Starting phenix.real_space_refine on Wed Jul 23 11:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp0_32665/07_2025/7wp0_32665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp0_32665/07_2025/7wp0_32665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wp0_32665/07_2025/7wp0_32665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp0_32665/07_2025/7wp0_32665.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp0_32665/07_2025/7wp0_32665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp0_32665/07_2025/7wp0_32665.cif" } resolution = 3.71 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= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2007 2.51 5 N 537 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 3174 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1332 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "F" 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: 5.31, per 1000 atoms: 1.67 Number of scatterers: 3174 At special positions: 0 Unit cell: (83.246, 63.018, 79.356, 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 13 16.00 O 617 8.00 N 537 7.00 C 2007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.02 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 F 601 " - " ASN F 343 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 380.2 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.760A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.174A pdb=" N TRP F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.492A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.568A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.568A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.746A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.936A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 374 through 379 removed outlier: 6.669A pdb=" N ALA F 435 " --> pdb=" O SER F 375 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE F 377 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL F 433 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS F 379 " --> pdb=" O GLY F 431 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY F 431 " --> pdb=" O CYS F 379 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP F 436 " --> pdb=" O ARG F 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 453 through 454 73 hydrogen bonds defined for protein. 165 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: 0.71 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 973 1.33 - 1.45: 693 1.45 - 1.57: 1569 1.57 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 3252 Sorted by residual: bond pdb=" C GLY H 99 " pdb=" N VAL H 100 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.57e-02 4.06e+03 8.43e+00 bond pdb=" C1 NAG F 601 " pdb=" O5 NAG F 601 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" CA ASP L 62 " pdb=" C ASP L 62 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.56e-02 4.11e+03 3.03e+00 bond pdb=" C CYS F 336 " pdb=" N PRO F 337 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.37e+00 ... (remaining 3247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 4240 2.23 - 4.46: 155 4.46 - 6.69: 16 6.69 - 8.92: 2 8.92 - 11.15: 1 Bond angle restraints: 4414 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" C TYR H 103 " ideal model delta sigma weight residual 110.44 105.25 5.19 1.20e+00 6.94e-01 1.87e+01 angle pdb=" C SER F 359 " pdb=" N ASN F 360 " pdb=" CA ASN F 360 " ideal model delta sigma weight residual 122.08 128.22 -6.14 1.47e+00 4.63e-01 1.75e+01 angle pdb=" CA ASP L 62 " pdb=" C ASP L 62 " pdb=" O ASP L 62 " ideal model delta sigma weight residual 119.43 123.76 -4.33 1.21e+00 6.83e-01 1.28e+01 angle pdb=" CA ASN F 360 " pdb=" CB ASN F 360 " pdb=" CG ASN F 360 " ideal model delta sigma weight residual 112.60 116.10 -3.50 1.00e+00 1.00e+00 1.23e+01 ... (remaining 4409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1677 16.84 - 33.68: 187 33.68 - 50.52: 33 50.52 - 67.36: 6 67.36 - 84.20: 3 Dihedral angle restraints: 1906 sinusoidal: 743 harmonic: 1163 Sorted by residual: dihedral pdb=" CA ARG H 16 " pdb=" C ARG H 16 " pdb=" N SER H 17 " pdb=" CA SER H 17 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 297 0.048 - 0.096: 121 0.096 - 0.144: 38 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 468 Sorted by residual: chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN F 360 " pdb=" N ASN F 360 " pdb=" C ASN F 360 " pdb=" CB ASN F 360 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PRO F 337 " pdb=" N PRO F 337 " pdb=" C PRO F 337 " pdb=" CB PRO F 337 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 465 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO F 463 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 411 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO F 412 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 412 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 412 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 6 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO L 7 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 7 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 7 " 0.027 5.00e-02 4.00e+02 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 968 2.80 - 3.33: 2577 3.33 - 3.85: 4987 3.85 - 4.38: 5544 4.38 - 4.90: 9966 Nonbonded interactions: 24042 Sorted by model distance: nonbonded pdb=" OH TYR L 51 " pdb=" O THR F 415 " model vdw 2.281 3.040 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.345 3.120 nonbonded pdb=" O THR F 430 " pdb=" OG1 THR F 430 " model vdw 2.350 3.040 nonbonded pdb=" O PRO L 7 " pdb=" OG1 THR L 106 " model vdw 2.362 3.040 nonbonded pdb=" NH1 ARG F 457 " pdb=" O SER F 459 " model vdw 2.377 3.120 ... (remaining 24037 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=0.00 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: 11.