Starting phenix.real_space_refine on Sat May 10 22:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtk_27703/05_2025/8dtk_27703_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtk_27703/05_2025/8dtk_27703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtk_27703/05_2025/8dtk_27703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtk_27703/05_2025/8dtk_27703.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtk_27703/05_2025/8dtk_27703_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtk_27703/05_2025/8dtk_27703_neut_trim.cif" } resolution = 3.77 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= -0.004 sd= 0.034 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 S 15 5.16 5 C 2248 2.51 5 N 596 2.21 5 O 692 1.98 5 H 3363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6914 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3134 Classifications: {'peptide': 203} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1749 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106} Chain: "C" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2003 Classifications: {'peptide': 133} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 129} 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: 5.08, per 1000 atoms: 0.73 Number of scatterers: 6914 At special positions: 0 Unit cell: (69.828, 92.046, 85.698, 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 15 16.00 O 692 8.00 N 596 7.00 C 2248 6.00 H 3363 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 331 " " NAG A 602 " - " ASN A 343 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 774.7 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.4% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.753A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.151A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.571A pdb=" N GLN C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.666A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.853A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.839A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.551A pdb=" N VAL B 85 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.968A pdb=" N VAL C 5 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 23 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.637A pdb=" N GLU C 10 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 110 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.543A pdb=" N VAL C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 82 " --> pdb=" O VAL C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 78 hydrogen bonds defined for protein. 177 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: 2.79 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3363 1.03 - 1.23: 9 1.23 - 1.42: 1608 1.42 - 1.62: 2005 1.62 - 1.81: 18 Bond restraints: 7003 Sorted by residual: bond pdb=" CB GLU C 81 " pdb=" CG GLU C 81 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CB ASP C 95 " pdb=" CG ASP C 95 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" CB ASP B 9 " pdb=" CG ASP B 9 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.56e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" CB MET B 4 " pdb=" CG MET B 4 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 6998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 12528 7.57 - 15.13: 2 15.13 - 22.70: 1 22.70 - 30.26: 2 30.26 - 37.83: 3 Bond angle restraints: 12536 Sorted by residual: angle pdb=" C PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 109.00 71.17 37.83 3.00e+00 1.11e-01 1.59e+02 angle pdb=" N PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 110.00 74.48 35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 109.00 78.57 30.43 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CB LEU C 4 " pdb=" CG LEU C 4 " pdb=" HG LEU C 4 " ideal model delta sigma weight residual 109.00 85.17 23.83 3.00e+00 1.11e-01 6.31e+01 angle pdb=" CD2 LEU C 4 " pdb=" CG LEU C 4 " pdb=" HG LEU C 4 " ideal model delta sigma weight residual 108.00 84.21 23.79 3.00e+00 1.11e-01 6.29e+01 ... (remaining 12531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 3126 22.08 - 44.16: 208 44.16 - 66.23: 51 66.23 - 88.31: 15 88.31 - 110.39: 5 Dihedral angle restraints: 3405 sinusoidal: 1818 harmonic: 1587 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA VAL A 524 " pdb=" C VAL A 524 " pdb=" N CYS A 525 " pdb=" CA CYS A 525 " ideal model delta harmonic sigma weight residual 180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 125.03 -32.03 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 3402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 537 0.352 - 0.705: 0 0.705 - 1.057: 0 1.057 - 1.409: 0 1.409 - 1.762: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" CG LEU C 4 " pdb=" CB LEU C 4 " pdb=" CD1 LEU C 4 " pdb=" CD2 LEU C 4 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.76e+01 chirality pdb=" CA PHE C 100N" pdb=" N PHE C 100N" pdb=" C PHE C 100N" pdb=" CB PHE C 100N" both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 535 not shown) Planarity restraints: 1068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 61 " 0.214 9.50e-02 1.11e+02 7.17e-02 6.49e+00 pdb=" NE ARG B 61 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 61 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 61 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 61 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 61 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG B 61 