Starting phenix.real_space_refine on Tue Mar 3 11:27:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp0_32665/03_2026/7wp0_32665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp0_32665/03_2026/7wp0_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wp0_32665/03_2026/7wp0_32665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp0_32665/03_2026/7wp0_32665.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wp0_32665/03_2026/7wp0_32665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp0_32665/03_2026/7wp0_32665.map" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.90, per 1000 atoms: 0.28 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: 0.20 Conformation dependent library (CDL) restraints added in 79.7 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: 0.11 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: 0.37 Time building geometry restraints manager: 0.27 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: 6.690 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.780 Find NCS groups from input model: 0.010 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- 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 : 5.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.000 ARG F 457 TYR 0.023 0.002 TYR F 453 PHE 0.014 0.003 PHE F 377 TRP 0.018 0.002 TRP F 436 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 3252) covalent geometry : angle 0.94376 ( 4414) SS BOND : bond 0.00595 ( 3) SS BOND : angle 1.05123 ( 6) hydrogen bonds : bond 0.29981 ( 64) hydrogen bonds : angle 13.58468 ( 165) link_NAG-ASN : bond 0.01246 ( 1) link_NAG-ASN : angle 3.50911 ( 3) *********************** 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 : 0.146 Fit side-chains REVERT: L 40 GLN cc_start: 0.8384 (tt0) cc_final: 0.8112 (tt0) REVERT: H 89 GLU cc_start: 0.7737 (pt0) cc_final: 0.7508 (pt0) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.0661 time to fit residues: 6.4379 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 : 0.124 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.154963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135317 restraints weight = 4719.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138948 restraints weight = 2930.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141519 restraints weight = 2094.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143216 restraints weight = 1626.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144606 restraints weight = 1345.564| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 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 = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3256 Z= 0.168 Angle : 0.655 6.915 4423 Z= 0.349 Chirality : 0.047 0.160 468 Planarity : 0.005 0.045 573 Dihedral : 6.214 46.893 478 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.64 % Allowed : 18.18 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.35), residues: 399 helix: -5.05 (0.22), residues: 27 sheet: -1.74 (0.41), residues: 141 loop : -3.00 (0.33), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 17 TYR 0.017 0.002 TYR F 369 PHE 0.011 0.001 PHE F 338 TRP 0.010 0.001 TRP F 436 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 3252) covalent geometry : angle 0.65394 ( 4414) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.64718 ( 6) hydrogen bonds : bond 0.04161 ( 64) hydrogen bonds : angle 7.31526 ( 165) link_NAG-ASN : bond 0.00544 ( 1) link_NAG-ASN : angle 1.40046 ( 3) *********************** 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 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.141 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.0771 time to fit residues: 6.8361 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 SER 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139625 restraints weight = 4704.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143335 restraints weight = 2895.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145892 restraints weight = 2062.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147819 restraints weight = 1600.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149132 restraints weight = 1306.472| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3256 Z= 0.112 Angle : 0.580 5.766 4423 Z= 0.306 Chirality : 0.045 0.181 468 Planarity : 0.005 0.043 573 Dihedral : 5.386 40.739 478 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.11 % Allowed : 21.99 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.38), residues: 399 helix: -4.80 (0.36), residues: 21 sheet: -1.04 (0.41), residues: 152 loop : -2.76 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 17 TYR 0.017 0.001 TYR F 369 PHE 0.014 0.001 PHE H 29 TRP 0.007 0.001 TRP F 353 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3252) covalent geometry : angle 0.57977 ( 4414) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.31965 ( 6) hydrogen bonds : bond 0.02943 ( 64) hydrogen bonds : angle 5.88649 ( 165) link_NAG-ASN : bond 0.00445 ( 1) link_NAG-ASN : angle 0.72078 ( 3) *********************** 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 82 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: F 452 ARG cc_start: 0.8754 (mtp85) cc_final: 0.8450 (mtm-85) REVERT: F 501 ASN cc_start: 0.7200 (m-40) cc_final: 0.6995 (m-40) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.0648 time to fit residues: 5.9837 Evaluate side-chains 72 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain H residue 2 VAL 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 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 360 ASN F 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134970 restraints weight = 4628.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138591 restraints weight = 2879.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141162 restraints weight = 2064.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142807 restraints weight = 1618.