Starting phenix.real_space_refine on Fri Aug 22 14:45:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsi_34998/08_2025/8hsi_34998_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsi_34998/08_2025/8hsi_34998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hsi_34998/08_2025/8hsi_34998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsi_34998/08_2025/8hsi_34998.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsi_34998/08_2025/8hsi_34998_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsi_34998/08_2025/8hsi_34998_trim.cif" } resolution = 3.1 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= 0.011 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 19 5.16 5 C 2352 2.51 5 N 541 2.21 5 O 603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3516 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3314 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 12, 'TRANS': 392} Chain breaks: 2 Chain: "B" 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 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 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'CLR': 2, 'L9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.96, per 1000 atoms: 0.27 Number of scatterers: 3516 At special positions: 0 Unit cell: (57.732, 60.279, 118.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 1 15.00 O 603 8.00 N 541 7.00 C 2352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.02 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN A 79 " " NAG C 1 " - " ASN A 62 " " NAG D 1 " - " ASN A 127 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 78.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 52.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 108 removed outlier: 4.391A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 Processing helix chain 'A' and resid 257 through 287 removed outlier: 3.932A pdb=" N TRP A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 317 Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 338 through 353 removed outlier: 3.566A pdb=" N LEU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 392 Proline residue: A 366 - end of helix removed outlier: 3.672A pdb=" N LEU A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 426 removed outlier: 3.686A pdb=" N SER A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 189 hydrogen bonds defined for protein. 552 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: 0.44 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 500 1.31 - 1.44: 1056 1.44 - 1.57: 2022 1.57 - 1.70: 2 1.70 - 1.83: 31 Bond restraints: 3611 Sorted by residual: bond pdb=" C GLU A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 1.331 1.384 -0.053 1.31e-02 5.83e+03 1.66e+01 bond pdb=" C GLY A 292 " pdb=" N ALA A 293 " ideal model delta sigma weight residual 1.332 1.276 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C31 L9Q A 601 " pdb=" O2 L9Q A 601 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C11 L9Q A 601 " pdb=" O3 L9Q A 601 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C4 CLR A 602 " pdb=" C5 CLR A 602 " ideal model delta sigma weight residual 1.506 1.440 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 3606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 4791 2.54 - 5.09: 84 5.09 - 7.63: 16 7.63 - 10.17: 3 10.17 - 12.71: 3 Bond angle restraints: 4897 Sorted by residual: angle pdb=" C PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta sigma weight residual 110.98 123.69 -12.71 1.31e+00 5.83e-01 9.42e+01 angle pdb=" CA ILE A 46 " pdb=" C ILE A 46 " pdb=" N PRO A 47 " ideal model delta sigma weight residual 120.83 124.77 -3.94 6.10e-01 2.69e+00 4.18e+01 angle pdb=" CA ILE A 46 " pdb=" C ILE A 46 " pdb=" O ILE A 46 " ideal model delta sigma weight residual 118.69 114.65 4.04 6.70e-01 2.23e+00 3.63e+01 angle pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta sigma weight residual 103.33 108.25 -4.92 9.30e-01 1.16e+00 2.80e+01 angle pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" CD PRO A 73 " ideal model delta sigma weight residual 112.00 104.62 7.38 1.40e+00 5.10e-01 2.78e+01 ... (remaining 4892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.28: 2094 22.28 - 44.56: 148 44.56 - 66.84: 29 66.84 - 89.12: 10 89.12 - 111.40: 21 Dihedral angle restraints: 2302 sinusoidal: 1113 harmonic: 1189 Sorted by residual: dihedral pdb=" C PRO A 73 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta harmonic sigma weight residual -120.70 -135.81 15.11 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -36.80 -49.20 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" N PRO A 73 " pdb=" C PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta harmonic sigma weight residual 115.10 127.29 -12.19 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 2299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 560 0.110 - 0.221: 11 0.221 - 0.331: 3 0.331 - 0.441: 0 0.441 - 0.552: 1 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" C PRO A 73 " pdb=" CB PRO A 73 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 127 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 572 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 73 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PRO A 73 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO A 73 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS A 74 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 292 " -0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLY A 292 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY A 292 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 293 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 293 " 0.015 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA A 293 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA A 293 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 294 " 0.019 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 974 2.82 - 3.34: 3205 3.34 - 3.86: 5273 3.86 - 4.38: 5675 4.38 - 4.90: 10482 Nonbonded interactions: 25609 Sorted by model distance: nonbonded pdb=" O ASN A 465 " pdb=" NH1 ARG A 468 " model vdw 2.299 3.120 nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.300 3.040 nonbonded pdb=" CD GLU A 279 " pdb=" CB ALA A 293 " model vdw 2.405 3.690 nonbonded pdb=" O5 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 2.453 2.432 nonbonded pdb=" N GLU A 217 " pdb=" OE1 GLU A 217 " model vdw 2.456 3.120 ... (remaining 25604 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 4.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.005 0.072 3620 Z= 0.270 Angle : 0.885 12.714 4922 Z= 0.461 Chirality : 0.051 0.552 575 Planarity : 0.004 0.037 564 Dihedral : 19.622 111.397 1526 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.26 % 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 aren not related in a simple way. whole: 0.27 (0.44), residues: 399 helix: 1.76 (0.38), residues: 206 sheet: 0.82 (0.64), residues: 65 loop : -3.00 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.008 0.001 TYR A 104 PHE 0.026 0.001 PHE A 364 TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 3611) covalent geometry : angle 0.84797 ( 4897) SS BOND : bond 0.00607 ( 2) SS BOND : angle 3.32056 ( 4) hydrogen bonds : bond 0.11749 ( 189) hydrogen bonds : angle 5.06371 ( 552) link_BETA1-4 : bond 0.00195 ( 4) link_BETA1-4 : angle 3.16151 ( 12) link_NAG-ASN : bond 0.00216 ( 3) link_NAG-ASN : angle 4.30231 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.103 Fit side-chains REVERT: A 112 ARG cc_start: 0.8856 (ptm-80) cc_final: 0.8337 (ttp80) REVERT: A 409 ILE cc_start: 0.8463 (tt) cc_final: 0.8209 (pt) REVERT: A 442 ASP cc_start: 0.8511 (m-30) cc_final: 0.8297 (m-30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0440 time to fit residues: 2.5901 Evaluate side-chains 35 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.111536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081540 restraints weight = 5906.382| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.62 r_work: 0.2931 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3620 Z= 0.116 Angle : 0.625 7.944 4922 Z= 0.290 Chirality : 0.042 0.245 575 Planarity : 0.004 0.053 564 Dihedral : 16.781 89.040 757 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.95 % Allowed : 6.13 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.45), residues: 399 helix: 2.40 (0.40), residues: 208 sheet: 1.54 (0.64), residues: 61 loop : -3.06 (0.44), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 468 TYR 0.007 0.001 TYR A 83 PHE 0.008 0.001 PHE A 276 TRP 0.007 0.001 TRP A 82 HIS 0.001 0.000 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3611) covalent geometry : angle 0.59259 ( 4897) SS BOND : bond 0.00477 ( 2) SS BOND : angle 1.82672 ( 4) hydrogen bonds : bond 0.03753 ( 189) hydrogen bonds : angle 3.54828 ( 552) link_BETA1-4 : bond 0.00531 ( 4) link_BETA1-4 : angle 3.56178 ( 12) link_NAG-ASN : bond 0.00123 ( 3) link_NAG-ASN : angle 2.10577 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8407 (mt) REVERT: A 112 ARG cc_start: 0.8981 (ptm-80) cc_final: 0.8460 (ttp80) REVERT: A 144 ARG cc_start: 0.8267 (ptp90) cc_final: 0.7799 (ptp90) REVERT: A 314 ILE cc_start: 0.8759 (tp) cc_final: 0.8557 (tp) REVERT: A 409 ILE cc_start: 0.8624 (tt) cc_final: 0.8360 (pt) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0495 time to fit residues: 2.6819 Evaluate side-chains 41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 420 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.110802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079826 restraints weight = 5758.032| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.74 r_work: 0.2874 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3620 Z= 0.134 Angle : 0.614 7.610 4922 Z= 0.284 Chirality : 0.041 0.232 575 Planarity : 0.003 0.043 564 Dihedral : 13.058 82.536 757 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.67 % Allowed : 11.70 % Favored : 86.63 % 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 aren not related in a simple way. whole: 1.02 (0.45), residues: 399 helix: 2.51 (0.39), residues: 209 sheet: 1.66 (0.65), residues: 63 loop : -3.32 (0.41), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.011 0.001 TYR A 319 PHE 0.008 0.001 PHE A 206 TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3611) covalent geometry : angle 0.57767 ( 4897) SS BOND : bond 0.00273 ( 2) SS BOND : angle 1.14136 ( 4) hydrogen bonds : bond 0.04442 ( 189) hydrogen bonds : angle 3.35810 ( 552) link_BETA1-4 : bond 0.00767 ( 4) link_BETA1-4 : angle 3.61828 ( 12) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 2.53929 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.122 Fit side-chains REVERT: A 112 ARG cc_start: 0.8992 (ptm-80) cc_final: 0.8458 (ttp80) REVERT: A 409 ILE cc_start: 0.8538 (tt) cc_final: 0.8264 (pt) outliers start: 6 outliers final: 6 residues processed: 40 average time/residue: 0.0433 time to fit residues: 2.2766 Evaluate side-chains 37 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 18 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.111532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080960 restraints weight = 5759.362| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.68 r_work: 0.2906 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3620 Z= 0.103 Angle : 0.578 7.844 4922 Z= 0.268 Chirality : 0.039 0.265 575 Planarity : 0.003 0.038 564 Dihedral : 11.398 80.432 757 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.23 % Allowed : 11.70 % Favored : 86.07 % 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 aren not related in a simple way. whole: 1.21 (0.45), residues: 399 helix: 2.70 (0.39), residues: 209 sheet: 1.73 (0.65), residues: 63 loop : -3.29 (0.42), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.007 0.001 TYR A 83 PHE 0.008 0.001 PHE A 55 TRP 0.007 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3611) covalent geometry : angle 0.54144 ( 4897) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.75791 ( 4) hydrogen bonds : bond 0.03810 ( 189) hydrogen bonds : angle 3.24537 ( 552) link_BETA1-4 : bond 0.00764 ( 4) link_BETA1-4 : angle 3.68573 ( 12) link_NAG-ASN : bond 0.00094 ( 3) link_NAG-ASN : angle 2.20121 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8407 (mt) REVERT: A 112 ARG cc_start: 0.9005 (ptm-80) cc_final: 0.8475 (ttp80) REVERT: A 409 ILE cc_start: 0.8487 (tt) cc_final: 0.8228 (pt) outliers start: 8 outliers final: 7 residues processed: 39 average time/residue: 0.0493 time to fit residues: 2.5031 Evaluate side-chains 39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.108992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.078712 restraints weight = 5728.245| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.65 r_work: 0.2861 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3620 Z= 0.149 Angle : 0.600 8.446 4922 Z= 0.281 Chirality : 0.040 0.243 575 Planarity : 0.003 0.037 564 Dihedral : 10.509 71.882 757 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.79 % Allowed : 12.53 % Favored : 84.68 % 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 aren not related in a simple way. whole: 1.23 (0.45), residues: 399 helix: 2.77 (0.39), residues: 209 sheet: 1.72 (0.64), residues: 63 loop : -3.37 (0.42), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 144 TYR 0.008 0.001 TYR A 401 PHE 0.007 0.001 PHE A 60 TRP 0.009 0.001 TRP A 82 HIS 0.001 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3611) covalent geometry : angle 0.56513 ( 4897) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.98989 ( 4) hydrogen bonds : bond 0.04642 ( 189) hydrogen bonds : angle 3.31771 ( 552) link_BETA1-4 : bond 0.00854 ( 4) link_BETA1-4 : angle 3.57427 ( 12) link_NAG-ASN : bond 0.00150 ( 3) link_NAG-ASN : angle 2.33944 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8992 (ptm-80) cc_final: 0.8456 (ttp80) REVERT: A 409 ILE cc_start: 0.8567 (tt) cc_final: 