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 61 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 61 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 497 " 0.013 2.00e-02 2.50e+03 1.04e-02 3.23e+00 pdb=" CG PHE A 497 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 497 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 497 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 497 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 497 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 497 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 497 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 497 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 497 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 497 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 497 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 13 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 14 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.024 5.00e-02 4.00e+02 ... (remaining 1065 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 838 2.24 - 2.83: 14848 2.83 - 3.42: 17054 3.42 - 4.01: 23693 4.01 - 4.60: 35931 Nonbonded interactions: 92364 Sorted by model distance: nonbonded pdb=" H PHE C 100N" pdb=" HA PHE C 100N" model vdw 1.653 1.816 nonbonded pdb=" HA PHE C 100N" pdb=" HB2 PHE C 100N" model vdw 1.710 1.952 nonbonded pdb=" H ALA A 363 " pdb=" O CYS A 525 " model vdw 1.732 2.450 nonbonded pdb="HH12 ARG A 454 " pdb=" O SER A 469 " model vdw 1.739 2.450 nonbonded pdb=" O VAL C 96 " pdb=" HG1 THR C 100L" model vdw 1.744 2.450 ... (remaining 92359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.050 Process input model: 21.420 Find NCS groups from input model: 0.110 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 0.044 3648 Z= 0.200 Angle : 0.794 10.998 4971 Z= 0.416 Chirality : 0.091 1.762 538 Planarity : 0.006 0.095 640 Dihedral : 16.060 110.391 1326 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.29 (0.37), residues: 443 helix: -3.24 (0.52), residues: 40 sheet: -1.95 (0.44), residues: 124 loop : -1.00 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 100B HIS 0.005 0.002 HIS C 32 PHE 0.031 0.002 PHE A 497 TYR 0.021 0.002 TYR B 49 ARG 0.016 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 2.53463 ( 6) hydrogen bonds : bond 0.31874 ( 73) hydrogen bonds : angle 11.46960 ( 177) SS BOND : bond 0.00468 ( 6) SS BOND : angle 1.42222 ( 12) covalent geometry : bond 0.00459 ( 3640) covalent geometry : angle 0.78779 ( 4953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3223 time to fit residues: 32.7751 Evaluate side-chains 69 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 42 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.168547 restraints weight = 11650.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.174923 restraints weight = 5997.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.178928 restraints weight = 3755.694| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3648 Z= 0.168 Angle : 0.655 10.369 4971 Z= 0.335 Chirality : 0.089 1.738 538 Planarity : 0.005 0.041 640 Dihedral : 8.737 59.299 541 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.52 % Allowed : 8.31 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.22 (0.37), residues: 443 helix: -3.14 (0.58), residues: 40 sheet: -1.78 (0.47), residues: 108 loop : -1.10 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 100B HIS 0.003 0.002 HIS C 32 PHE 0.015 0.001 PHE A 490 TYR 0.014 0.001 TYR B 49 ARG 0.005 0.001 ARG C 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 2) link_NAG-ASN : angle 2.05118 ( 6) hydrogen bonds : bond 0.04984 ( 73) hydrogen bonds : angle 7.58081 ( 177) SS BOND : bond 0.00471 ( 6) SS BOND : angle 0.87987 ( 12) covalent geometry : bond 0.00381 ( 3640) covalent geometry : angle 0.65126 ( 4953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 76 average time/residue: 0.3282 time to fit residues: 30.5826 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 27 GLN B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.186552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162787 restraints weight = 12017.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168982 restraints weight = 6283.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172937 restraints weight = 3992.946| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3648 Z= 0.134 Angle : 0.582 10.211 4971 Z= 0.297 Chirality : 0.088 1.736 538 Planarity : 0.004 0.046 640 Dihedral : 7.185 53.668 541 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.30 % Allowed : 9.61 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.26 (0.37), residues: 443 helix: -3.19 (0.58), residues: 40 sheet: -1.86 (0.47), residues: 108 loop : -1.09 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 47 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE A 490 TYR 0.012 0.001 TYR B 49 ARG 0.006 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 1.84662 ( 6) hydrogen bonds : bond 0.04217 ( 73) hydrogen bonds : angle 6.84075 ( 177) SS BOND : bond 0.00421 ( 6) SS BOND : angle 0.77557 ( 12) covalent geometry : bond 0.00307 ( 3640) covalent geometry : angle 0.57832 ( 4953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.3937 time to fit residues: 35.0135 Evaluate side-chains 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 8 optimal weight: 0.0060 overall best weight: 0.2892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.186322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163591 restraints weight = 11946.