Starting phenix.real_space_refine on Fri Jul 25 03:14:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtk_27703/07_2025/8dtk_27703_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtk_27703/07_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_27703/07_2025/8dtk_27703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtk_27703/07_2025/8dtk_27703.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtk_27703/07_2025/8dtk_27703_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtk_27703/07_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-5711/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: 4.75, per 1000 atoms: 0.69 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 668.4 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: 0.79 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: 2.53 Time building geometry restraints manager: 2.27 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: 3.750 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: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- 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 : 0.573 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: 0.3346 time to fit residues: 33.9881 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 : 0.592 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 388 ASN B 42 GLN ** C 35 HIS ** 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 = 0.4007 r_free = 0.4007 target = 0.177212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157747 restraints weight = 12017.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162737 restraints weight = 6632.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166051 restraints weight = 4304.020| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1450 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= 0.179 Angle : 0.664 10.372 4971 Z= 0.340 Chirality : 0.089 1.739 538 Planarity : 0.005 0.041 640 Dihedral : 8.897 58.529 541 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.78 % Allowed : 8.31 % Favored : 90.91 % 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 (0.37), residues: 443 helix: -3.15 (0.58), residues: 40 sheet: -1.79 (0.47), residues: 108 loop : -1.12 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 100B HIS 0.004 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 0.00299 ( 2) link_NAG-ASN : angle 2.09850 ( 6) hydrogen bonds : bond 0.05111 ( 73) hydrogen bonds : angle 7.61051 ( 177) SS BOND : bond 0.00480 ( 6) SS BOND : angle 0.90587 ( 12) covalent geometry : bond 0.00403 ( 3640) covalent geometry : angle 0.65978 ( 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 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.3980 time to fit residues: 38.6178 Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN ** C 3 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.187562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.163758 restraints weight = 12012.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169946 restraints weight = 6260.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173960 restraints weight = 3974.416| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1764 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= 0.126 Angle : 0.576 10.183 4971 Z= 0.294 Chirality : 0.088 1.733 538 Planarity : 0.004 0.040 640 Dihedral : 7.194 55.120 541 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.78 % Allowed : 9.35 % Favored : 89.87 % 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: -2.23 (0.37), residues: 443 helix: -3.15 (0.58), residues: 40 sheet: -1.83 (0.47), residues: 108 loop : -1.08 (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 0.005 0.000 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 1.80003 ( 6) hydrogen bonds : bond 0.04146 ( 73) hydrogen bonds : angle 6.87268 ( 177) SS BOND : bond 0.00395 ( 6) SS BOND : angle 0.74956 ( 12) covalent geometry : bond 0.00291 ( 3640) covalent geometry : angle 0.57225 ( 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 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.722 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: 1 residues processed: 76 average time/residue: 0.4315 time to fit residues: 40.2376 Evaluate side-chains 70 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 0.3980 chunk 14 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.185284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.163234 restraints weight = 12005.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168948 restraints weight = 6522.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172439 restraints weight = 4200.799| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2140 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= 0.117 Angle : 0.553 10.303 4971 Z= 0.281 Chirality : 0.087 1.733 538 Planarity : 0.004 0.041 640 Dihedral : 6.551 50.669 541 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.56 % Allowed : 11.17 % Favored : 87.27 % 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: -2.11 (0.37), residues: 443 helix: -2.94 (0.68), residues: 33 sheet: -1.80 (0.47), residues: 109 loop : -1.06 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 35 HIS 0.002 0.001 HIS C 32 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 0.00223 ( 2) link_NAG-ASN : angle 2.07701 ( 6) hydrogen bonds : bond 0.03377 ( 73) hydrogen bonds : angle 6.32478 ( 177) SS BOND : bond 0.00419 ( 6) SS BOND : angle 0.70377 ( 12) covalent geometry : bond 0.00274 ( 3640) covalent geometry : angle 0.54845 ( 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 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 73 average time/residue: 0.3806 time to fit residues: 33.7511 Evaluate side-chains 69 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155387 restraints weight = 12055.