Starting phenix.real_space_refine on Tue Aug 4 15:24:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yt4_73441/08_2026/9yt4_73441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yt4_73441/08_2026/9yt4_73441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yt4_73441/08_2026/9yt4_73441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yt4_73441/08_2026/9yt4_73441.map" model { file = "/net/cci-nas-00/data/ceres_data/9yt4_73441/08_2026/9yt4_73441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yt4_73441/08_2026/9yt4_73441.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2725 2.51 5 N 677 2.21 5 O 809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4229 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1961 Classifications: {'peptide': 244} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2114 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 17, 'TRANS': 248} Chain breaks: 1 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: "D" 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: "E" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.79, per 1000 atoms: 0.19 Number of scatterers: 4229 At special positions: 0 Unit cell: (84.032, 86.528, 85.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 809 8.00 N 677 7.00 C 2725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B 1 " - " ASN C 120 " " NAG C1301 " - " ASN C 230 " " NAG C1302 " - " ASN C 241 " " NAG C1303 " - " ASN C 162 " " NAG D 1 " - " ASN C 278 " " NAG E 1 " - " ASN A 354 " Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 97.8 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 958 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 7.1% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.006A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.361A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 29 removed outlier: 7.872A pdb=" N ASN C 61 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR C 265 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE C 198 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP C 224 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE C 200 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.729A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.869A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.677A pdb=" N GLY C 101 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA C 239 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE C 99 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 118 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 169 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 165 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU C 130 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N CYS C 163 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLN C 132 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N ASN C 161 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.013A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 133 hydrogen bonds defined for protein. 327 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: 0.55 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1285 1.34 - 1.46: 1143 1.46 - 1.58: 1891 1.58 - 1.70: 0 1.70 - 1.83: 21 Bond restraints: 4340 Sorted by residual: bond pdb=" N ASN C 185 " pdb=" CA ASN C 185 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.25e-02 6.40e+03 6.29e+00 bond pdb=" N LEU C 186 " pdb=" CA LEU C 186 " ideal model delta sigma weight residual 1.461 1.487 -0.025 1.38e-02 5.25e+03 3.39e+00 bond pdb=" N PHE C 212 " pdb=" CA PHE C 212 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.37e+00 bond pdb=" C PHE C 212 " pdb=" N PRO C 213 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.34e-02 5.57e+03 2.30e+00 bond pdb=" N LYS C 184 " pdb=" CA LYS C 184 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.30e+00 ... (remaining 4335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 5793 2.12 - 4.24: 95 4.24 - 6.36: 6 6.36 - 8.48: 3 8.48 - 10.60: 1 Bond angle restraints: 5898 Sorted by residual: angle pdb=" C SER C 69 " pdb=" CA SER C 69 " pdb=" CB SER C 69 " ideal model delta sigma weight residual 116.54 110.80 5.74 1.15e+00 7.56e-01 2.49e+01 angle pdb=" CB MET C 16 " pdb=" CG MET C 16 " pdb=" SD MET C 16 " ideal model delta sigma weight residual 112.70 