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144107 restraints weight = 1350.101| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 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 = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3256 Z= 0.208 Angle : 0.662 6.140 4423 Z= 0.350 Chirality : 0.047 0.159 468 Planarity : 0.005 0.048 573 Dihedral : 6.036 46.887 478 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.28 % Allowed : 22.29 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.39), residues: 399 helix: -4.78 (0.39), residues: 27 sheet: -1.10 (0.43), residues: 144 loop : -2.44 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 17 TYR 0.016 0.002 TYR F 380 PHE 0.015 0.002 PHE F 377 TRP 0.013 0.002 TRP F 436 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 3252) covalent geometry : angle 0.66173 ( 4414) SS BOND : bond 0.00372 ( 3) SS BOND : angle 0.58082 ( 6) hydrogen bonds : bond 0.03277 ( 64) hydrogen bonds : angle 5.90683 ( 165) link_NAG-ASN : bond 0.00608 ( 1) link_NAG-ASN : angle 1.30228 ( 3) *********************** 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 87 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: H 53 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7551 (t80) outliers start: 18 outliers final: 12 residues processed: 80 average time/residue: 0.0654 time to fit residues: 6.3195 Evaluate side-chains 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 53 ASN 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 118 MET Chi-restraints excluded: chain F residue 360 ASN 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 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 33 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 360 ASN F 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135816 restraints weight = 4661.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139363 restraints weight = 2928.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141720 restraints weight = 2111.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143602 restraints weight = 1671.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144810 restraints weight = 1381.907| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 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 = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3256 Z= 0.147 Angle : 0.616 5.576 4423 Z= 0.326 Chirality : 0.046 0.180 468 Planarity : 0.005 0.044 573 Dihedral : 5.711 45.225 478 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.99 % Allowed : 24.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.39), residues: 399 helix: -4.81 (0.42), residues: 27 sheet: -0.91 (0.44), residues: 141 loop : -2.30 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 17 TYR 0.016 0.001 TYR F 369 PHE 0.014 0.002 PHE H 29 TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3252) covalent geometry : angle 0.61656 ( 4414) SS BOND : bond 0.00243 ( 3) SS BOND : angle 0.34168 ( 6) hydrogen bonds : bond 0.02964 ( 64) hydrogen bonds : angle 5.48355 ( 165) link_NAG-ASN : bond 0.00479 ( 1) link_NAG-ASN : angle 0.71099 ( 3) *********************** 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 83 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.108 Fit side-chains REVERT: H 51 MET cc_start: 0.7574 (tpt) cc_final: 0.7275 (tpp) REVERT: H 53 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7562 (t80) REVERT: F 452 ARG cc_start: 0.8799 (mtp85) cc_final: 0.8400 (mtm-85) REVERT: F 511 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8653 (m) outliers start: 17 outliers final: 13 residues processed: 76 average time/residue: 0.0618 time to fit residues: 5.7271 Evaluate side-chains 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 53 ASN 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 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 360 ASN 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 Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 360 ASN F 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135876 restraints weight = 4646.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139327 restraints weight = 2929.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141958 restraints weight = 2125.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143762 restraints weight = 1655.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144957 restraints weight = 1363.194| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 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 = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3256 Z= 0.152 Angle : 0.620 6.724 4423 Z= 0.327 Chirality : 0.045 0.156 468 Planarity : 0.005 0.041 573 Dihedral : 5.688 45.063 478 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.99 % Allowed : 23.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.39), residues: 399 helix: -4.79 (0.43), residues: 27 sheet: -0.85 (0.44), residues: 139 loop : -2.26 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.015 0.001 TYR F 369 PHE 0.014 0.002 PHE H 68 TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3252) covalent geometry : angle 0.61981 ( 4414) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.37652 ( 6) hydrogen bonds : bond 0.02896 ( 64) hydrogen bonds : angle 5.37551 ( 165) link_NAG-ASN : bond 0.00481 ( 1) link_NAG-ASN : angle 0.68260 ( 3) *********************** 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 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.118 Fit side-chains REVERT: H 51 MET cc_start: 0.7596 (tpt) cc_final: 0.7395 (tpp) REVERT: H 53 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7446 (t80) REVERT: F 452 ARG cc_start: 0.8801 (mtp85) cc_final: 0.8407 (mtm-85) REVERT: F 511 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8629 (m) outliers start: 17 outliers final: 14 residues processed: 72 average time/residue: 0.0607 time to fit residues: 5.3789 Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 53 ASN 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 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 360 ASN 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 Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** F 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134172 restraints weight = 4710.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137897 restraints weight = 2876.