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161021 restraints weight = 6595.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164701 restraints weight = 4295.708| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3648 Z= 0.214 Angle : 0.643 10.965 4971 Z= 0.328 Chirality : 0.089 1.770 538 Planarity : 0.005 0.048 640 Dihedral : 6.874 55.960 541 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 1.04 % Allowed : 13.25 % Favored : 85.71 % 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: -2.34 (0.37), residues: 443 helix: -2.90 (0.69), residues: 33 sheet: -1.73 (0.46), residues: 118 loop : -1.32 (0.35), residues: 292 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 0.013 0.002 PHE A 429 TYR 0.015 0.002 TYR B 49 ARG 0.005 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 2) link_NAG-ASN : angle 3.73676 ( 6) hydrogen bonds : bond 0.03806 ( 73) hydrogen bonds : angle 6.24179 ( 177) SS BOND : bond 0.00622 ( 6) SS BOND : angle 1.25534 ( 12) covalent geometry : bond 0.00489 ( 3640) covalent geometry : angle 0.62743 ( 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 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.3171 time to fit residues: 29.2231 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 : 0.516 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.176546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152512 restraints weight = 12488.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158624 restraints weight = 6432.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162582 restraints weight = 4057.315| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3648 Z= 0.157 Angle : 0.594 10.470 4971 Z= 0.300 Chirality : 0.088 1.755 538 Planarity : 0.004 0.056 640 Dihedral : 6.459 51.725 541 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.78 % Allowed : 14.29 % Favored : 84.94 % 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: -2.24 (0.37), residues: 443 helix: -2.75 (0.72), residues: 33 sheet: -1.43 (0.49), residues: 102 loop : -1.40 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 100B HIS 0.003 0.002 HIS C 32 PHE 0.008 0.001 PHE A 429 TYR 0.013 0.001 TYR B 49 ARG 0.009 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 2) link_NAG-ASN : angle 3.50440 ( 6) hydrogen bonds : bond 0.03331 ( 73) hydrogen bonds : angle 6.06868 ( 177) SS BOND : bond 0.00549 ( 6) SS BOND : angle 1.02652 ( 12) covalent geometry : bond 0.00359 ( 3640) covalent geometry : angle 0.58048 ( 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 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.586 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: 73 average time/residue: 0.3659 time to fit residues: 32.6953 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 : 0.506 ------------------------------------------------------------------------------- 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 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.177837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153683 restraints weight = 12258.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159860 restraints weight = 6362.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163830 restraints weight = 4011.217| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3648 Z= 0.128 Angle : 0.570 10.539 4971 Z= 0.286 Chirality : 0.087 1.740 538 Planarity : 0.004 0.060 640 Dihedral : 6.268 52.053 541 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.78 % Allowed : 15.06 % Favored : 84.16 % 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: -2.16 (0.38), residues: 443 helix: -2.61 (0.80), residues: 27 sheet: -1.61 (0.46), residues: 120 loop : -1.25 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 100B HIS 0.003 0.001 HIS C 35 PHE 0.006 0.001 PHE A 490 TYR 0.013 0.001 TYR B 49 ARG 0.010 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 2) link_NAG-ASN : angle 3.16807 ( 6) hydrogen bonds : bond 0.03097 ( 73) hydrogen bonds : angle 5.90467 ( 177) SS BOND : bond 0.00544 ( 6) SS BOND : angle 0.87856 ( 12) covalent geometry : bond 0.00297 ( 3640) covalent geometry : angle 0.55845 ( 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 79 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 78 average time/residue: 0.3582 time to fit residues: 34.2821 Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 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=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: 2.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN ** C 3 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.176510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152772 restraints weight = 12496.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158745 restraints weight = 6392.