123.30 -10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA LYS C 111 " pdb=" CB LYS C 111 " pdb=" CG LYS C 111 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CB LYS C 111 " pdb=" CG LYS C 111 " pdb=" CD LYS C 111 " ideal model delta sigma weight residual 111.30 118.36 -7.06 2.30e+00 1.89e-01 9.41e+00 angle pdb=" CA CYS C 14 " pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " ideal model delta sigma weight residual 114.40 120.91 -6.51 2.30e+00 1.89e-01 8.02e+00 ... (remaining 5893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 2425 17.41 - 34.82: 206 34.82 - 52.23: 49 52.23 - 69.65: 9 69.65 - 87.06: 3 Dihedral angle restraints: 2692 sinusoidal: 1203 harmonic: 1489 Sorted by residual: dihedral pdb=" CA GLU C 94 " pdb=" C GLU C 94 " pdb=" N LYS C 95 " pdb=" CA LYS C 95 " ideal model delta harmonic sigma weight residual -180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 122.00 -29.00 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta harmonic sigma weight residual -180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 2689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 402 0.031 - 0.063: 167 0.063 - 0.094: 56 0.094 - 0.125: 46 0.125 - 0.156: 7 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA ASP C 195 " pdb=" N ASP C 195 " pdb=" C ASP C 195 " pdb=" CB ASP C 195 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 675 not shown) Planarity restraints: 750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 452 " -0.009 2.00e-02 2.50e+03 1.11e-02 3.06e+00 pdb=" CG TRP A 452 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 452 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 452 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 452 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 452 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 452 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 452 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 452 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 452 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 277 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" CD GLU C 277 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU C 277 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 277 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 153 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.50e+00 pdb=" CD GLU C 153 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU C 153 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU C 153 " 0.008 2.00e-02 2.50e+03 ... (remaining 747 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 2567 3.04 - 3.51: 3825 3.51 - 3.97: 6634 3.97 - 4.43: 7861 4.43 - 4.90: 12856 Nonbonded interactions: 33743 Sorted by model distance: nonbonded pdb=" OG1 THR C 122 " pdb=" OD1 ASN C 123 " model vdw 2.575 3.040 nonbonded pdb=" N GLU C 277 " pdb=" OE1 GLU C 277 " model vdw 2.589 3.120 nonbonded pdb=" O LYS C 184 " pdb=" N ILE C 207 " model vdw 2.591 3.120 nonbonded pdb=" N VAL A 570 " pdb=" N ASP A 571 " model vdw 2.620 2.560 nonbonded pdb=" N ALA A 411 " pdb=" O ALA A 411 " model vdw 2.629 2.496 ... (remaining 33738 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 'D' selection = chain 'E' } 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: 4.840 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.540 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: 0.010 Load rotamer database and sin/cos tables:5.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4356 Z= 0.183 Angle : 0.664 10.599 5941 Z= 0.358 Chirality : 0.047 0.156 678 Planarity : 0.004 0.029 742 Dihedral : 13.446 87.057 1719 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.22 % Allowed : 16.70 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.37), residues: 496 helix: -2.47 (0.91), residues: 19 sheet: -0.52 (0.42), residues: 148 loop : -0.49 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 76 TYR 0.013 0.001 TYR A 489 PHE 0.021 0.001 PHE C 125 TRP 0.029 0.002 TRP A 452 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 4340) covalent geometry : angle 0.65434 / 0.36 ( 5898) SS BOND : bond 0.00161 / 0.09 ( 5) SS BOND : angle 0.55597 / 0.36 ( 10) hydrogen bonds : bond 0.20664 / 13.61 ( 131) hydrogen bonds : angle 10.16713 / 7.05 ( 327) link_BETA1-4 : bond 0.00240 / 0.12 ( 3) link_BETA1-4 : angle 2.18065 / 1.07 ( 9) link_NAG-ASN : bond 0.00197 / 0.14 ( 8) link_NAG-ASN : angle 1.46645 / 0.