Starting phenix.real_space_refine on Tue Mar 3 11:34:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrz_32738/03_2026/7wrz_32738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrz_32738/03_2026/7wrz_32738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wrz_32738/03_2026/7wrz_32738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrz_32738/03_2026/7wrz_32738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrz_32738/03_2026/7wrz_32738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrz_32738/03_2026/7wrz_32738.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 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 14 5.16 5 C 2077 2.51 5 N 553 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3270 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "R" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.77, per 1000 atoms: 0.24 Number of scatterers: 3270 At special positions: 0 Unit cell: (84.24, 64.8, 71.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 626 8.00 N 553 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " 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 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 " NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 74.6 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 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: 9 helices and 8 sheets defined 12.8% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.795A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.506A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.567A pdb=" N TYR R 369 " --> pdb=" O TYR R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 390 removed outlier: 3.550A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.622A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS H 96 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.539A pdb=" N ILE H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.596A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.343A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 356 through 358 Processing sheet with id=AA7, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'R' and resid 473 through 474 103 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.29 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 834 1.46 - 1.57: 1460 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3355 Sorted by residual: bond pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" N ILE R 410 " pdb=" CA ILE R 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.22e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 3350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 4498 2.18 - 4.36: 56 4.36 - 6.55: 4 6.55 - 8.73: 0 8.73 - 10.91: 1 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta sigma weight residual 121.72 132.63 -10.91 1.54e+00 4.22e-01 5.02e+01 angle pdb=" C VAL R 382 " pdb=" N SER R 383 " pdb=" CA SER R 383 " ideal model delta sigma weight residual 120.49 114.45 6.04 1.42e+00 4.96e-01 1.81e+01 angle pdb=" N PHE R 374 " pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 110.79 114.90 -4.11 1.63e+00 3.76e-01 6.35e+00 angle pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " pdb=" CG PHE R 374 " ideal model delta sigma weight residual 113.80 116.26 -2.46 1.00e+00 1.00e+00 6.06e+00 angle pdb=" N TRP L 96 " pdb=" CA TRP L 96 " pdb=" C TRP L 96 " ideal model delta sigma weight residual 109.81 114.95 -5.14 2.21e+00 2.05e-01 5.42e+00 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1774 15.87 - 31.74: 168 31.74 - 47.61: 33 47.61 - 63.48: 9 63.48 - 79.34: 6 Dihedral angle restraints: 1990 sinusoidal: 794 harmonic: 1196 Sorted by residual: dihedral pdb=" CA TRP L 96 " pdb=" C TRP L 96 " pdb=" N PRO L 97 " pdb=" CA PRO L 97 " ideal model delta harmonic sigma weight residual 180.00 134.00 46.00 0 5.00e+00 4.00e-02 8.47e+01 dihedral pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASP H 104 " pdb=" C ASP H 104 " pdb=" N TYR H 105 " pdb=" CA TYR H 105 " ideal model delta harmonic sigma weight residual -180.00 -164.30 -15.70 0 5.00e+00 4.00e-02 9.86e+00 ... (remaining 1987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 310 0.034 - 0.067: 124 0.067 - 0.101: 36 0.101 - 0.134: 21 0.134 - 0.168: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 489 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 96 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO L 97 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 41 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO L 42 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO L 46 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " -0.018 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 243 2.74 - 3.28: 3077 3.28 - 3.82: 5219 3.82 - 4.36: 6717 4.36 - 4.90: 11797 Nonbonded interactions: 27053 Sorted by model distance: nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.201 3.040 nonbonded pdb=" NH1 ARG L 56 " pdb=" O ILE L 60 " model vdw 2.301 3.120 nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR R 369 " pdb=" O PRO R 384 " model vdw 2.314 3.040 nonbonded pdb=" O ASP R 442 " pdb=" ND2 ASN R 448 " model vdw 2.367 3.120 ... (remaining 27048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.160 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.004 0.029 3363 Z= 0.169 Angle : 0.619 10.910 4577 Z= 0.355 Chirality : 0.044 0.168 492 Planarity : 0.005 0.066 587 Dihedral : 13.598 79.345 1212 