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169660 restraints weight = 6291.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173531 restraints weight = 3981.641| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3648 Z= 0.106 Angle : 0.549 10.192 4971 Z= 0.278 Chirality : 0.087 1.730 538 Planarity : 0.004 0.047 640 Dihedral : 6.477 49.273 541 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.30 % Allowed : 11.69 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.08 (0.37), residues: 443 helix: -2.94 (0.69), residues: 33 sheet: -1.78 (0.47), residues: 109 loop : -1.03 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 35 HIS 0.002 0.001 HIS C 35 PHE 0.008 0.001 PHE A 490 TYR 0.012 0.001 TYR B 49 ARG 0.006 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 2) link_NAG-ASN : angle 1.85232 ( 6) hydrogen bonds : bond 0.03351 ( 73) hydrogen bonds : angle 6.34621 ( 177) SS BOND : bond 0.00430 ( 6) SS BOND : angle 0.96525 ( 12) covalent geometry : bond 0.00250 ( 3640) covalent geometry : angle 0.54382 ( 4953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.3741 time to fit residues: 34.0524 Evaluate side-chains 70 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153616 restraints weight = 12069.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159631 restraints weight = 6273.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.163573 restraints weight = 3985.894| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3648 Z= 0.215 Angle : 0.637 10.823 4971 Z= 0.326 Chirality : 0.089 1.758 538 Planarity : 0.004 0.048 640 Dihedral : 6.798 56.026 541 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.78 % Allowed : 13.77 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.25 (0.38), residues: 443 helix: -2.89 (0.71), residues: 33 sheet: -1.83 (0.48), residues: 108 loop : -1.21 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 100B HIS 0.005 0.002 HIS C 32 PHE 0.014 0.002 PHE A 429 TYR 0.014 0.002 TYR B 49 ARG 0.008 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 2) link_NAG-ASN : angle 3.61061 ( 6) hydrogen bonds : bond 0.03764 ( 73) hydrogen bonds : angle 6.25562 ( 177) SS BOND : bond 0.00563 ( 6) SS BOND : angle 1.10672 ( 12) covalent geometry : bond 0.00494 ( 3640) covalent geometry : angle 0.62305 ( 4953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.3230 time to fit residues: 29.3480 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152357 restraints weight = 12498.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158367 restraints weight = 6471.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162246 restraints weight = 4084.905| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3648 Z= 0.168 Angle : 0.600 10.507 4971 Z= 0.304 Chirality : 0.088 1.757 538 Planarity : 0.004 0.057 640 Dihedral : 6.490 52.128 541 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.04 % Allowed : 15.06 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.20 (0.38), residues: 443 helix: -2.67 (0.82), residues: 27 sheet: -1.84 (0.48), residues: 110 loop : -1.21 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 103 HIS 0.003 0.002 HIS C 32 PHE 0.010 0.001 PHE A 429 TYR 0.015 0.001 TYR B 49 ARG 0.007 0.000 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 2) link_NAG-ASN : angle 3.57176 ( 6) hydrogen bonds : bond 0.03373 ( 73) hydrogen bonds : angle 6.09847 ( 177) SS BOND : bond 0.00526 ( 6) SS BOND : angle 1.03395 ( 12) covalent geometry : bond 0.00382 ( 3640) covalent geometry : angle 0.58611 ( 4953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.3779 time to fit residues: 34.6504 Evaluate side-chains 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.173741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149897 restraints weight = 12383.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155837 restraints weight = 6498.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159697 restraints weight = 4143.909| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3648 Z= 0.189 Angle : 0.624 10.645 4971 Z= 0.316 Chirality : 0.088 1.758 538 Planarity : 0.005 0.061 640 Dihedral : 6.695 53.847 541 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.78 % Allowed : 15.84 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.29 (0.37), residues: 443 helix: -2.70 (0.80), residues: 27 sheet: -1.44 (0.49), residues: 103 loop : -1.51 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 100B HIS 0.004 0.002 HIS C 32 PHE 0.009 0.001 PHE A 429 TYR 0.014 0.001 TYR B 49 ARG 0.010 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 2) link_NAG-ASN : angle 3.81010 ( 6) hydrogen bonds : bond 0.03433 ( 73) hydrogen bonds : angle 6.09690 ( 177) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.12413 ( 12) covalent geometry : bond 0.00433 ( 3640) covalent geometry : angle 0.60808 ( 4953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7212 (tmtt) cc_final: 0.6962 (tmtt) outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 0.3555 time to fit residues: 31.2958 Evaluate side-chains 72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 3 GLN ** 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 = 0.3961 r_free = 0.3961 target = 0.172701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148960 restraints weight = 12637.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154844 restraints weight = 6573.