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 SER cc_start: 0.9004 (m) cc_final: 0.8689 (p) REVERT: C 142 TYR cc_start: 0.7500 (p90) cc_final: 0.7262 (p90) REVERT: C 151 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7695 (tm-30) REVERT: C 194 ILE cc_start: 0.9411 (pt) cc_final: 0.9051 (pp) REVERT: A 406 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 478 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8737 (tmtt) REVERT: A 498 ARG cc_start: 0.8498 (ptp-170) cc_final: 0.8261 (ptp-110) REVERT: A 506 GLN cc_start: 0.8265 (mt0) cc_final: 0.7972 (mt0) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.6066 time to fit residues: 38.5708 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN A 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067301 restraints weight = 7982.151| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.42 r_work: 0.2772 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4356 Z= 0.178 Angle : 0.580 5.055 5941 Z= 0.299 Chirality : 0.048 0.167 678 Planarity : 0.004 0.028 742 Dihedral : 6.597 53.446 782 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.52 % Allowed : 16.48 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.36), residues: 496 helix: -2.88 (0.90), residues: 13 sheet: -0.64 (0.39), residues: 159 loop : -0.38 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 76 TYR 0.017 0.001 TYR C 261 PHE 0.025 0.001 PHE C 125 TRP 0.014 0.001 TRP A 452 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 4340) covalent geometry : angle 0.56827 / 0.30 ( 5898) SS BOND : bond 0.00102 / 0.05 ( 5) SS BOND : angle 0.72989 / 0.48 ( 10) hydrogen bonds : bond 0.04242 / 2.70 ( 131) hydrogen bonds : angle 7.59194 / 5.16 ( 327) link_BETA1-4 : bond 0.00302 / 0.15 ( 3) link_BETA1-4 : angle 2.16961 / 1.05 ( 9) link_NAG-ASN : bond 0.00143 / 0.11 ( 8) link_NAG-ASN : angle 1.39833 / 0.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: C 52 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8487 (tp40) REVERT: C 75 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8976 (mmmm) REVERT: C 76 ARG cc_start: 0.8398 (ptm160) cc_final: 0.8153 (ptm160) REVERT: C 78 ASP cc_start: 0.7964 (p0) cc_final: 0.7759 (p0) REVERT: C 109 ASP cc_start: 0.8787 (t0) cc_final: 0.8445 (t0) REVERT: C 111 LYS cc_start: 0.9000 (mmpt) cc_final: 0.8469 (mmpt) REVERT: C 132 GLN cc_start: 0.8841 (tp40) cc_final: 0.7672 (tp40) REVERT: A 478 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8708 (tmtt) REVERT: A 498 ARG cc_start: 0.8484 (ptp-170) cc_final: 0.8262 (ptp-110) REVERT: A 506 GLN cc_start: 0.8389 (mt0) cc_final: 0.8051 (mt0) REVERT: A 509 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (mmm-85) outliers start: 16 outliers final: 3 residues processed: 68 average time/residue: 0.4342 time to fit residues: 30.5134 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 509 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067597 restraints weight = 7948.240| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.42 r_work: 0.2801 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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 0.031 4356 Z= 0.144 Angle : 0.576 7.971 5941 Z= 0.291 Chirality : 0.047 0.166 678 Planarity : 0.003 0.026 742 Dihedral : 6.441 53.496 780 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.52 % Allowed : 17.36 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.36), residues: 496 helix: -2.64 (0.98), residues: 13 sheet: -0.59 (0.39), residues: 159 loop : -0.41 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 76 TYR 0.014 0.001 TYR C 261 PHE 0.024 0.001 PHE C 125 TRP 0.017 0.001 TRP A 452 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4340) covalent geometry : angle 0.56507 / 0.29 ( 5898) SS BOND : bond 0.00077 / 0.04 ( 5) SS BOND : angle 0.62259 / 0.40 ( 10) hydrogen bonds : bond 0.03847 / 2.40 ( 131) hydrogen bonds : angle 7.04925 / 4.77 ( 327) link_BETA1-4 : bond 0.00314 / 0.16 ( 3) link_BETA1-4 : angle 2.16332 / 1.03 ( 9) link_NAG-ASN : bond 0.00173 / 0.12 ( 8) link_NAG-ASN : angle 1.32710 / 0.