Starting phenix.real_space_refine on Wed Jun 4 22:42:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsi_34998/06_2025/8hsi_34998_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsi_34998/06_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_34998/06_2025/8hsi_34998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsi_34998/06_2025/8hsi_34998.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsi_34998/06_2025/8hsi_34998_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsi_34998/06_2025/8hsi_34998_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.40, per 1000 atoms: 0.97 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: 1.16 Conformation dependent library (CDL) restraints added in 866.8 milliseconds 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: 0.30 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: 0.90 Time building geometry restraints manager: 1.35 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- 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 : 14.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 43 PHE 0.026 0.001 PHE A 364 TYR 0.008 0.001 TYR A 104 ARG 0.005 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 3) link_NAG-ASN : angle 4.30231 ( 9) link_BETA1-4 : bond 0.00195 ( 4) link_BETA1-4 : angle 3.16151 ( 12) hydrogen bonds : bond 0.11749 ( 189) hydrogen bonds : angle 5.06371 ( 552) SS BOND : bond 0.00607 ( 2) SS BOND : angle 3.32056 ( 4) covalent geometry : bond 0.00494 ( 3611) covalent geometry : angle 0.84797 ( 4897) *********************** 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 : 0.364 Fit side-chains REVERT: A 112 ARG cc_start: 0.8856 (ptm-80) cc_final: 0.8337 (ttp80) REVERT: A 222 GLU cc_start: 0.6901 (tp30) cc_final: 0.6524 (tp30) 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: 0.8298 (m-30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1403 time to fit residues: 8.1079 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 : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.110423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080075 restraints weight = 5818.431| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.61 r_work: 0.2910 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3620 Z= 0.138 Angle : 0.630 7.767 4922 Z= 0.295 Chirality : 0.042 0.226 575 Planarity : 0.004 0.058 564 Dihedral : 16.985 88.860 757 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.23 % Allowed : 6.13 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.45), residues: 399 helix: 2.35 (0.40), residues: 208 sheet: 1.34 (0.64), residues: 63 loop : -3.03 (0.44), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 171 PHE 0.008 0.001 PHE A 276 TYR 0.006 0.001 TYR A 83 ARG 0.004 0.000 ARG A 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 3) link_NAG-ASN : angle 2.19315 ( 9) link_BETA1-4 : bond 0.00588 ( 4) link_BETA1-4 : angle 3.50023 ( 12) hydrogen bonds : bond 0.04197 ( 189) hydrogen bonds : angle 3.61278 ( 552) SS BOND : bond 0.00477 ( 2) SS BOND : angle 1.82316 ( 4) covalent geometry : bond 0.00332 ( 3611) covalent geometry : angle 0.59746 ( 4897) *********************** 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 44 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8989 (ptm-80) cc_final: 0.8457 (ttp80) REVERT: A 314 ILE cc_start: 0.8749 (tp) cc_final: 0.8529 (tp) REVERT: A 409 ILE cc_start: 0.8644 (tt) cc_final: 0.8377 (pt) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.1325 time to fit residues: 7.1635 Evaluate side-chains 42 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 31 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.0010 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5566 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.110464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079597 restraints weight = 5807.562| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.73 r_work: 0.2888 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3620 Z= 0.122 Angle : 0.613 7.789 4922 Z= 0.285 Chirality : 0.041 0.242 575 Planarity : 0.003 0.044 564 Dihedral : 13.102 81.670 757 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.39 % Allowed : 11.