0.8291 (pt) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.0480 time to fit residues: 2.5311 Evaluate side-chains 39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 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 = 0.3534 r_free = 0.3534 target = 0.109298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078969 restraints weight = 5801.456| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.67 r_work: 0.2866 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3620 Z= 0.131 Angle : 0.604 8.476 4922 Z= 0.283 Chirality : 0.039 0.222 575 Planarity : 0.003 0.035 564 Dihedral : 9.827 66.175 757 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.34 % Allowed : 13.37 % Favored : 83.29 % 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 aren not related in a simple way. whole: 1.34 (0.46), residues: 399 helix: 2.87 (0.39), residues: 209 sheet: 1.74 (0.65), residues: 63 loop : -3.34 (0.43), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 144 TYR 0.007 0.001 TYR A 83 PHE 0.008 0.001 PHE A 55 TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3611) covalent geometry : angle 0.56705 ( 4897) SS BOND : bond 0.00674 ( 2) SS BOND : angle 2.23669 ( 4) hydrogen bonds : bond 0.04424 ( 189) hydrogen bonds : angle 3.27672 ( 552) link_BETA1-4 : bond 0.00873 ( 4) link_BETA1-4 : angle 3.60592 ( 12) link_NAG-ASN : bond 0.00060 ( 3) link_NAG-ASN : angle 2.27205 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.9007 (ptm-80) cc_final: 0.8477 (ttp80) REVERT: A 279 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 409 ILE cc_start: 0.8546 (tt) cc_final: 0.8267 (pt) outliers start: 12 outliers final: 8 residues processed: 43 average time/residue: 0.0540 time to fit residues: 3.0641 Evaluate side-chains 39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.107438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077203 restraints weight = 5945.139| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.64 r_work: 0.2848 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3620 Z= 0.152 Angle : 0.612 8.054 4922 Z= 0.292 Chirality : 0.039 0.179 575 Planarity : 0.003 0.036 564 Dihedral : 9.418 59.747 757 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.79 % Allowed : 13.93 % Favored : 83.29 % 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 aren not related in a simple way. whole: 1.35 (0.46), residues: 399 helix: 2.90 (0.39), residues: 209 sheet: 1.77 (0.65), residues: 63 loop : -3.41 (0.42), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 144 TYR 0.008 0.001 TYR A 401 PHE 0.007 0.001 PHE A 55 TRP 0.009 0.001 TRP A 82 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3611) covalent geometry : angle 0.57629 ( 4897) SS BOND : bond 0.00620 ( 2) SS BOND : angle 1.68614 ( 4) hydrogen bonds : bond 0.04737 ( 189) hydrogen bonds : angle 3.30259 ( 552) link_BETA1-4 : bond 0.00942 ( 4) link_BETA1-4 : angle 3.59159 ( 12) link_NAG-ASN : bond 0.00113 ( 3) link_NAG-ASN : angle 2.34364 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8616 (tm-30) REVERT: A 409 ILE cc_start: 0.8622 (tt) cc_final: 0.8353 (pt) outliers start: 10 outliers final: 9 residues processed: 40 average time/residue: 0.0588 time to fit residues: 3.0669 Evaluate side-chains 39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.106568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.076465 restraints weight = 5966.950| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.62 r_work: 0.2837 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3620 Z= 0.160 Angle : 0.608 8.036 4922 Z= 0.292 Chirality : 0.039 0.146 575 Planarity : 0.003 0.039 564 Dihedral : 9.063 58.233 757 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.51 % Allowed : 15.32 % Favored : 82.17 % 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 aren not related in a simple way. whole: 1.39 (0.46), residues: 399 helix: 2.91 (0.39), residues: 210 sheet: 1.75 (0.65), residues: 63 loop : -3.35 (0.43), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 144 TYR 0.007 0.001 TYR A 401 PHE 0.008 0.001 PHE A 364 TRP 0.008 0.001 TRP A 82 HIS 0.001 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3611) covalent geometry : angle 0.57290 ( 4897) SS BOND : bond 0.00543 ( 2) SS BOND : angle 1.64646 ( 4) hydrogen bonds : bond 0.04931 ( 189) hydrogen bonds : angle 3.34530 ( 552) link_BETA1-4 : bond 0.00983 ( 4) link_BETA1-4 : angle 3.58722 ( 12) link_NAG-ASN : bond 0.00113 ( 3) link_NAG-ASN : angle 2.34316 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8990 (ptm-80) cc_final: 0.8417 (ttp80) REVERT: A 279 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 409 ILE cc_start: 0.8635 (tt) cc_final: 