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162761 restraints weight = 4029.930| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3648 Z= 0.150 Angle : 0.585 10.567 4971 Z= 0.294 Chirality : 0.088 1.743 538 Planarity : 0.004 0.068 640 Dihedral : 6.307 53.035 541 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.78 % Allowed : 14.81 % Favored : 84.42 % 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: -2.19 (0.38), residues: 443 helix: -2.70 (0.80), residues: 27 sheet: -1.59 (0.46), residues: 120 loop : -1.28 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100B HIS 0.003 0.001 HIS C 32 PHE 0.006 0.001 PHE A 490 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 0.00322 ( 2) link_NAG-ASN : angle 3.37593 ( 6) hydrogen bonds : bond 0.03192 ( 73) hydrogen bonds : angle 5.86954 ( 177) SS BOND : bond 0.00511 ( 6) SS BOND : angle 0.96297 ( 12) covalent geometry : bond 0.00348 ( 3640) covalent geometry : angle 0.57209 ( 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 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7213 (tmtt) cc_final: 0.6967 (tmtt) outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.3553 time to fit residues: 31.8663 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 : 0.569 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 overall best weight: 0.1898 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.179216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156313 restraints weight = 12240.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162231 restraints weight = 6426.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165732 restraints weight = 4076.616| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3648 Z= 0.095 Angle : 0.546 10.430 4971 Z= 0.272 Chirality : 0.087 1.727 538 Planarity : 0.004 0.072 640 Dihedral : 5.748 47.614 541 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.26 % Allowed : 15.06 % Favored : 84.68 % 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: -2.02 (0.38), residues: 443 helix: -2.58 (0.82), residues: 27 sheet: -1.42 (0.46), residues: 120 loop : -1.19 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100B HIS 0.004 0.001 HIS C 35 PHE 0.007 0.001 PHE A 497 TYR 0.012 0.001 TYR B 49 ARG 0.011 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 2.56361 ( 6) hydrogen bonds : bond 0.02829 ( 73) hydrogen bonds : angle 5.69259 ( 177) SS BOND : bond 0.00392 ( 6) SS BOND : angle 0.70754 ( 12) covalent geometry : bond 0.00226 ( 3640) covalent geometry : angle 0.53879 ( 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 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ILE cc_start: 0.8971 (tt) cc_final: 0.8593 (pt) outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.3455 time to fit residues: 29.7935 Evaluate side-chains 70 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.173853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150557 restraints weight = 12760.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156335 restraints weight = 6810.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160135 restraints weight = 4361.534| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3648 Z= 0.192 Angle : 0.617 10.556 4971 Z= 0.312 Chirality : 0.088 1.751 538 Planarity : 0.005 0.074 640 Dihedral : 6.345 55.563 541 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.52 % Allowed : 14.55 % Favored : 84.94 % 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: -2.13 (0.39), residues: 443 helix: -2.43 (0.83), residues: 27 sheet: -1.45 (0.47), residues: 120 loop : -1.32 (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 0.00438 ( 2) link_NAG-ASN : angle 3.69029 ( 6) hydrogen bonds : bond 0.03267 ( 73) hydrogen bonds : angle 5.81611 ( 177) SS BOND : bond 0.00573 ( 6) SS BOND : angle 0.99328 ( 12) covalent geometry : bond 0.00440 ( 3640) covalent geometry : angle 0.60315 ( 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 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7226 (tmtt) cc_final: 0.6961 (tmtt) REVERT: B 5 THR cc_start: 0.7716 (t) cc_final: 0.7467 (p) REVERT: C 38 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7893 (ttm170) outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.3782 time to fit residues: 33.1718 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 : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 0 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.175454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152627 restraints weight = 12553.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158436 restraints weight = 6646.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162193 restraints weight = 4229.757| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3648 Z= 0.134 Angle : 0.580 10.473 4971 Z= 0.291 Chirality : 0.087 1.742 538 Planarity : 0.005 0.076 640 Dihedral : 5.956 50.470 541 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.52 % Allowed : 14.81 % Favored : 84.68 % 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: -2.09 (0.39), residues: 443 helix: -2.37 (0.84), residues: 27 sheet: -1.42 (0.47), residues: 120 loop : -1.30 (0.36), 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 35 PHE 0.006 0.001 PHE A 490 TYR 0.015 0.001 TYR B 49 ARG 0.011 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 2) link_NAG-ASN : angle 3.26821 ( 6) hydrogen bonds : bond 0.03021 ( 73) hydrogen bonds : angle 5.72482 ( 177) SS BOND : bond 0.00481 ( 6) SS BOND : angle 0.92154 ( 12) covalent geometry : bond 0.00310 ( 3640) covalent geometry : angle 0.56762 ( 4953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.67 seconds wall clock time: 74 minutes 22.54 seconds (4462.54 seconds total)