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.45), residues: 399 helix: 2.57 (0.39), residues: 208 sheet: 1.58 (0.64), residues: 63 loop : -3.35 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 43 PHE 0.013 0.001 PHE A 132 TYR 0.007 0.001 TYR A 83 ARG 0.003 0.000 ARG A 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 3) link_NAG-ASN : angle 2.47968 ( 9) link_BETA1-4 : bond 0.00803 ( 4) link_BETA1-4 : angle 3.64360 ( 12) hydrogen bonds : bond 0.04185 ( 189) hydrogen bonds : angle 3.30580 ( 552) SS BOND : bond 0.00254 ( 2) SS BOND : angle 1.12452 ( 4) covalent geometry : bond 0.00282 ( 3611) covalent geometry : angle 0.57709 ( 4897) *********************** 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 42 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8998 (ptm-80) cc_final: 0.8463 (ttp80) REVERT: A 208 MET cc_start: 0.9007 (ttp) cc_final: 0.8741 (ttp) REVERT: A 409 ILE cc_start: 0.8552 (tt) cc_final: 0.8288 (pt) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.1365 time to fit residues: 7.1904 Evaluate side-chains 37 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.108653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.077749 restraints weight = 5833.203| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.71 r_work: 0.2851 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3620 Z= 0.146 Angle : 0.607 7.954 4922 Z= 0.287 Chirality : 0.040 0.255 575 Planarity : 0.003 0.040 564 Dihedral : 11.304 73.707 757 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.95 % Allowed : 13.09 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.45), residues: 399 helix: 2.67 (0.39), residues: 209 sheet: 1.67 (0.64), residues: 63 loop : -3.35 (0.42), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 82 HIS 0.001 0.001 HIS A 143 PHE 0.008 0.001 PHE A 60 TYR 0.008 0.001 TYR A 401 ARG 0.002 0.000 ARG A 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 3) link_NAG-ASN : angle 2.37032 ( 9) link_BETA1-4 : bond 0.00747 ( 4) link_BETA1-4 : angle 3.60336 ( 12) hydrogen bonds : bond 0.04719 ( 189) hydrogen bonds : angle 3.34657 ( 552) SS BOND : bond 0.00392 ( 2) SS BOND : angle 0.94706 ( 4) covalent geometry : bond 0.00348 ( 3611) covalent geometry : angle 0.57268 ( 4897) *********************** 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 40 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 409 ILE cc_start: 0.8532 (tt) cc_final: 0.8254 (pt) outliers start: 7 outliers final: 7 residues processed: 38 average time/residue: 0.1402 time to fit residues: 7.0363 Evaluate side-chains 38 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.109941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.079243 restraints weight = 5822.297| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.72 r_work: 0.2810 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3620 Z= 0.112 Angle : 0.587 8.470 4922 Z= 0.274 Chirality : 0.039 0.250 575 Planarity : 0.003 0.036 564 Dihedral : 10.448 68.761 757 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.46), residues: 399 helix: 2.88 (0.39), residues: 208 sheet: 1.70 (0.64), residues: 63 loop : -3.35 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 PHE 0.008 0.001 PHE A 55 TYR 0.007 0.001 TYR A 83 ARG 0.004 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 3) link_NAG-ASN : angle 2.29002 ( 9) link_BETA1-4 : bond 0.00853 ( 4) link_BETA1-4 : angle 3.62815 ( 12) hydrogen bonds : bond 0.04169 ( 189) hydrogen bonds : angle 3.24207 ( 552) SS BOND : bond 0.00312 ( 2) SS BOND : angle 0.85227 ( 4) covalent geometry : bond 0.00255 ( 3611) covalent geometry : angle 0.55098 ( 4897) *********************** 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 41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 112 ARG cc_start: 0.9016 (ptm-80) cc_final: 0.8446 (ttp80) REVERT: A 279 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 409 ILE cc_start: 0.8425 (tt) cc_final: 0.8159 (pt) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.1267 time to fit residues: 6.5757 Evaluate side-chains 37 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.0010 chunk 24 optimal weight: 0.