0.8347 (pt) outliers start: 9 outliers final: 8 residues processed: 39 average time/residue: 0.0574 time to fit residues: 2.8718 Evaluate side-chains 40 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.107955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078200 restraints weight = 5753.302| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.55 r_work: 0.2871 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3620 Z= 0.125 Angle : 0.580 8.089 4922 Z= 0.279 Chirality : 0.038 0.141 575 Planarity : 0.003 0.040 564 Dihedral : 8.729 57.711 757 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.51 % Allowed : 15.32 % Favored : 82.17 % 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 aren not related in a simple way. whole: 1.48 (0.46), residues: 399 helix: 3.07 (0.39), residues: 208 sheet: 1.78 (0.65), residues: 63 loop : -3.38 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 144 TYR 0.007 0.001 TYR A 224 PHE 0.010 0.001 PHE A 55 TRP 0.008 0.001 TRP A 376 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3611) covalent geometry : angle 0.54298 ( 4897) SS BOND : bond 0.00436 ( 2) SS BOND : angle 1.46389 ( 4) hydrogen bonds : bond 0.04424 ( 189) hydrogen bonds : angle 3.28392 ( 552) link_BETA1-4 : bond 0.01011 ( 4) link_BETA1-4 : angle 3.58776 ( 12) link_NAG-ASN : bond 0.00046 ( 3) link_NAG-ASN : angle 2.27195 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8586 (tm-30) REVERT: A 409 ILE cc_start: 0.8586 (tt) cc_final: 0.8326 (pt) REVERT: A 466 ASN cc_start: 0.8542 (t0) cc_final: 0.8179 (t0) outliers start: 9 outliers final: 7 residues processed: 40 average time/residue: 0.0425 time to fit residues: 2.2846 Evaluate side-chains 39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.107476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077119 restraints weight = 5954.470| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.66 r_work: 0.2863 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3620 Z= 0.138 Angle : 0.586 7.963 4922 Z= 0.284 Chirality : 0.038 0.139 575 Planarity : 0.003 0.042 564 Dihedral : 8.661 57.398 757 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.95 % Allowed : 15.88 % Favored : 82.17 % 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 aren not related in a simple way. whole: 1.48 (0.46), residues: 399 helix: 3.03 (0.39), residues: 209 sheet: 1.77 (0.65), residues: 63 loop : -3.35 (0.43), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 144 TYR 0.008 0.001 TYR A 319 PHE 0.009 0.001 PHE A 364 TRP 0.008 0.001 TRP A 82 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3611) covalent geometry : angle 0.55046 ( 4897) SS BOND : bond 0.00438 ( 2) SS BOND : angle 1.51722 ( 4) hydrogen bonds : bond 0.04569 ( 189) hydrogen bonds : angle 3.28664 ( 552) link_BETA1-4 : bond 0.01040 ( 4) link_BETA1-4 : angle 3.52694 ( 12) link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 2.26425 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8614 (tm-30) REVERT: A 409 ILE cc_start: 0.8625 (tt) cc_final: 0.8360 (pt) REVERT: A 466 ASN cc_start: 0.8522 (t0) cc_final: 0.8161 (t0) outliers start: 7 outliers final: 7 residues processed: 38 average time/residue: 0.0492 time to fit residues: 2.4292 Evaluate side-chains 39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 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 = 0.3521 r_free = 0.3521 target = 0.107302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.077456 restraints weight = 5812.701| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.57 r_work: 0.2858 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3620 Z= 0.141 Angle : 0.579 7.670 4922 Z= 0.281 Chirality : 0.038 0.139 575 Planarity : 0.003 0.045 564 Dihedral : 8.644 57.619 757 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.23 % Allowed : 15.88 % Favored : 81.89 % 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 aren not related in a simple way. whole: 1.50 (0.46), residues: 399 helix: 3.07 (0.39), residues: 208 sheet: 1.80 (0.65), residues: 63 loop : -3.35 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 144 TYR 0.007 0.001 TYR A 401 PHE 0.009 0.001 PHE A 55 TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3611) covalent geometry : angle 0.54421 ( 4897) SS BOND : bond 0.00416 ( 2) SS BOND : angle 1.53072 ( 4) hydrogen bonds : bond 0.04626 ( 189) hydrogen bonds : angle 3.28325 ( 552) link_BETA1-4 : bond 0.01008 ( 4) link_BETA1-4 : angle 3.45296 ( 12) link_NAG-ASN : bond 0.00037 ( 3) link_NAG-ASN : angle 2.29255 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 886.45 seconds wall clock time: 15 minutes 57.50 seconds (957.50 seconds total)