Starting phenix.real_space_refine on Wed Jul 23 13:33:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k9i_22749/07_2025/7k9i_22749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k9i_22749/07_2025/7k9i_22749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2025/7k9i_22749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2025/7k9i_22749.map" model { file = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2025/7k9i_22749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2025/7k9i_22749.cif" } resolution = 3.3 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= 0.002 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2095 2.51 5 N 554 2.21 5 O 632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3295 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.09, per 1000 atoms: 1.24 Number of scatterers: 3295 At special positions: 0 Unit cell: (64.9, 85.8, 86.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 632 8.00 N 554 7.00 C 2095 6.00 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 343 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.605A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.200A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.896A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.277A 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 'H' and resid 86 through 90 removed outlier: 3.569A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.306A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.846A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1051 1.34 - 1.47: 910 1.47 - 1.59: 1402 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3379 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.340 1.269 0.071 5.87e-02 2.90e+02 1.47e+00 bond pdb=" CB ASN L 36 " pdb=" CG ASN L 36 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB ILE A 434 " pdb=" CG2 ILE A 434 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.69e-01 ... (remaining 3374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4390 1.51 - 3.01: 171 3.01 - 4.52: 31 4.52 - 6.03: 6 6.03 - 7.54: 3 Bond angle restraints: 4601 Sorted by residual: angle pdb=" CA CYS H 95 " pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " ideal model delta sigma weight residual 114.40 120.30 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" N CYS H 95 " pdb=" CA CYS H 95 " pdb=" C CYS H 95 " ideal model delta sigma weight residual 110.32 106.37 3.95 1.59e+00 3.96e-01 6.17e+00 angle pdb=" CA GLU A 516 " pdb=" CB GLU A 516 " pdb=" CG GLU A 516 " ideal model delta sigma weight residual 114.10 118.67 -4.57 2.00e+00 2.50e-01 5.23e+00 angle pdb=" C GLY L 52 " pdb=" N THR L 53 " pdb=" CA THR L 53 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 angle pdb=" N GLY L 70 " pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 112.10 108.16 3.94 1.82e+00 3.02e-01 4.68e+00 ... (remaining 4596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 1821 17.83 - 35.66: 139 35.66 - 53.48: 17 53.48 - 71.31: 4 71.31 - 89.14: 2 Dihedral angle restraints: 1983 sinusoidal: 770 harmonic: 1213 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual 93.00 51.32 41.68 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA TRP L 93 " pdb=" C TRP L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.94 -36.94 1 1.00e+01 1.00e-02 1.93e+01 ... (remaining 1980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 317 0.039 - 0.078: 118 0.078 - 0.116: 59 0.116 - 0.155: 8 0.155 - 0.193: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE L 87 " pdb=" N ILE L 87 " pdb=" C ILE L 87 " pdb=" CB ILE L 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 500 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.073 9.50e-02 1.11e+02 4.13e-02 8.64e+00 pdb=" NE ARG A 355 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 41 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO L 42 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 463 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.019 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 72 2.67 - 3.23: 3219 3.23 - 3.79: 4886 3.79 - 4.34: 6660 4.34 - 4.90: 11314 Nonbonded interactions: 26151 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.118 3.040 nonbonded pdb=" O ILE H 30 " pdb=" OG1 THR H 53 " model vdw 2.140 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.173 3.120 nonbonded pdb=" OG1 THR L 12 " pdb=" O GLU L 16 " model vdw 2.189 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 82 " model vdw 2.239 3.040 ... (remaining 26146 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.790 Find NCS groups from input model: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 0.071 3386 Z= 0.237 Angle : 0.723 7.536 4616 Z= 0.386 Chirality : 0.049 0.193 503 Planarity : 0.005 0.043 591 Dihedral : 12.862 89.140 1199 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.40), residues: 417 helix: -1.66 (0.85), residues: 32 sheet: 0.51 (0.45), residues: 133 loop : -1.05 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.012 0.002 PHE A 490 TYR 0.015 0.001 TYR A 380 ARG 0.049 0.003 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 