) covalent geometry : angle 0.57676 / 0.30 ( 4708) SS BOND : bond 0.00213 / 0.11 ( 6) SS BOND : angle 0.84158 / 0.49 ( 12) hydrogen bonds : bond 0.03885 / 2.41 ( 63) hydrogen bonds : angle 6.99747 / 5.36 ( 141) link_NAG-ASN : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : angle 1.50841 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.138 Fit side-chains REVERT: A 93 TYR cc_start: 0.4317 (OUTLIER) cc_final: 0.3093 (p90) REVERT: R 493 GLN cc_start: 0.6588 (mp10) cc_final: 0.5946 (mp10) REVERT: B 80 TYR cc_start: 0.4518 (m-80) cc_final: 0.4124 (m-10) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.0659 time to fit residues: 2.1274 Evaluate side-chains 25 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 400 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.230486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.222378 restraints weight = 5602.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.223534 restraints weight = 4266.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.224896 restraints weight = 3452.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.225533 restraints weight = 2803.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.226396 restraints weight = 2377.721| |-----------------------------------------------------------------------------| r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4853 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3476 Z= 0.175 Angle : 0.631 7.062 4723 Z= 0.340 Chirality : 0.046 0.189 506 Planarity : 0.004 0.033 614 Dihedral : 7.042 86.809 490 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.97 % Allowed : 13.80 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.38), residues: 429 helix: -3.09 (0.62), residues: 40 sheet: -1.84 (0.45), residues: 110 loop : -1.65 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 36 TYR 0.019 0.002 TYR R 453 PHE 0.013 0.002 PHE B 47 TRP 0.016 0.002 TRP R 353 HIS 0.001 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 3469) covalent geometry : angle 0.62784 / 0.34 ( 4708) SS BOND : bond 0.00255 / 0.13 ( 6) SS BOND : angle 1.06369 / 0.62 ( 12) hydrogen bonds : bond 0.04319 / 2.68 ( 63) hydrogen bonds : angle 7.29288 / 5.47 ( 141) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 1.91063 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.121 Fit side-chains REVERT: A 93 TYR cc_start: 0.4685 (OUTLIER) cc_final: 0.3313 (p90) REVERT: A 114 THR cc_start: 0.5784 (OUTLIER) cc_final: 0.5444 (m) REVERT: B 80 TYR cc_start: 0.4665 (m-80) cc_final: 0.4299 (m-10) outliers start: 7 outliers final: 5 residues processed: 25 average time/residue: 0.0671 time to fit residues: 2.2170 Evaluate side-chains 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 9 optimal weight: 0.0970 overall best weight: 0.2350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.232991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.226102 restraints weight = 5694.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.227305 restraints weight = 4478.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.228208 restraints weight = 3617.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.228753 restraints weight = 3000.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.229006 restraints weight = 2597.508| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4749 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3476 Z= 0.109 Angle : 0.555 6.982 4723 Z= 0.294 Chirality : 0.044 0.197 506 Planarity : 0.003 0.034 614 Dihedral : 6.572 88.399 490 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.25 % Allowed : 13.52 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.38), residues: 429 helix: -2.98 (0.64), residues: 40 sheet: -1.79 (0.45), residues: 111 loop : -1.70 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.015 0.001 TYR R 453 PHE 0.011 0.001 PHE B 47 TRP 0.009 0.001 TRP R 353 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 3469) covalent geometry : angle 0.55367 / 0.29 ( 4708) SS BOND : bond 0.00173 / 0.08 ( 6) SS BOND : angle 0.72140 / 0.42 ( 12) hydrogen bonds : bond 0.03514 / 2.16 ( 63) hydrogen bonds : angle 6.87113 / 5.28 ( 141) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 1.27447 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.117 Fit side-chains REVERT: A 93 TYR cc_start: 0.4710 (OUTLIER) cc_final: 0.3691 (p90) REVERT: A 114 THR cc_start: 0.5472 (OUTLIER) cc_final: 0.5123 (m) REVERT: B 51 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5594 (mt) outliers start: 8 outliers final: 4 residues processed: 26 average time/residue: 0.0665 time to fit residues: 2.3056 Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.0570 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.232114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.223847 restraints weight = 5709.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.225368 restraints weight = 4421.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.226264 restraints weight = 3451.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.227434 restraints weight = 2865.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.227968 restraints weight = 2358.457| |-----------------------------------------------------------------------------| r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4772 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3476 Z= 0.122 Angle : 0.559 7.108 4723 Z= 0.297 Chirality : 0.044 0.199 506 Planarity : 0.003 0.033 614 Dihedral : 6.546 87.879 490 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.25 % Allowed : 14.08 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.78 (0.37), residues: 429 helix: -3.01 (0.63), residues: 40 sheet: -1.84 (0.45), residues: 111 loop : -1.70 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.016 0.001 TYR R 453 PHE 0.011 0.001 PHE B 47 TRP 0.010 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 3469) covalent geometry : angle 0.55704 / 0.30 ( 4708) SS BOND : bond 0.00208 / 0.10 ( 6) SS BOND : angle 0.77882 / 0.45 ( 12) hydrogen bonds : bond 0.03541 / 2.18 ( 63) hydrogen bonds : angle 6.86935 / 5.24 ( 141) link_NAG-ASN : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : angle 1.31271 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.159 Fit side-chains REVERT: A 93 TYR cc_start: 0.4761 (OUTLIER) cc_final: 0.3691 (p90) REVERT: A 114 THR cc_start: 0.5521 (OUTLIER) cc_final: 0.5159 (m) REVERT: B 51 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5617 (mt) outliers start: 8 outliers final: 5 residues processed: 26 average time/residue: 0.0781 time to fit residues: 2.6946 Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.0370 chunk 41 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 15 optimal weight: 0.0010 chunk 10 optimal weight: 0.9990 overall best weight: 0.