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.03 (0.40), residues: 406 helix: -3.69 (0.60), residues: 27 sheet: -0.30 (0.41), residues: 152 loop : -0.47 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 357 TYR 0.015 0.001 TYR L 93 PHE 0.012 0.001 PHE R 347 TRP 0.006 0.001 TRP R 436 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3355) covalent geometry : angle 0.61825 ( 4559) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.37689 ( 12) hydrogen bonds : bond 0.24946 ( 99) hydrogen bonds : angle 11.75452 ( 243) link_BETA1-4 : bond 0.00073 ( 1) link_BETA1-4 : angle 1.24355 ( 3) link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 1.24696 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 GLU cc_start: 0.7412 (pm20) cc_final: 0.7186 (pm20) REVERT: L 84 ASP cc_start: 0.8096 (m-30) cc_final: 0.7859 (m-30) REVERT: R 340 GLU cc_start: 0.8305 (mp0) cc_final: 0.8014 (mm-30) REVERT: R 356 LYS cc_start: 0.9212 (mttp) cc_final: 0.8991 (mttm) REVERT: R 369 TYR cc_start: 0.7160 (m-80) cc_final: 0.6940 (m-80) REVERT: R 483 VAL cc_start: 0.7956 (t) cc_final: 0.7741 (m) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0962 time to fit residues: 8.1278 Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 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 = 0.3145 r_free = 0.3145 target = 0.106083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.088102 restraints weight = 4861.252| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.92 r_work: 0.3109 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3363 Z= 0.195 Angle : 0.579 5.661 4577 Z= 0.306 Chirality : 0.046 0.174 492 Planarity : 0.005 0.067 587 Dihedral : 5.547 45.095 502 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % Rotamer: Outliers : 1.44 % Allowed : 9.77 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.13 (0.39), residues: 406 helix: -3.54 (0.56), residues: 33 sheet: -0.40 (0.39), residues: 154 loop : -0.43 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 357 TYR 0.015 0.001 TYR L 93 PHE 0.015 0.001 PHE R 347 TRP 0.012 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3355) covalent geometry : angle 0.57633 ( 4559) SS BOND : bond 0.00246 ( 6) SS BOND : angle 0.81262 ( 12) hydrogen bonds : bond 0.04819 ( 99) hydrogen bonds : angle 7.68472 ( 243) link_BETA1-4 : bond 0.00268 ( 1) link_BETA1-4 : angle 1.30642 ( 3) link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 1.40819 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: R 420 ASP cc_start: 0.8946 (m-30) cc_final: 0.8557 (m-30) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.0979 time to fit residues: 7.6332 Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.087662 restraints weight = 4756.155| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.83 r_work: 0.2768 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3363 Z= 0.170 Angle : 0.550 5.967 4577 Z= 0.288 Chirality : 0.045 0.161 492 Planarity : 0.005 0.067 587 Dihedral : 5.484 45.054 502 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer: Outliers : 1.72 % Allowed : 12.64 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.20 (0.40), residues: 406 helix: -3.77 (0.49), residues: 33 sheet: -0.54 (0.39), residues: 153 loop : -0.37 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.012 0.001 PHE R 347 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3355) covalent geometry : angle 0.54782 ( 4559) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.61516 ( 12) hydrogen bonds : bond 0.03803 ( 99) hydrogen bonds : angle 7.00954 ( 243) link_BETA1-4 : bond 0.00134 ( 1) link_BETA1-4 : angle 1.43725 ( 3) link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 1.17377 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8564 (mp10) cc_final: 0.7722 (mp10) REVERT: R 420 ASP cc_start: 0.8987 (m-30) cc_final: 0.8428 (m-30) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.0886 time to fit residues: 6.9230 Evaluate side-chains 64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.087221 restraints weight = 4713.621| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.87 r_work: 0.2761 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3363 Z= 0.166 Angle : 0.534 6.149 4577 Z= 0.278 Chirality : 0.045 0.159 492 Planarity : 0.005 0.067 587 Dihedral : 5.431 44.647 502 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.68 % Favored : 95.07 % Rotamer: Outliers : 2.01 % Allowed : 14.94 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.21 (0.40), residues: 406 helix: -3.87 (0.45), residues: 33 sheet: -0.50 (0.40), residues: 153 loop : -0.40 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.011 0.001 PHE R 347 TRP 0.009 0.001 TRP H 50 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3355) covalent geometry : angle 0.53181 ( 4559) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.67704 ( 12) hydrogen bonds : bond 0.03477 ( 99) hydrogen bonds : angle 6.79833 ( 243) link_BETA1-4 : bond 0.00063 ( 1) link_BETA1-4 : angle 1.47009 ( 3) link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.11741 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8567 (mp10) cc_final: 0.7712 (mp10) REVERT: R 420 ASP cc_start: 0.8999 (m-30) cc_final: 0.8365 (m-30) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.1037 time to fit residues: 8.0929 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 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 = 0.3106 r_free = 0.3106 