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: C 75 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8949 (mmmm) REVERT: C 76 ARG cc_start: 0.8398 (ptm160) cc_final: 0.8128 (ptm160) REVERT: C 78 ASP cc_start: 0.7977 (p0) cc_final: 0.7691 (p0) REVERT: C 212 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.5632 (m-80) REVERT: A 406 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 478 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8703 (tmtt) REVERT: A 498 ARG cc_start: 0.8474 (ptp-170) cc_final: 0.8207 (ptp-110) REVERT: A 506 GLN cc_start: 0.8479 (mt0) cc_final: 0.8203 (mt0) REVERT: A 509 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8150 (mmm-85) outliers start: 16 outliers final: 5 residues processed: 60 average time/residue: 0.5355 time to fit residues: 33.0818 Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068044 restraints weight = 7855.473| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.42 r_work: 0.2804 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4356 Z= 0.134 Angle : 0.555 6.847 5941 Z= 0.282 Chirality : 0.047 0.160 678 Planarity : 0.003 0.027 742 Dihedral : 6.412 54.299 780 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.52 % Allowed : 18.02 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.36), residues: 496 helix: -2.44 (1.02), residues: 13 sheet: -0.47 (0.38), residues: 160 loop : -0.44 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 76 TYR 0.015 0.001 TYR C 28 PHE 0.023 0.001 PHE C 125 TRP 0.019 0.001 TRP A 452 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4340) covalent geometry : angle 0.54386 / 0.28 ( 5898) SS BOND : bond 0.00073 / 0.04 ( 5) SS BOND : angle 0.53852 / 0.35 ( 10) hydrogen bonds : bond 0.03476 / 2.18 ( 131) hydrogen bonds : angle 6.76935 / 4.58 ( 327) link_BETA1-4 : bond 0.00232 / 0.12 ( 3) link_BETA1-4 : angle 2.12172 / 1.02 ( 9) link_NAG-ASN : bond 0.00160 / 0.11 ( 8) link_NAG-ASN : angle 1.36995 / 0.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: C 52 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8442 (tp40) REVERT: C 75 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8939 (mmmm) REVERT: C 76 ARG cc_start: 0.8384 (ptm160) cc_final: 0.8103 (ptm160) REVERT: C 78 ASP cc_start: 0.8007 (p0) cc_final: 0.7752 (p0) REVERT: C 100 ARG cc_start: 0.8275 (ptm160) cc_final: 0.8003 (ptm-80) REVERT: C 132 GLN cc_start: 0.8846 (tp40) cc_final: 0.7746 (tp40) REVERT: C 212 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.5603 (m-80) REVERT: A 478 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8701 (tmtt) REVERT: A 498 ARG cc_start: 0.8457 (ptp-170) cc_final: 0.8255 (ptp-170) REVERT: A 506 GLN cc_start: 0.8504 (mt0) cc_final: 0.8225 (mt0) REVERT: A 509 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8116 (mmm-85) outliers start: 16 outliers final: 4 residues processed: 63 average time/residue: 0.5013 time to fit residues: 32.4797 Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.097299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067222 restraints weight = 7995.615| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.45 r_work: 0.2798 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4356 Z= 0.153 Angle : 0.555 6.569 5941 Z= 0.283 Chirality : 0.047 0.164 678 Planarity : 0.003 0.026 742 Dihedral : 6.439 54.308 780 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.30 % Allowed : 19.78 % Favored : 76.92 % 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 are not related in a simple way. whole: -0.79 (0.36), residues: 496 helix: -2.41 (1.03), residues: 13 sheet: -0.41 (0.38), residues: 160 loop : -0.45 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 76 TYR 0.015 0.001 TYR C 28 PHE 0.023 0.001 PHE C 125 TRP 0.017 0.001 TRP A 452 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4340) covalent geometry : angle 0.54321 / 0.28 ( 5898) SS BOND : bond 0.00107 / 0.07 ( 5) SS BOND : angle 0.53982 / 0.38 ( 10) hydrogen bonds : bond 0.03500 / 2.19 ( 131) hydrogen bonds : angle 6.63990 / 4.50 ( 327) link_BETA1-4 : bond 0.00189 / 0.09 ( 3) link_BETA1-4 : angle 2.10125 / 1.01 ( 9) link_NAG-ASN : bond 0.00143 / 0.10 ( 8) link_NAG-ASN : angle 1.40674 / 0.