2.19598 ( 3) hydrogen bonds : bond 0.24723 ( 94) hydrogen bonds : angle 9.73332 ( 291) SS BOND : bond 0.00560 ( 6) SS BOND : angle 1.22432 ( 12) covalent geometry : bond 0.00541 ( 3379) covalent geometry : angle 0.71925 ( 4601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7615 (pt0) cc_final: 0.7371 (pt0) REVERT: H 108 ASP cc_start: 0.7834 (t0) cc_final: 0.7624 (t0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2275 time to fit residues: 16.9069 Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 3 GLN ** L 36 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.091850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076316 restraints weight = 7931.960| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.35 r_work: 0.3180 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3386 Z= 0.140 Angle : 0.680 6.856 4616 Z= 0.353 Chirality : 0.047 0.134 503 Planarity : 0.005 0.040 591 Dihedral : 6.503 54.734 485 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.13 % Allowed : 13.52 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.41), residues: 417 helix: -1.31 (0.97), residues: 33 sheet: 0.13 (0.44), residues: 142 loop : -0.73 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.008 0.001 TYR A 451 ARG 0.005 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 1.86939 ( 3) hydrogen bonds : bond 0.04336 ( 94) hydrogen bonds : angle 6.79483 ( 291) SS BOND : bond 0.00562 ( 6) SS BOND : angle 0.83584 ( 12) covalent geometry : bond 0.00304 ( 3379) covalent geometry : angle 0.67832 ( 4601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8522 (tppt) REVERT: A 420 ASP cc_start: 0.8767 (m-30) cc_final: 0.8210 (m-30) REVERT: H 108 ASP cc_start: 0.8074 (t0) cc_final: 0.7727 (t0) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2885 time to fit residues: 25.8120 Evaluate side-chains 67 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3557 r_free = 0.3557 target = 0.089837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074257 restraints weight = 7923.541| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.32 r_work: 0.3141 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3386 Z= 0.207 Angle : 0.682 6.303 4616 Z= 0.353 Chirality : 0.046 0.155 503 Planarity : 0.005 0.041 591 Dihedral : 6.508 54.789 485 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.38 % Allowed : 16.62 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.40), residues: 417 helix: -1.31 (1.12), residues: 26 sheet: 0.11 (0.43), residues: 142 loop : -0.88 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS L 97 PHE 0.011 0.001 PHE A 490 TYR 0.017 0.001 TYR A 380 ARG 0.006 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 1) link_NAG-ASN : angle 2.10487 ( 3) hydrogen bonds : bond 0.03880 ( 94) hydrogen bonds : angle 6.41416 ( 291) SS BOND : bond 0.00503 ( 6) SS BOND : angle 0.74613 ( 12) covalent geometry : bond 0.00473 ( 3379) covalent geometry : angle 0.67961 ( 4601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.451 Fit side-chains REVERT: A 414 GLN cc_start: 0.8027 (mp10) cc_final: 0.7775 (mp10) REVERT: A 417 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8566 (tppt) REVERT: A 420 ASP cc_start: 0.8754 (m-30) cc_final: 0.8229 (m-30) REVERT: H 16 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: H 108 ASP cc_start: 0.8319 (t0) cc_final: 0.8016 (t0) REVERT: L 7 GLU cc_start: 0.7368 (pm20) cc_final: 0.7127 (pm20) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.2388 time to fit residues: 21.9055 Evaluate side-chains 69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 50 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3570 r_free = 0.3570 target = 0.090538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074829 restraints weight = 8060.542| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.36 r_work: 0.3152 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3386 Z= 0.164 Angle : 0.639 6.143 4616 Z= 0.330 Chirality : 0.046 0.135 503 Planarity : 0.005 0.041 591 Dihedral : 6.369 54.390 485 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.66 % Allowed : 18.59 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.40), residues: 417 helix: -1.53 (1.02), residues: 26 sheet: 0.17 (0.43), residues: 142 loop : -0.92 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS L 97 PHE 0.010 0.001 PHE A 490 TYR 0.012 0.001 TYR A 380 ARG 0.005 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 1.92070 ( 3) hydrogen bonds : bond 0.03502 ( 94) hydrogen bonds : angle 6.22406 ( 291) SS BOND : bond 0.00452 ( 6) SS BOND : angle 0.68673 ( 12) covalent geometry : bond 0.00377 ( 3379) covalent geometry : angle 0.63738 ( 4601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8561 (tppt) REVERT: A 420 ASP cc_start: 0.8754 (m-30) cc_final: 0.8229 (m-30) REVERT: H 4 LEU cc_start: 0.8816 (mm) cc_final: 0.8602 (mm) REVERT: H 16 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: H 72 ASP cc_start: 0.8272 (t0) cc_final: 0.7820 (p0) REVERT: H 108 ASP cc_start: 0.8399 (t0) cc_final: 0.8031 (t0) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.1837 