target = 0.103470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.086265 restraints weight = 4733.807| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.85 r_work: 0.2755 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3363 Z= 0.188 Angle : 0.547 6.279 4577 Z= 0.284 Chirality : 0.046 0.184 492 Planarity : 0.005 0.067 587 Dihedral : 5.504 45.036 502 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer: Outliers : 3.16 % Allowed : 14.66 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.14 (0.40), residues: 406 helix: -3.83 (0.47), residues: 33 sheet: -0.43 (0.40), residues: 152 loop : -0.37 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.010 0.001 PHE R 347 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3355) covalent geometry : angle 0.54489 ( 4559) SS BOND : bond 0.00193 ( 6) SS BOND : angle 0.73777 ( 12) hydrogen bonds : bond 0.03409 ( 99) hydrogen bonds : angle 6.75829 ( 243) link_BETA1-4 : bond 0.00109 ( 1) link_BETA1-4 : angle 1.53223 ( 3) link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 1.20510 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8581 (mp10) cc_final: 0.7807 (mp10) REVERT: R 357 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8207 (ttt90) REVERT: R 369 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: R 420 ASP cc_start: 0.9023 (m-30) cc_final: 0.8432 (m-30) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.0995 time to fit residues: 7.7590 Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 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 = 0.3113 r_free = 0.3113 target = 0.103974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.086813 restraints weight = 4687.577| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.85 r_work: 0.2773 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3363 Z= 0.158 Angle : 0.529 6.303 4577 Z= 0.275 Chirality : 0.045 0.170 492 Planarity : 0.005 0.066 587 Dihedral : 5.420 44.858 502 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.19 % Favored : 95.57 % Rotamer: Outliers : 3.74 % Allowed : 14.66 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.08 (0.41), residues: 406 helix: -4.08 (0.51), residues: 26 sheet: -0.34 (0.41), residues: 152 loop : -0.47 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.008 0.001 PHE R 347 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3355) covalent geometry : angle 0.52636 ( 4559) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.77618 ( 12) hydrogen bonds : bond 0.03290 ( 99) hydrogen bonds : angle 6.67846 ( 243) link_BETA1-4 : bond 0.00128 ( 1) link_BETA1-4 : angle 1.54154 ( 3) link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 1.10929 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8560 (mp10) cc_final: 0.7920 (mp10) REVERT: R 369 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: R 394 ASN cc_start: 0.7811 (m-40) cc_final: 0.7458 (m110) REVERT: R 420 ASP cc_start: 0.9019 (m-30) cc_final: 0.8434 (m-30) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.1005 time to fit residues: 8.3620 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 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 = 0.3129 r_free = 0.3129 target = 0.104800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.087517 restraints weight = 4758.861| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.87 r_work: 0.2776 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3363 Z= 0.155 Angle : 0.531 6.227 4577 Z= 0.278 Chirality : 0.045 0.193 492 Planarity : 0.005 0.066 587 Dihedral : 5.379 44.728 502 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer: Outliers : 2.87 % Allowed : 15.80 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.06 (0.41), residues: 406 helix: -4.03 (0.52), residues: 26 sheet: -0.30 (0.41), residues: 152 loop : -0.48 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.008 0.001 PHE R 347 TRP 0.008 0.001 TRP H 50 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3355) covalent geometry : angle 0.52847 ( 4559) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.82292 ( 12) hydrogen bonds : bond 0.03171 ( 99) hydrogen bonds : angle 6.60524 ( 243) link_BETA1-4 : bond 0.00121 ( 1) link_BETA1-4 : angle 1.55686 ( 3) link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.06619 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: R 369 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: R 394 ASN cc_start: 0.7845 (m-40) cc_final: 0.7414 (m110) REVERT: R 420 ASP cc_start: 0.8997 (m-30) cc_final: 0.8457 (m-30) REVERT: R 494 SER cc_start: 0.9090 (m) cc_final: 0.8797 (p) outliers start: 10 outliers final: 9 residues processed: 65 average time/residue: 0.0903 time to fit residues: 6.8452 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.086434 restraints weight = 4817.172| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.84 r_work: 0.2751 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3363 Z= 0.182 Angle : 0.545 6.309 4577 Z= 0.284 Chirality : 0.045 0.199 492 Planarity : 0.005 0.067 587 Dihedral : 5.455 45.063 502 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 3.45 % Allowed : 15.80 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.09 (0.41), residues: 406 helix: -4.03 (0.52), residues: 26 sheet: -0.35 (0.41), residues: 152 loop : -0.48 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.008 0.001 PHE R 374 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3355) covalent geometry : angle 