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: C 52 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8437 (tp40) REVERT: C 75 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8931 (mmmm) REVERT: C 76 ARG cc_start: 0.8415 (ptm160) cc_final: 0.8098 (ptm160) REVERT: C 78 ASP cc_start: 0.7988 (p0) cc_final: 0.7691 (p0) REVERT: C 100 ARG cc_start: 0.8378 (ptm160) cc_final: 0.8091 (ptm-80) REVERT: C 111 LYS cc_start: 0.9410 (mmmm) cc_final: 0.8813 (mmpt) REVERT: C 132 GLN cc_start: 0.8820 (tp40) cc_final: 0.8509 (tp40) REVERT: A 478 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8702 (tmtt) REVERT: A 506 GLN cc_start: 0.8514 (mt0) cc_final: 0.8219 (mt0) REVERT: A 509 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8127 (mmm-85) outliers start: 15 outliers final: 7 residues processed: 59 average time/residue: 0.6158 time to fit residues: 37.2289 Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067613 restraints weight = 8050.666| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.45 r_work: 0.2787 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.129 Angle : 0.542 6.214 5941 Z= 0.277 Chirality : 0.047 0.169 678 Planarity : 0.003 0.026 742 Dihedral : 6.383 54.131 780 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.74 % Allowed : 19.34 % Favored : 76.92 % 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 are not related in a simple way. whole: -0.75 (0.36), residues: 496 helix: -2.32 (1.06), residues: 13 sheet: -0.33 (0.39), residues: 160 loop : -0.46 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 76 TYR 0.014 0.001 TYR C 28 PHE 0.026 0.001 PHE C 165 TRP 0.014 0.001 TRP A 452 HIS 0.001 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4340) covalent geometry : angle 0.53093 / 0.27 ( 5898) SS BOND : bond 0.00068 / 0.04 ( 5) SS BOND : angle 0.48968 / 0.34 ( 10) hydrogen bonds : bond 0.03320 / 2.07 ( 131) hydrogen bonds : angle 6.50963 / 4.41 ( 327) link_BETA1-4 : bond 0.00289 / 0.14 ( 3) link_BETA1-4 : angle 2.07845 / 1.01 ( 9) link_NAG-ASN : bond 0.00147 / 0.09 ( 8) link_NAG-ASN : angle 1.36140 / 0.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8940 (mmmm) REVERT: C 76 ARG cc_start: 0.8406 (ptm160) cc_final: 0.8110 (ptm160) REVERT: C 78 ASP cc_start: 0.8011 (p0) cc_final: 0.7682 (p0) REVERT: C 100 ARG cc_start: 0.8307 (ptm160) cc_final: 0.8034 (ptm-80) REVERT: C 111 LYS cc_start: 0.9414 (mmmm) cc_final: 0.8781 (mmpt) REVERT: C 132 GLN cc_start: 0.8826 (tp40) cc_final: 0.8539 (tp40) REVERT: A 406 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8055 (mp0) REVERT: A 466 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8546 (mtp85) REVERT: A 478 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8702 (tmtt) REVERT: A 506 GLN cc_start: 0.8489 (mt0) cc_final: 0.8116 (mt0) REVERT: A 509 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8084 (mmm-85) REVERT: A 531 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8951 (p) REVERT: A 568 ASP cc_start: 0.8188 (m-30) cc_final: 0.7926 (m-30) REVERT: A 574 ASP cc_start: 0.7973 (p0) cc_final: 0.7619 (p0) outliers start: 17 outliers final: 4 residues processed: 68 average time/residue: 0.5712 time to fit residues: 39.9412 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.067481 restraints weight = 8062.590| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.43 r_work: 0.2777 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 : 0.003 0.029 4356 Z= 0.144 Angle : 0.574 8.794 5941 Z= 0.291 Chirality : 0.047 0.159 678 Planarity : 0.004 0.033 742 Dihedral : 6.414 54.207 780 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.30 % Allowed : 20.44 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.36), residues: 496 helix: -2.33 (1.05), residues: 13 sheet: -0.31 (0.38), residues: 159 loop : -0.48 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 242 TYR 0.016 0.001 TYR C 28 PHE 0.024 0.001 PHE C 165 TRP 0.022 0.002 TRP A 452 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4340) covalent geometry : angle 0.56346 / 0.29 ( 5898) SS BOND : bond 0.00084 / 0.05 ( 5) SS BOND : angle 0.48543 / 0.34 ( 10) hydrogen bonds : bond 0.03352 / 2.08 ( 131) hydrogen bonds : angle 6.44274 / 4.37 ( 327) link_BETA1-4 : bond 0.00248 / 0.12 ( 3) link_BETA1-4 : angle 2.08570 / 1.01 ( 9) link_NAG-ASN : bond 0.00136 / 0.08 ( 8) link_NAG-ASN : angle 1.37576 / 0.