time to fit residues: 16.8430 Evaluate side-chains 79 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3574 r_free = 0.3574 target = 0.090699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074905 restraints weight = 8051.364| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.44 r_work: 0.3151 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3386 Z= 0.154 Angle : 0.629 6.197 4616 Z= 0.323 Chirality : 0.045 0.133 503 Planarity : 0.004 0.040 591 Dihedral : 6.295 54.393 485 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.23 % Allowed : 18.87 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.40), residues: 417 helix: -1.59 (0.99), residues: 27 sheet: 0.01 (0.43), residues: 145 loop : -0.78 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS L 97 PHE 0.009 0.001 PHE A 490 TYR 0.016 0.001 TYR A 451 ARG 0.006 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 1.85991 ( 3) hydrogen bonds : bond 0.03365 ( 94) hydrogen bonds : angle 6.10295 ( 291) SS BOND : bond 0.00425 ( 6) SS BOND : angle 0.61316 ( 12) covalent geometry : bond 0.00353 ( 3379) covalent geometry : angle 0.62724 ( 4601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8514 (tppt) REVERT: A 420 ASP cc_start: 0.8768 (m-30) cc_final: 0.8279 (m-30) REVERT: H 16 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: H 18 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7141 (mm) REVERT: H 72 ASP cc_start: 0.8222 (t0) cc_final: 0.7843 (p0) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.1866 time to fit residues: 17.2117 Evaluate side-chains 79 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3559 r_free = 0.3559 target = 0.089822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074053 restraints weight = 8264.720| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.42 r_work: 0.3136 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3386 Z= 0.199 Angle : 0.654 7.093 4616 Z= 0.336 Chirality : 0.046 0.147 503 Planarity : 0.005 0.041 591 Dihedral : 6.389 54.383 485 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.63 % Allowed : 19.15 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.40), residues: 417 helix: -1.64 (0.98), residues: 27 sheet: -0.09 (0.43), residues: 145 loop : -0.78 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS L 97 PHE 0.011 0.001 PHE A 490 TYR 0.016 0.001 TYR A 451 ARG 0.004 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 1) link_NAG-ASN : angle 2.00493 ( 3) hydrogen bonds : bond 0.03427 ( 94) hydrogen bonds : angle 6.10836 ( 291) SS BOND : bond 0.00419 ( 6) SS BOND : angle 0.61828 ( 12) covalent geometry : bond 0.00453 ( 3379) covalent geometry : angle 0.65266 ( 4601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8539 (tppt) REVERT: A 420 ASP cc_start: 0.8788 (m-30) cc_final: 0.8299 (m-30) REVERT: A 517 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8354 (tt) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.1659 time to fit residues: 16.5538 Evaluate side-chains 80 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3573 r_free = 0.3573 target = 0.090614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.075044 restraints weight = 8072.875| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.37 r_work: 0.3157 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3386 Z= 0.164 Angle : 0.655 7.581 4616 Z= 0.333 Chirality : 0.046 0.137 503 Planarity : 0.004 0.040 591 Dihedral : 6.303 54.435 485 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.51 % Allowed : 21.97 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.40), residues: 417 helix: -1.60 (0.98), residues: 27 sheet: -0.14 (0.43), residues: 145 loop : -0.76 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS L 97 PHE 0.009 0.001 PHE A 490 TYR 0.013 0.001 TYR A 451 ARG 0.005 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00027 ( 1) link_NAG-ASN : angle 1.96889 ( 3) hydrogen bonds : bond 0.03282 ( 94) hydrogen bonds : angle 6.05598 ( 291) SS BOND : bond 0.00396 ( 6) SS BOND : angle 0.57458 ( 12) covalent geometry : bond 0.00378 ( 3379) covalent geometry : angle 0.65312 ( 4601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.359 Fit side-chains REVERT: A 417 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8529 (tppt) REVERT: A 420 ASP cc_start: 0.8781 (m-30) cc_final: 0.8280 (m-30) REVERT: A 493 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7869 (mm-40) REVERT: A 517 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8385 (tt) outliers start: 16 outliers final: 13 residues processed: 78 average time/residue: 0.2380 time to fit residues: 23.0748 Evaluate side-chains 81 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 26 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3608 r_free = 0.3608 target = 0.092602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077092 restraints weight = 7878.557| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.34 r_work: 0.3203 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3386 Z= 0.110 Angle : 0.619 7.226 4616 Z= 0.313 Chirality : 0.045 0.129 503 Planarity : 0.004 0.037 591 Dihedral : 6.026 54.593 485 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.94 % Allowed : 21.41 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.40), residues: 417 helix: -2.10 (0.85), residues: 33 sheet: 0.03 (0.44), residues: 134 loop : -0.73 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS L 44 PHE 0.006 0.001 PHE A 400 TYR 0.013 0.001 TYR A 451 ARG 0.007 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 1.68332 ( 3) hydrogen bonds : bond 0.02967 ( 94) hydrogen bonds : angle 5.80607 ( 291) SS BOND : bond 0.00342 ( 6) SS BOND : angle 0.47053 ( 12) covalent geometry : bond 0.00259 ( 3379) covalent geometry : angle 0.61784 ( 4601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8533 (tppt) REVERT: A 420 ASP cc_start: 0.8808 (m-30) cc_final: 0.8291 (m-30) REVERT: A 517 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8431 (tt) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.2657 time to fit residues: 26.6985 Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.093053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077535 restraints weight = 8046.521| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.37 r_work: 0.3209 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3386 Z= 0.116 Angle : 0.648 9.071 4616 Z= 0.322 Chirality : 0.045 0.129 503 Planarity : 0.004 0.037 591 Dihedral : 6.038 54.384 485 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.23 % Allowed : 22.82 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.40), residues: 417 helix: -1.54 (1.01), residues: 27 sheet: 0.01 (0.44), residues: 134 loop : -0.65 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 490 TYR 0.009 0.001 TYR H 104 ARG 0.006 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 1.70041 ( 3) hydrogen bonds : bond 0.02959 ( 94) hydrogen bonds : angle 5.78716 ( 291) SS BOND : bond 0.00347 ( 6) SS BOND : angle 0.48902 ( 12) covalent geometry : bond 0.00273 ( 3379) covalent geometry : angle 0.64729 ( 4601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8407 (tppt) REVERT: A 420 ASP cc_start: 0.8736 (m-30) cc_final: 0.8243 (m-30) REVERT: A 517 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8397 (tt) REVERT: H 107 MET cc_start: 0.8686 (mpp) cc_final: 0.8167 (mpp) REVERT: L 39 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7643 (tm-30) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.2150 time to fit residues: 20.9636 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 0.0270 chunk 18 optimal weight: 0.0040 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.094340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.079124 restraints weight = 7874.539| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.25 r_work: 0.3248 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3386 Z= 0.107 Angle : 0.652 9.022 4616 Z= 0.324 Chirality : 0.045 0.144 503 Planarity : 0.004 0.036 591 Dihedral : 5.930 54.404 485 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.66 % Allowed : 23.38 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.40), residues: 417 helix: -2.15 (0.84), residues: 33 sheet: 0.02 (0.44), residues: 133 loop : -0.65 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 400 TYR 0.015 0.001 TYR A 451 ARG 0.008 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 1) link_NAG-ASN : angle 1.54797 ( 3) hydrogen bonds : bond 0.02796 ( 94) hydrogen bonds : angle 5.68594 ( 291) SS BOND : bond 0.00330 ( 6) SS BOND : angle 0.45923 ( 12) covalent geometry : bond 0.00255 ( 3379) covalent geometry : angle 0.65139 ( 4601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8496 (tppt) REVERT: A 420 ASP cc_start: 0.8622 (m-30) cc_final: 0.8124 (m-30) REVERT: A 517 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8369 (tt) REVERT: H 107 MET cc_start: 0.8570 (mpp) cc_final: 0.8046 (mpp) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.3277 time to fit residues: 31.3390 Evaluate side-chains 77 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.091170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075495 restraints weight = 8052.790| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.36 r_work: 0.3169 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3386 Z= 0.185 Angle : 0.673 8.477 4616 Z= 0.339 Chirality : 0.046 0.147 503 Planarity : 0.005 0.041 591 Dihedral : 6.144 54.720 485 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.66 % Allowed : 23.38 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.40), residues: 417 helix: -2.14 (0.84), residues: 33 sheet: -0.02 (0.44), residues: 133 loop : -0.66 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS L 97 PHE 0.010 0.001 PHE A 490 TYR 0.015 0.001 TYR A 451 ARG 0.008 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 1.88015 ( 3) hydrogen bonds : bond 0.03097 ( 94) hydrogen bonds : angle 5.90706 ( 291) SS BOND : bond 0.00387 ( 6) SS BOND : angle 0.51751 ( 12) covalent geometry : bond 0.00428 ( 3379) covalent geometry : angle 0.67210 ( 4601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.65 seconds wall clock time: 53 minutes 56.43 seconds (3236.43 seconds total)