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.110185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.079581 restraints weight = 5864.844| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.71 r_work: 0.2820 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1830 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= 0.112 Angle : 0.596 8.442 4922 Z= 0.278 Chirality : 0.039 0.220 575 Planarity : 0.003 0.034 564 Dihedral : 9.715 64.825 757 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.79 % Allowed : 12.81 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.46), residues: 399 helix: 2.99 (0.39), residues: 208 sheet: 1.79 (0.64), residues: 63 loop : -3.37 (0.43), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 PHE 0.009 0.001 PHE A 55 TYR 0.008 0.001 TYR A 83 ARG 0.005 0.000 ARG A 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 2.26754 ( 9) link_BETA1-4 : bond 0.00901 ( 4) link_BETA1-4 : angle 3.61218 ( 12) hydrogen bonds : bond 0.04026 ( 189) hydrogen bonds : angle 3.19986 ( 552) SS BOND : bond 0.01015 ( 2) SS BOND : angle 2.22457 ( 4) covalent geometry : bond 0.00253 ( 3611) covalent geometry : angle 0.55849 ( 4897) *********************** 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 44 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8377 (mt) REVERT: A 112 ARG cc_start: 0.8992 (ptm-80) cc_final: 0.8428 (ttp80) REVERT: A 279 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 409 ILE cc_start: 0.8420 (tt) cc_final: 0.8168 (pt) outliers start: 10 outliers final: 7 residues processed: 41 average time/residue: 0.1395 time to fit residues: 7.5321 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 : 0.386 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076896 restraints weight = 5876.626| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.60 r_work: 0.2787 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3620 Z= 0.157 Angle : 0.613 7.914 4922 Z= 0.291 Chirality : 0.039 0.172 575 Planarity : 0.003 0.036 564 Dihedral : 9.350 57.363 757 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.46), residues: 399 helix: 2.95 (0.39), residues: 210 sheet: 1.83 (0.64), residues: 63 loop : -3.40 (0.42), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 82 HIS 0.001 0.001 HIS A 187 PHE 0.008 0.001 PHE A 132 TYR 0.008 0.001 TYR A 401 ARG 0.006 0.000 ARG A 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 3) link_NAG-ASN : angle 2.36252 ( 9) link_BETA1-4 : bond 0.00926 ( 4) link_BETA1-4 : angle 3.58429 ( 12) hydrogen bonds : bond 0.04817 ( 189) hydrogen bonds : angle 3.29073 ( 552) SS BOND : bond 0.00638 ( 2) SS BOND : angle 1.74391 ( 4) covalent geometry : bond 0.00373 ( 3611) covalent geometry : angle 0.57780 ( 4897) *********************** 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 42 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 409 ILE cc_start: 0.8529 (tt) cc_final: 0.8254 (pt) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.1402 time to fit residues: 7.1755 Evaluate side-chains 41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 328 VAL 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 17 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 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 = 0.3483 r_free = 0.3483 target = 0.106777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.075918 restraints weight = 5846.564| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.66 r_work: 0.2800 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2073 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= 0.127 Angle : 0.584 8.056 4922 Z= 0.277 Chirality : 0.038 0.150 575 Planarity : 0.003 0.037 564 Dihedral : 8.920 57.472 757 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.23 % Allowed : 14.76 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.46), residues: 399 helix: 3.05 (0.39), residues: 209 sheet: 1.82 (0.64), residues: 63 loop : -3.33 (0.43), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 143 PHE 0.009 0.001 PHE A 55 TYR 0.007 0.001 TYR A 224 ARG 0.007 0.000 ARG A 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 3) link_NAG-ASN : angle 2.28104 ( 9) link_BETA1-4 : bond 0.01010 ( 4) link_BETA1-4 : angle 3.62126 ( 12) hydrogen bonds : bond 0.04422 ( 189) hydrogen bonds : angle 3.23881 ( 552) SS BOND : bond 0.00456 ( 2) SS BOND : angle 1.56798 ( 4) covalent geometry : bond 0.00296 ( 3611) covalent geometry : angle 0.54710 ( 4897) *********************** 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 43 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 409 ILE cc_start: 0.8573 (tt) cc_final: 0.8305 (pt) REVERT: A 466 ASN cc_start: 0.8567 (t0) cc_final: 0.8198 (t0) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.1402 time to fit residues: 7.5480 Evaluate side-chains 40 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 328 VAL 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 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.077324 restraints weight = 5798.555| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.59 r_work: 0.2872 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3620 Z= 0.139 Angle : 0.588 8.137 4922 Z= 0.282 Chirality : 0.039 0.139 575 Planarity : 0.003 0.037 564 Dihedral : 8.732 57.414 757 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.95 % Allowed : 15.32 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.46), residues: 399 helix: 3.00 (0.39), residues: 210 sheet: 1.84 (0.64), residues: 63 loop : -3.38 (0.43), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.002 0.001 HIS A 143 PHE 0.025 0.001 PHE A 206 TYR 0.009 0.001 TYR A 319 ARG 0.006 0.000 ARG A 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 2.28585 ( 9) link_BETA1-4 : bond 0.00998 ( 4) link_BETA1-4 : angle 3.57908 ( 12) hydrogen bonds : bond 0.04585 ( 189) hydrogen bonds : angle 3.28229 ( 552) SS BOND : bond 0.00451 ( 2) SS BOND : angle 1.54091 ( 4) covalent geometry : bond 0.00328 ( 3611) covalent geometry : angle 0.55153 ( 4897) *********************** 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: 7 poor density : 35 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8601 (tm-30) REVERT: A 409 ILE cc_start: 0.8601 (tt) cc_final: 0.8335 (pt) REVERT: A 466 ASN cc_start: 0.8506 (t0) cc_final: 0.8143 (t0) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.1432 time to fit residues: 7.7384 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 : 0.404 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 328 VAL 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 5 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.108031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.077937 restraints weight = 5896.647| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.60 r_work: 0.2816 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2183 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= 0.124 Angle : 0.579 8.014 4922 Z= 0.278 Chirality : 0.039 0.140 575 Planarity : 0.003 0.037 564 Dihedral : 8.602 57.262 757 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.23 % Allowed : 15.04 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.46), residues: 399 helix: 3.06 (0.39), residues: 209 sheet: 1.83 (0.64), residues: 63 loop : -3.34 (0.43), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.001 0.000 HIS A 171 PHE 0.018 0.001 PHE A 206 TYR 0.007 0.001 TYR A 83 ARG 0.009 0.001 ARG A 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 3) link_NAG-ASN : angle 2.24251 ( 9) link_BETA1-4 : bond 0.01026 ( 4) link_BETA1-4 : angle 3.55757 ( 12) hydrogen bonds : bond 0.04332 ( 189) hydrogen bonds : angle 3.23963 ( 552) SS BOND : bond 0.00390 ( 2) SS BOND : angle 1.48605 ( 4) covalent geometry : bond 0.00288 ( 3611) covalent geometry : angle 0.54266 ( 4897) ********************** 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 41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 409 ILE cc_start: 0.8522 (tt) cc_final: 0.8264 (pt) REVERT: A 466 ASN cc_start: 0.8564 (t0) cc_final: 0.8190 (t0) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.1318 time to fit residues: 6.9498 Evaluate side-chains 40 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 328 VAL 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 30 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 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 = 0.3522 r_free = 0.3522 target = 0.107024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076888 restraints weight = 5855.248| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.58 r_work: 0.2856 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3620 Z= 0.141 Angle : 0.572 7.729 4922 Z= 0.278 Chirality : 0.038 0.139 575 Planarity : 0.003 0.037 564 Dihedral : 8.622 57.330 757 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.95 % Allowed : 15.32 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.46), residues: 399 helix: 2.98 (0.39), residues: 210 sheet: 1.85 (0.64), residues: 63 loop : -3.34 (0.43), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.000 HIS A 171 PHE 0.017 0.001 PHE A 206 TYR 0.007 0.001 TYR A 401 ARG 0.010 0.001 ARG A 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 3) link_NAG-ASN : angle 2.27761 ( 9) link_BETA1-4 : bond 0.01015 ( 4) link_BETA1-4 : angle 3.46750 ( 12) hydrogen bonds : bond 0.04628 ( 189) hydrogen bonds : angle 3.25664 ( 552) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.54625 ( 4) covalent geometry : bond 0.00334 ( 3611) covalent geometry : angle 0.53653 ( 4897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.37 seconds wall clock time: 37 minutes 36.65 seconds (2256.65 seconds total)