0.54133 ( 4559) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.92080 ( 12) hydrogen bonds : bond 0.03243 ( 99) hydrogen bonds : angle 6.64067 ( 243) link_BETA1-4 : bond 0.00216 ( 1) link_BETA1-4 : angle 1.60958 ( 3) link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 1.14136 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.129 Fit side-chains REVERT: L 81 GLN cc_start: 0.8653 (mp10) cc_final: 0.7911 (mp10) REVERT: R 357 ARG cc_start: 0.8437 (ttt90) cc_final: 0.7957 (ttt90) REVERT: R 369 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: R 394 ASN cc_start: 0.7848 (m-40) cc_final: 0.7215 (m110) REVERT: R 420 ASP cc_start: 0.9022 (m-30) cc_final: 0.8368 (m-30) REVERT: R 494 SER cc_start: 0.9169 (m) cc_final: 0.8876 (p) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.0975 time to fit residues: 7.3966 Evaluate side-chains 71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.087537 restraints weight = 4730.768| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.85 r_work: 0.2760 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3363 Z= 0.162 Angle : 0.532 6.193 4577 Z= 0.278 Chirality : 0.045 0.195 492 Planarity : 0.005 0.066 587 Dihedral : 5.422 44.900 502 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 3.45 % Allowed : 15.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.03 (0.41), residues: 406 helix: -3.99 (0.53), residues: 26 sheet: -0.28 (0.41), residues: 152 loop : -0.46 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.007 0.001 PHE R 347 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3355) covalent geometry : angle 0.52859 ( 4559) SS BOND : bond 0.00199 ( 6) SS BOND : angle 0.85316 ( 12) hydrogen bonds : bond 0.03178 ( 99) hydrogen bonds : angle 6.62036 ( 243) link_BETA1-4 : bond 0.00125 ( 1) link_BETA1-4 : angle 1.58663 ( 3) link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 1.10211 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: H 105 TYR cc_start: 0.9105 (m-80) cc_final: 0.8867 (m-80) REVERT: L 81 GLN cc_start: 0.8598 (mp10) cc_final: 0.7816 (mp10) REVERT: L 84 ASP cc_start: 0.8213 (m-30) cc_final: 0.7952 (m-30) REVERT: R 369 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: R 394 ASN cc_start: 0.7901 (m-40) cc_final: 0.7621 (m110) REVERT: R 420 ASP cc_start: 0.8989 (m-30) cc_final: 0.8345 (m-30) REVERT: R 494 SER cc_start: 0.9156 (m) cc_final: 0.8872 (p) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.0880 time to fit residues: 6.8956 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.086744 restraints weight = 4645.951| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.83 r_work: 0.2762 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3363 Z= 0.167 Angle : 0.546 6.363 4577 Z= 0.286 Chirality : 0.046 0.193 492 Planarity : 0.005 0.067 587 Dihedral : 5.460 45.012 502 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 2.87 % Allowed : 16.38 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.01 (0.41), residues: 406 helix: -3.99 (0.53), residues: 26 sheet: -0.28 (0.42), residues: 152 loop : -0.43 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.007 0.001 PHE R 374 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 3355) covalent geometry : angle 0.54268 ( 4559) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.91007 ( 12) hydrogen bonds : bond 0.03179 ( 99) hydrogen bonds : angle 6.66216 ( 243) link_BETA1-4 : bond 0.00143 ( 1) link_BETA1-4 : angle 1.59974 ( 3) link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.11797 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.083 Fit side-chains REVERT: H 105 TYR cc_start: 0.9096 (m-80) cc_final: 0.8887 (m-80) REVERT: L 81 GLN cc_start: 0.8553 (mp10) cc_final: 0.7916 (mt0) REVERT: L 84 ASP cc_start: 0.8556 (m-30) cc_final: 0.8048 (m-30) REVERT: R 369 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: R 394 ASN cc_start: 0.7888 (m-40) cc_final: 0.7632 (m110) REVERT: R 420 ASP cc_start: 0.9017 (m-30) cc_final: 0.8371 (m-30) REVERT: R 494 SER cc_start: 0.9134 (m) cc_final: 0.8857 (p) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.0896 time to fit residues: 6.6157 Evaluate side-chains 67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.0010 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088079 restraints weight = 4759.401| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.86 r_work: 0.2778 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3363 Z= 0.124 Angle : 0.512 6.014 4577 Z= 0.268 Chirality : 0.045 0.180 492 Planarity : 0.005 0.066 587 Dihedral : 5.302 44.260 502 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.68 % Favored : 95.07 % Rotamer: Outliers : 3.16 % Allowed : 16.38 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.41), residues: 406 helix: -3.89 (0.55), residues: 26 sheet: -0.22 (0.42), residues: 152 loop : -0.41 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.006 0.001 PHE R 347 TRP 0.006 0.001 TRP L 96 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3355) covalent geometry : angle 0.50969 ( 4559) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.76764 ( 12) hydrogen bonds : bond 0.03033 ( 99) hydrogen bonds : angle 6.55677 ( 243) link_BETA1-4 : bond 0.00183 ( 1) link_BETA1-4 : angle 1.57858 ( 3) link_NAG-ASN : bond 0.00116 ( 1) link_NAG-ASN : angle 0.97049 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 990.92 seconds wall clock time: 17 minutes 35.57 seconds (1055.57 seconds total)