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8935 (mmmm) REVERT: C 76 ARG cc_start: 0.8386 (ptm160) cc_final: 0.8074 (ptm160) REVERT: C 78 ASP cc_start: 0.8035 (p0) cc_final: 0.7690 (p0) REVERT: C 100 ARG cc_start: 0.8317 (ptm160) cc_final: 0.8070 (ptm-80) REVERT: C 111 LYS cc_start: 0.9415 (mmmm) cc_final: 0.8808 (mmpt) REVERT: C 132 GLN cc_start: 0.8808 (tp40) cc_final: 0.8505 (tp40) REVERT: A 406 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8015 (mp0) REVERT: A 478 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8686 (tmtt) REVERT: A 506 GLN cc_start: 0.8498 (mt0) cc_final: 0.8132 (mt0) REVERT: A 509 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8068 (mmm-85) REVERT: A 531 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8967 (p) REVERT: A 568 ASP cc_start: 0.8191 (m-30) cc_final: 0.7896 (m-30) REVERT: A 574 ASP cc_start: 0.8017 (p0) cc_final: 0.7610 (p0) outliers start: 15 outliers final: 6 residues processed: 59 average time/residue: 0.6190 time to fit residues: 37.4815 Evaluate side-chains 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.068281 restraints weight = 7909.000| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.40 r_work: 0.2824 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4356 Z= 0.122 Angle : 0.568 8.663 5941 Z= 0.286 Chirality : 0.047 0.168 678 Planarity : 0.003 0.027 742 Dihedral : 6.341 53.959 780 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.42 % Allowed : 21.10 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.36), residues: 496 helix: -2.23 (1.08), residues: 13 sheet: -0.26 (0.39), residues: 159 loop : -0.48 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 242 TYR 0.016 0.001 TYR C 28 PHE 0.025 0.001 PHE C 165 TRP 0.016 0.001 TRP A 452 HIS 0.001 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4340) covalent geometry : angle 0.55823 / 0.28 ( 5898) SS BOND : bond 0.00053 / 0.03 ( 5) SS BOND : angle 0.42927 / 0.30 ( 10) hydrogen bonds : bond 0.03240 / 2.02 ( 131) hydrogen bonds : angle 6.32626 / 4.29 ( 327) link_BETA1-4 : bond 0.00293 / 0.15 ( 3) link_BETA1-4 : angle 2.03228 / 1.00 ( 9) link_NAG-ASN : bond 0.00156 / 0.09 ( 8) link_NAG-ASN : angle 1.32577 / 0.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8924 (mmmm) REVERT: C 76 ARG cc_start: 0.8451 (ptm160) cc_final: 0.8152 (ptm160) REVERT: C 78 ASP cc_start: 0.8065 (p0) cc_final: 0.7730 (p0) REVERT: C 100 ARG cc_start: 0.8268 (ptm160) cc_final: 0.7999 (ptm-80) REVERT: C 132 GLN cc_start: 0.8820 (tp40) cc_final: 0.8554 (tp40) REVERT: A 340 GLU cc_start: 0.8157 (mp0) cc_final: 0.7905 (mp0) REVERT: A 406 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8033 (mp0) REVERT: A 478 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8694 (tmtt) REVERT: A 498 ARG cc_start: 0.8209 (ptp-170) cc_final: 0.7929 (ptp-110) REVERT: A 506 GLN cc_start: 0.8487 (mt0) cc_final: 0.8165 (mt0) REVERT: A 509 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8025 (mmm-85) REVERT: A 531 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8964 (p) REVERT: A 568 ASP cc_start: 0.8128 (m-30) cc_final: 0.7777 (m-30) REVERT: A 574 ASP cc_start: 0.7992 (p0) cc_final: 0.7550 (p0) outliers start: 11 outliers final: 4 residues processed: 58 average time/residue: 0.6599 time to fit residues: 39.3249 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067537 restraints weight = 7953.976| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.40 r_work: 0.2807 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4356 Z= 0.152 Angle : 0.589 7.194 5941 Z= 0.300 Chirality : 0.047 0.168 678 Planarity : 0.003 0.028 742 Dihedral : 6.394 54.090 780 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.20 % Allowed : 21.10 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.36), residues: 496 helix: -2.32 (1.05), residues: 13 sheet: -0.28 (0.39), residues: 159 loop : -0.50 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 242 TYR 0.017 0.001 TYR C 28 PHE 0.022 0.001 PHE C 165 TRP 0.016 0.001 TRP A 452 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4340) covalent geometry : angle 0.57883 / 0.30 ( 5898) SS BOND : bond 0.00085 / 0.05 ( 5) SS BOND : angle 0.47602 / 0.34 ( 10) hydrogen bonds : bond 0.03397 / 2.11 ( 131) hydrogen bonds : angle 6.34074 / 4.31 ( 327) link_BETA1-4 : bond 0.00236 / 0.12 ( 3) link_BETA1-4 : angle 2.03557 / 1.00 ( 9) link_NAG-ASN : bond 0.00130 / 0.08 ( 8) link_NAG-ASN : angle 1.38819 / 0.