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.007 0.063 3256 Z= 0.308 Angle : 0.948 11.148 4423 Z= 0.547 Chirality : 0.060 0.240 468 Planarity : 0.007 0.067 573 Dihedral : 14.465 84.198 1167 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.59 % Allowed : 11.14 % Favored : 88.27 % 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: -4.57 (0.33), residues: 399 helix: -5.05 (0.23), residues: 21 sheet: -2.27 (0.39), residues: 149 loop : -3.48 (0.30), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.014 0.003 PHE F 377 TYR 0.023 0.002 TYR F 453 ARG 0.004 0.000 ARG F 457 Details of bonding type rmsd link_NAG-ASN : bond 0.01246 ( 1) link_NAG-ASN : angle 3.50911 ( 3) hydrogen bonds : bond 0.29981 ( 64) hydrogen bonds : angle 13.58468 ( 165) SS BOND : bond 0.00595 ( 3) SS BOND : angle 1.05123 ( 6) covalent geometry : bond 0.00691 ( 3252) covalent geometry : angle 0.94376 ( 4414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.403 Fit side-chains REVERT: L 40 GLN cc_start: 0.8384 (tt0) cc_final: 0.8114 (tt0) REVERT: H 89 GLU cc_start: 0.7737 (pt0) cc_final: 0.7511 (pt0) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.1743 time to fit residues: 16.9525 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0170 chunk 30 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140083 restraints weight = 4754.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143921 restraints weight = 2858.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146624 restraints weight = 1996.773| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3256 Z= 0.119 Angle : 0.619 7.160 4423 Z= 0.329 Chirality : 0.046 0.156 468 Planarity : 0.005 0.047 573 Dihedral : 5.876 43.614 478 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.35 % Allowed : 17.60 % Favored : 80.06 % 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: -3.88 (0.36), residues: 399 helix: -5.07 (0.21), residues: 27 sheet: -1.62 (0.41), residues: 141 loop : -2.99 (0.33), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.001 0.001 HIS H 35 PHE 0.008 0.001 PHE H 68 TYR 0.017 0.001 TYR F 369 ARG 0.005 0.001 ARG L 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 1) link_NAG-ASN : angle 1.11516 ( 3) hydrogen bonds : bond 0.03895 ( 64) hydrogen bonds : angle 7.13650 ( 165) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.47706 ( 6) covalent geometry : bond 0.00272 ( 3252) covalent geometry : angle 0.61890 ( 4414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.361 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 0.1794 time to fit residues: 17.2437 Evaluate side-chains 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136225 restraints weight = 4689.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140039 restraints weight = 2847.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142776 restraints weight = 2021.755| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3256 Z= 0.147 Angle : 0.620 6.951 4423 Z= 0.327 Chirality : 0.047 0.185 468 Planarity : 0.005 0.039 573 Dihedral : 5.730 43.233 478 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.11 % Allowed : 20.53 % Favored : 75.37 % 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: -3.29 (0.37), residues: 399 helix: -4.94 (0.30), residues: 27 sheet: -1.13 (0.43), residues: 141 loop : -2.61 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.001 0.001 HIS H 35 PHE 0.015 0.002 PHE H 29 TYR 0.023 0.001 TYR F 369 ARG 0.005 0.001 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 1) link_NAG-ASN : angle 1.23816 ( 3) hydrogen bonds : bond 0.03291 ( 64) hydrogen bonds : angle 6.15300 ( 165) SS BOND : bond 0.00256 ( 3) SS BOND : angle 0.50383 ( 6) covalent geometry : bond 0.00348 ( 3252) covalent geometry : angle 0.61968 ( 4414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.363 Fit side-chains REVERT: L 68 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8458 (tttm) REVERT: L 80 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8455 (pp) REVERT: F 452 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8437 (mtm-85) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.1772 time to fit residues: 17.3095 Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.0050 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137998 restraints weight = 4654.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141447 restraints weight = 2914.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144044 restraints weight = 2094.985| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3256 Z= 0.138 Angle : 0.605 6.555 4423 Z= 0.317 Chirality : 0.046 0.154 468 Planarity : 0.005 0.048 573 Dihedral : 5.578 41.881 478 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.93 % Allowed : 25.51 % Favored : 71.55 % 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: -2.96 (0.38), residues: 399 helix: -4.43 (0.68), residues: 14 sheet: -0.95 (0.42), residues: 144 loop : -2.59 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 436 HIS 0.003 0.001 HIS L 36 PHE 0.009 0.001 PHE F 338 TYR 0.022 0.001 TYR F 369 ARG 0.004 0.000 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 1) link_NAG-ASN : angle 0.89792 ( 3) hydrogen bonds : bond 0.02901 ( 64) hydrogen bonds : angle 5.47675 ( 165) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.32747 ( 6) covalent geometry : bond 0.00328 ( 3252) covalent geometry : angle 0.60544 ( 4414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.451 Fit side-chains REVERT: L 68 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8358 (tttp) REVERT: F 452 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8467 (mtm-85) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.2110 time to fit residues: 18.5532 Evaluate side-chains 71 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136908 restraints weight = 4664.