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158686 restraints weight = 4168.849| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3648 Z= 0.200 Angle : 0.640 10.723 4971 Z= 0.324 Chirality : 0.089 1.769 538 Planarity : 0.005 0.068 640 Dihedral : 6.797 53.679 541 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 1.04 % Allowed : 15.32 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.45 (0.37), residues: 443 helix: -2.71 (0.80), residues: 27 sheet: -1.51 (0.49), residues: 105 loop : -1.65 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100B HIS 0.004 0.002 HIS C 32 PHE 0.011 0.001 PHE C 29 TYR 0.014 0.002 TYR B 49 ARG 0.010 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 2) link_NAG-ASN : angle 4.00119 ( 6) hydrogen bonds : bond 0.03529 ( 73) hydrogen bonds : angle 6.07878 ( 177) SS BOND : bond 0.00609 ( 6) SS BOND : angle 1.17232 ( 12) covalent geometry : bond 0.00459 ( 3640) covalent geometry : angle 0.62325 ( 4953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7219 (tmtt) cc_final: 0.6968 (tmtt) REVERT: C 38 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7862 (ttm170) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.3822 time to fit residues: 33.2418 Evaluate side-chains 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 10 optimal weight: 0.3980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152955 restraints weight = 12323.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.158900 restraints weight = 6327.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162768 restraints weight = 3954.560| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3648 Z= 0.132 Angle : 0.591 10.479 4971 Z= 0.296 Chirality : 0.088 1.744 538 Planarity : 0.005 0.071 640 Dihedral : 6.326 50.194 541 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 1.04 % Allowed : 15.32 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.30 (0.38), residues: 443 helix: -2.66 (0.81), residues: 27 sheet: -1.62 (0.46), residues: 120 loop : -1.40 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 100B HIS 0.003 0.002 HIS C 35 PHE 0.006 0.001 PHE C 29 TYR 0.013 0.001 TYR B 49 ARG 0.011 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 2) link_NAG-ASN : angle 3.41805 ( 6) hydrogen bonds : bond 0.03145 ( 73) hydrogen bonds : angle 5.91493 ( 177) SS BOND : bond 0.00473 ( 6) SS BOND : angle 0.93421 ( 12) covalent geometry : bond 0.00306 ( 3640) covalent geometry : angle 0.57767 ( 4953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7202 (tmtt) cc_final: 0.6948 (tmtt) REVERT: C 38 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7780 (ttm170) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.3647 time to fit residues: 33.3797 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.173106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150219 restraints weight = 12762.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155972 restraints weight = 6745.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159648 restraints weight = 4311.120| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3648 Z= 0.174 Angle : 0.619 10.526 4971 Z= 0.312 Chirality : 0.088 1.750 538 Planarity : 0.005 0.074 640 Dihedral : 6.524 54.012 541 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 1.04 % Allowed : 15.32 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.36 (0.38), residues: 443 helix: -2.64 (0.80), residues: 27 sheet: -1.65 (0.46), residues: 120 loop : -1.46 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 100B HIS 0.004 0.002 HIS C 32 PHE 0.010 0.001 PHE C 29 TYR 0.014 0.001 TYR B 49 ARG 0.012 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 2) link_NAG-ASN : angle 3.72801 ( 6) hydrogen bonds : bond 0.03300 ( 73) hydrogen bonds : angle 5.95070 ( 177) SS BOND : bond 0.00533 ( 6) SS BOND : angle 1.09963 ( 12) covalent geometry : bond 0.00401 ( 3640) covalent geometry : angle 0.60368 ( 4953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7240 (tmtt) cc_final: 0.6977 (tmtt) REVERT: C 38 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7852 (ttm170) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.3805 time to fit residues: 33.6955 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** 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 = 0.3969 r_free = 0.3969 target = 0.173391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150612 restraints weight = 12639.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156391 restraints weight = 6710.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160060 restraints weight = 4291.262| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3648 Z= 0.164 Angle : 0.613 10.500 4971 Z= 0.308 Chirality : 0.088 1.748 538 Planarity : 0.005 0.074 640 Dihedral : 6.399 52.600 541 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.04 % Allowed : 15.32 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.35 (0.38), residues: 443 helix: -2.64 (0.80), residues: 27 sheet: -1.53 (0.47), residues: 118 loop : -1.51 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 100B HIS 0.003 0.002 HIS C 32 PHE 0.009 0.001 PHE C 29 TYR 0.018 0.001 TYR B 49 ARG 0.012 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 2) link_NAG-ASN : angle 3.67990 ( 6) hydrogen bonds : bond 0.03265 ( 73) hydrogen bonds : angle 5.90828 ( 177) SS BOND : bond 0.00524 ( 6) SS BOND : angle 1.07016 ( 12) covalent geometry : bond 0.00378 ( 3640) covalent geometry : angle 0.59792 ( 4953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.10 seconds wall clock time: 60 minutes 20.49 seconds (3620.49 seconds total)