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.232407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.217741 restraints weight = 5292.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.221143 restraints weight = 3521.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.223598 restraints weight = 2481.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.225117 restraints weight = 1850.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.226551 restraints weight = 1461.834| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4682 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3476 Z= 0.083 Angle : 0.506 6.329 4723 Z= 0.266 Chirality : 0.043 0.191 506 Planarity : 0.003 0.035 614 Dihedral : 6.053 89.350 490 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.69 % Allowed : 15.49 % Favored : 82.82 % 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 (0.38), residues: 429 helix: -2.80 (0.61), residues: 46 sheet: -1.67 (0.49), residues: 92 loop : -1.63 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 457 TYR 0.011 0.001 TYR R 453 PHE 0.008 0.001 PHE B 47 TRP 0.008 0.001 TRP B 104 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.08 ( 3469) covalent geometry : angle 0.50498 / 0.27 ( 4708) SS BOND : bond 0.00131 / 0.06 ( 6) SS BOND : angle 0.53970 / 0.31 ( 12) hydrogen bonds : bond 0.02883 / 1.79 ( 63) hydrogen bonds : angle 6.39961 / 5.04 ( 141) link_NAG-ASN : bond 0.00185 / 0.10 ( 1) link_NAG-ASN : angle 1.04011 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.114 Fit side-chains REVERT: A 93 TYR cc_start: 0.4530 (OUTLIER) cc_final: 0.3606 (p90) REVERT: A 114 THR cc_start: 0.5355 (OUTLIER) cc_final: 0.5025 (m) REVERT: B 51 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5588 (mt) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.0654 time to fit residues: 2.0770 Evaluate side-chains 25 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.0170 chunk 11 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.233013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.225974 restraints weight = 5636.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.227027 restraints weight = 4393.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.228053 restraints weight = 3578.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.228552 restraints weight = 2975.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.229121 restraints weight = 2575.092| |-----------------------------------------------------------------------------| r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4736 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3476 Z= 0.115 Angle : 0.538 7.877 4723 Z= 0.285 Chirality : 0.043 0.197 506 Planarity : 0.003 0.032 614 Dihedral : 6.314 89.056 490 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.97 % Allowed : 15.77 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.38), residues: 429 helix: -2.90 (0.66), residues: 40 sheet: -1.67 (0.49), residues: 92 loop : -1.65 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.014 0.001 TYR R 453 PHE 0.010 0.001 PHE R 400 TRP 0.009 0.001 TRP R 353 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 3469) covalent geometry : angle 0.53718 / 0.28 ( 4708) SS BOND : bond 0.00189 / 0.09 ( 6) SS BOND : angle 0.70497 / 0.41 ( 12) hydrogen bonds : bond 0.03275 / 2.01 ( 63) hydrogen bonds : angle 6.60351 / 5.10 ( 141) link_NAG-ASN : bond 0.00084 / 0.04 ( 1) link_NAG-ASN : angle 1.18530 / 0.69 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.117 Fit side-chains REVERT: A 93 TYR cc_start: 0.4573 (OUTLIER) cc_final: 0.3601 (p90) REVERT: A 114 THR cc_start: 0.5487 (OUTLIER) cc_final: 0.5144 (m) REVERT: B 51 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5679 (mt) outliers start: 7 outliers final: 3 residues processed: 24 average time/residue: 0.0676 time to fit residues: 2.1419 Evaluate side-chains 24 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 11 optimal weight: 0.0060 chunk 13 optimal weight: 0.9990 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.229782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.222934 restraints weight = 5690.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.223926 restraints weight = 4429.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.224872 restraints weight = 3619.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.225750 restraints weight = 3001.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.226103 restraints weight = 2526.756| |-----------------------------------------------------------------------------| r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4856 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3476 Z= 0.170 Angle : 0.619 8.787 4723 Z= 0.331 Chirality : 0.046 0.201 506 Planarity : 0.004 0.031 614 Dihedral : 6.905 87.918 490 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.25 % Allowed : 14.93 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.87 (0.38), residues: 429 helix: -3.05 (0.63), residues: 40 sheet: -1.84 (0.44), residues: 111 loop : -1.80 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 36 TYR 0.014 0.002 TYR B 32 PHE 0.012 0.002 PHE B 47 TRP 0.014 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 3469) covalent geometry : angle 0.61592 / 0.33 ( 4708) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 1.05307 / 0.62 ( 12) hydrogen bonds : bond 0.04024 / 2.49 ( 63) hydrogen bonds : angle 7.02758 / 5.26 ( 141) link_NAG-ASN : bond 0.00081 / 0.04 ( 1) link_NAG-ASN : angle 1.69384 / 0.97 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 878.66 seconds wall clock time: 15 minutes 50.87 seconds (950.87 seconds total)