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140722 restraints weight = 2823.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143395 restraints weight = 1995.307| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3256 Z= 0.138 Angle : 0.601 5.423 4423 Z= 0.314 Chirality : 0.045 0.177 468 Planarity : 0.004 0.040 573 Dihedral : 5.486 43.546 478 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.81 % Allowed : 24.34 % Favored : 71.85 % 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: -2.73 (0.39), residues: 399 helix: -4.30 (0.77), residues: 14 sheet: -0.70 (0.44), residues: 147 loop : -2.51 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.013 0.001 PHE H 29 TYR 0.021 0.001 TYR F 369 ARG 0.002 0.000 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 1) link_NAG-ASN : angle 0.80926 ( 3) hydrogen bonds : bond 0.02735 ( 64) hydrogen bonds : angle 5.36377 ( 165) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.35331 ( 6) covalent geometry : bond 0.00329 ( 3252) covalent geometry : angle 0.60085 ( 4414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.316 Fit side-chains REVERT: L 68 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8401 (tttp) REVERT: H 53 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7487 (t80) REVERT: H 114 TYR cc_start: 0.8458 (m-10) cc_final: 0.8211 (m-10) REVERT: F 417 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8321 (ttpt) REVERT: F 452 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8392 (mtm-85) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.1580 time to fit residues: 14.0776 Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134743 restraints weight = 4792.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138290 restraints weight = 2982.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140787 restraints weight = 2138.704| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3256 Z= 0.176 Angle : 0.628 6.242 4423 Z= 0.329 Chirality : 0.046 0.155 468 Planarity : 0.005 0.042 573 Dihedral : 5.723 46.095 478 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.11 % Allowed : 24.05 % Favored : 71.85 % 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: -2.76 (0.39), residues: 399 helix: -4.27 (0.82), residues: 14 sheet: -0.90 (0.45), residues: 135 loop : -2.33 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.011 0.002 PHE F 338 TYR 0.019 0.002 TYR F 369 ARG 0.003 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 1) link_NAG-ASN : angle 0.89820 ( 3) hydrogen bonds : bond 0.02886 ( 64) hydrogen bonds : angle 5.49829 ( 165) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.52256 ( 6) covalent geometry : bond 0.00422 ( 3252) covalent geometry : angle 0.62814 ( 4414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.446 Fit side-chains REVERT: L 68 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8375 (tttp) REVERT: F 417 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8222 (ttpt) REVERT: F 452 ARG cc_start: 0.8736 (mtp85) cc_final: 0.8375 (mtm-85) outliers start: 14 outliers final: 12 residues processed: 71 average time/residue: 0.2193 time to fit residues: 18.9580 Evaluate side-chains 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135039 restraints weight = 4643.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138477 restraints weight = 2937.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140908 restraints weight = 2117.273| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3256 Z= 0.180 Angle : 0.654 7.431 4423 Z= 0.338 Chirality : 0.047 0.178 468 Planarity : 0.005 0.038 573 Dihedral : 5.774 47.380 478 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.11 % Allowed : 24.93 % Favored : 70.97 % 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: -2.67 (0.40), residues: 399 helix: -4.61 (0.59), residues: 20 sheet: -0.81 (0.45), residues: 140 loop : -2.20 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.011 0.002 PHE F 338 TYR 0.018 0.001 TYR F 369 ARG 0.003 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 1) link_NAG-ASN : angle 0.73318 ( 3) hydrogen bonds : bond 0.02884 ( 64) hydrogen bonds : angle 5.60575 ( 165) SS BOND : bond 0.00317 ( 3) SS BOND : angle 0.54049 ( 6) covalent geometry : bond 0.00433 ( 3252) covalent geometry : angle 0.65458 ( 4414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.232 Fit side-chains REVERT: L 68 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8363 (tttp) REVERT: F 417 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8320 (ttpt) REVERT: F 452 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8360 (mtm110) outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.3148 time to fit residues: 26.6889 Evaluate side-chains 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0970 chunk 24 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 overall best weight: 0.1434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142182 restraints weight = 4606.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145740 restraints weight = 2819.