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8933 (mmmm) REVERT: C 76 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8123 (ptm160) REVERT: C 78 ASP cc_start: 0.8076 (p0) cc_final: 0.7717 (p0) REVERT: C 100 ARG cc_start: 0.8351 (ptm160) cc_final: 0.8112 (ptm-80) REVERT: C 132 GLN cc_start: 0.8800 (tp40) cc_final: 0.8515 (tp40) REVERT: A 340 GLU cc_start: 0.8172 (mp0) cc_final: 0.7919 (mp0) REVERT: A 406 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8050 (mp0) REVERT: A 478 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8676 (tmtt) REVERT: A 498 ARG cc_start: 0.8227 (ptp-170) cc_final: 0.7951 (ptp-110) REVERT: A 506 GLN cc_start: 0.8433 (mt0) cc_final: 0.8115 (mt0) REVERT: A 509 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (mmm-85) REVERT: A 531 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8966 (p) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.6006 time to fit residues: 32.6798 Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 0.0050 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.068683 restraints weight = 7766.445| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.38 r_work: 0.2832 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4356 Z= 0.118 Angle : 0.583 7.020 5941 Z= 0.296 Chirality : 0.047 0.161 678 Planarity : 0.004 0.035 742 Dihedral : 6.315 53.216 780 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.76 % Allowed : 21.76 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.36), residues: 496 helix: -2.20 (1.09), residues: 13 sheet: -0.22 (0.39), residues: 159 loop : -0.48 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 242 TYR 0.017 0.001 TYR C 28 PHE 0.022 0.001 PHE C 125 TRP 0.015 0.001 TRP A 452 HIS 0.001 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4340) covalent geometry : angle 0.57334 / 0.29 ( 5898) SS BOND : bond 0.00042 / 0.02 ( 5) SS BOND : angle 0.39530 / 0.28 ( 10) hydrogen bonds : bond 0.03239 / 2.00 ( 131) hydrogen bonds : angle 6.25292 / 4.25 ( 327) link_BETA1-4 : bond 0.00308 / 0.15 ( 3) link_BETA1-4 : angle 1.99466 / 0.99 ( 9) link_NAG-ASN : bond 0.00157 / 0.10 ( 8) link_NAG-ASN : angle 1.36535 / 0.90 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8969 (mmmm) REVERT: C 76 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8038 (ptm160) REVERT: C 78 ASP cc_start: 0.8084 (p0) cc_final: 0.7576 (p0) REVERT: C 100 ARG cc_start: 0.8289 (ptm160) cc_final: 0.8020 (ptm-80) REVERT: C 132 GLN cc_start: 0.8817 (tp40) cc_final: 0.8551 (tp40) REVERT: A 340 GLU cc_start: 0.8146 (mp0) cc_final: 0.7893 (mp0) REVERT: A 406 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8060 (mp0) REVERT: A 478 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8689 (tmtt) REVERT: A 498 ARG cc_start: 0.8247 (ptp-170) cc_final: 0.7976 (ptp-110) REVERT: A 506 GLN cc_start: 0.8430 (mt0) cc_final: 0.8147 (mt0) REVERT: A 509 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8022 (mmm-85) REVERT: A 531 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8967 (p) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.5702 time to fit residues: 33.3504 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069215 restraints weight = 7859.993| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.39 r_work: 0.2844 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4356 Z= 0.116 Angle : 0.593 6.879 5941 Z= 0.301 Chirality : 0.047 0.152 678 Planarity : 0.003 0.028 742 Dihedral : 6.304 53.300 780 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.20 % Allowed : 21.10 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.36), residues: 496 helix: -2.17 (1.10), residues: 13 sheet: -0.17 (0.39), residues: 159 loop : -0.47 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 242 TYR 0.018 0.001 TYR C 28 PHE 0.026 0.001 PHE C 165 TRP 0.013 0.001 TRP A 452 HIS 0.001 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4340) covalent geometry : angle 0.58301 / 0.30 ( 5898) SS BOND : bond 0.00038 / 0.02 ( 5) SS BOND : angle 0.33814 / 0.23 ( 10) hydrogen bonds : bond 0.03168 / 1.95 ( 131) hydrogen bonds : angle 6.17493 / 4.20 ( 327) link_BETA1-4 : bond 0.00285 / 0.14 ( 3) link_BETA1-4 : angle 1.99279 / 0.98 ( 9) link_NAG-ASN : bond 0.00182 / 0.12 ( 8) link_NAG-ASN : angle 1.37859 / 0.93 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.89 seconds wall clock time: 23 minutes 55.51 seconds (1435.51 seconds total)