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148218 restraints weight = 2001.806| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3256 Z= 0.101 Angle : 0.596 7.690 4423 Z= 0.308 Chirality : 0.044 0.150 468 Planarity : 0.004 0.040 573 Dihedral : 5.183 41.010 478 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.23 % Allowed : 25.51 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.44 (0.40), residues: 399 helix: -4.39 (0.72), residues: 14 sheet: -0.82 (0.47), residues: 126 loop : -1.97 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.007 0.001 PHE H 27 TYR 0.021 0.001 TYR F 369 ARG 0.002 0.000 ARG L 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 1) link_NAG-ASN : angle 0.36037 ( 3) hydrogen bonds : bond 0.02522 ( 64) hydrogen bonds : angle 5.07681 ( 165) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.26028 ( 6) covalent geometry : bond 0.00232 ( 3252) covalent geometry : angle 0.59624 ( 4414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.699 Fit side-chains REVERT: L 68 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8387 (tttp) REVERT: F 408 ARG cc_start: 0.7922 (mpt-90) cc_final: 0.7545 (mpt-90) REVERT: F 454 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8290 (mtp-110) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 0.2647 time to fit residues: 26.4545 Evaluate side-chains 75 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.0270 chunk 10 optimal weight: 0.4980 chunk 12 optimal weight: 0.3980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139447 restraints weight = 4673.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143051 restraints weight = 2866.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145547 restraints weight = 2038.254| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3256 Z= 0.125 Angle : 0.617 9.617 4423 Z= 0.318 Chirality : 0.044 0.172 468 Planarity : 0.004 0.034 573 Dihedral : 5.282 42.130 478 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.64 % Allowed : 26.69 % Favored : 70.67 % 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: -2.41 (0.40), residues: 399 helix: -4.34 (0.76), residues: 14 sheet: -0.69 (0.47), residues: 129 loop : -2.02 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.011 0.001 PHE H 68 TYR 0.019 0.001 TYR F 369 ARG 0.002 0.000 ARG L 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 1) link_NAG-ASN : angle 0.58546 ( 3) hydrogen bonds : bond 0.02534 ( 64) hydrogen bonds : angle 5.04384 ( 165) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.38787 ( 6) covalent geometry : bond 0.00297 ( 3252) covalent geometry : angle 0.61762 ( 4414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.394 Fit side-chains REVERT: L 68 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8394 (tttp) REVERT: F 408 ARG cc_start: 0.7903 (mpt-90) cc_final: 0.7510 (mmt90) REVERT: F 454 ARG cc_start: 0.8604 (mtp-110) cc_final: 0.8325 (mtp-110) outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.2893 time to fit residues: 25.3981 Evaluate side-chains 75 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.0970 chunk 8 optimal weight: 0.2980 chunk 1 optimal weight: 0.0050 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN ** L 81 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 = 0.3839 r_free = 0.3839 target = 0.160239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140918 restraints weight = 4578.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144567 restraints weight = 2830.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.147042 restraints weight = 2008.319| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3256 Z= 0.117 Angle : 0.620 9.423 4423 Z= 0.318 Chirality : 0.044 0.168 468 Planarity : 0.005 0.043 573 Dihedral : 5.180 40.762 478 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.35 % Allowed : 28.15 % Favored : 69.50 % 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: -2.30 (0.41), residues: 399 helix: -4.28 (0.83), residues: 14 sheet: -0.57 (0.48), residues: 129 loop : -1.98 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE H 68 TYR 0.019 0.001 TYR F 369 ARG 0.010 0.001 ARG F 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 1) link_NAG-ASN : angle 0.50637 ( 3) hydrogen bonds : bond 0.02535 ( 64) hydrogen bonds : angle 5.06180 ( 165) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.42699 ( 6) covalent geometry : bond 0.00274 ( 3252) covalent geometry : angle 0.62009 ( 4414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.409 Fit side-chains REVERT: L 68 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8385 (tttp) REVERT: H 116 TYR cc_start: 0.8318 (m-80) cc_final: 0.8060 (m-80) REVERT: F 408 ARG cc_start: 0.7848 (mpt-90) cc_final: 0.7443 (mmt90) REVERT: F 454 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8273 (mtp-110) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.3504 time to fit residues: 31.3838 Evaluate side-chains 75 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 36 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138112 restraints weight = 4615.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141898 restraints weight = 2744.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144348 restraints weight = 1920.944| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3256 Z= 0.140 Angle : 0.632 9.826 4423 Z= 0.324 Chirality : 0.045 0.170 468 Planarity : 0.004 0.035 573 Dihedral : 5.312 42.653 478 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.64 % Allowed : 27.57 % Favored : 69.79 % 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: -2.30 (0.41), residues: 399 helix: -4.25 (0.86), residues: 14 sheet: -0.57 (0.48), residues: 129 loop : -1.97 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.012 0.001 PHE H 29 TYR 0.018 0.001 TYR F 369 ARG 0.009 0.001 ARG F 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 1) link_NAG-ASN : angle 0.62032 ( 3) hydrogen bonds : bond 0.02552 ( 64) hydrogen bonds : angle 5.09284 ( 165) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.55275 ( 6) covalent geometry : bond 0.00333 ( 3252) covalent geometry : angle 0.63238 ( 4414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3103.59 seconds wall clock time: 57 minutes 57.61 seconds (3477.61 seconds total)