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140606 restraints weight = 2045.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142472 restraints weight = 1586.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143732 restraints weight = 1305.557| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 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 = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3256 Z= 0.165 Angle : 0.623 6.244 4423 Z= 0.329 Chirality : 0.045 0.157 468 Planarity : 0.005 0.039 573 Dihedral : 5.695 45.562 478 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.87 % Allowed : 24.05 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.40), residues: 399 helix: -4.61 (0.55), residues: 21 sheet: -0.81 (0.44), residues: 139 loop : -2.34 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.016 0.001 TYR H 59 PHE 0.012 0.002 PHE H 68 TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3252) covalent geometry : angle 0.62326 ( 4414) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.42368 ( 6) hydrogen bonds : bond 0.02888 ( 64) hydrogen bonds : angle 5.38942 ( 165) link_NAG-ASN : bond 0.00474 ( 1) link_NAG-ASN : angle 0.70912 ( 3) *********************** 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 82 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.104 Fit side-chains REVERT: H 51 MET cc_start: 0.7592 (tpt) cc_final: 0.7390 (tpp) REVERT: H 53 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7538 (t80) REVERT: F 452 ARG cc_start: 0.8807 (mtp85) cc_final: 0.8421 (mtm-85) REVERT: F 511 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8562 (m) outliers start: 20 outliers final: 15 residues processed: 74 average time/residue: 0.0581 time to fit residues: 5.2641 Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 53 ASN 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 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 360 ASN 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 Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136649 restraints weight = 4674.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140436 restraints weight = 2815.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143043 restraints weight = 1976.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144886 restraints weight = 1519.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146124 restraints weight = 1242.429| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3256 Z= 0.168 Angle : 0.632 6.737 4423 Z= 0.333 Chirality : 0.045 0.157 468 Planarity : 0.005 0.038 573 Dihedral : 5.690 46.303 478 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.57 % Allowed : 23.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.40), residues: 399 helix: -4.79 (0.44), residues: 27 sheet: -0.76 (0.45), residues: 139 loop : -2.23 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.015 0.001 TYR F 369 PHE 0.011 0.002 PHE H 68 TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3252) covalent geometry : angle 0.63251 ( 4414) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.46047 ( 6) hydrogen bonds : bond 0.02871 ( 64) hydrogen bonds : angle 5.40044 ( 165) link_NAG-ASN : bond 0.00459 ( 1) link_NAG-ASN : angle 0.66315 ( 3) *********************** 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 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.108 Fit side-chains REVERT: H 51 MET cc_start: 0.7617 (tpt) cc_final: 0.7402 (tpp) REVERT: H 53 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7552 (t80) REVERT: F 452 ARG cc_start: 0.8790 (mtp85) cc_final: 0.8402 (mtm-85) REVERT: F 511 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8516 (m) outliers start: 19 outliers final: 16 residues processed: 72 average time/residue: 0.0583 time to fit residues: 5.1971 Evaluate side-chains 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 53 ASN 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 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 360 ASN 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 Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136976 restraints weight = 4687.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140503 restraints weight = 2929.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142899 restraints weight = 2098.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144895 restraints weight = 1634.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146091 restraints weight = 1325.642| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 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 = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3256 Z= 0.147 Angle : 0.650 12.018 4423 Z= 0.332 Chirality : 0.045 0.176 468 Planarity : 0.005 0.039 573 Dihedral : 5.550 46.101 478 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.28 % Allowed : 24.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.40), residues: 399 helix: -4.81 (0.42), residues: 27 sheet: -0.68 (0.43), residues: 150 loop : -2.20 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.015 0.001 TYR F 369 PHE 0.010 0.001 PHE H 68 TRP 0.009 0.001 TRP H 36 HIS 0.001 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3252) covalent geometry : angle 0.65071 ( 4414) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.39616 ( 6) hydrogen bonds : bond 0.02764 ( 64) hydrogen bonds : angle 5.33825 ( 165) link_NAG-ASN : bond 0.00420 ( 1) link_NAG-ASN : angle 0.52154 ( 3) *********************** 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 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.090 Fit side-chains REVERT: H 53 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7547 (t80) REVERT: F 408 ARG cc_start: 0.8047 (mpt-90) cc_final: 0.7539 (mpt-90) REVERT: F 452 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8314 (mtm110) REVERT: F 511 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8534 (m) outliers start: 18 outliers final: 14 residues processed: 72 average time/residue: 0.0697 time to fit residues: 6.0021 Evaluate side-chains 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 53 ASN 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 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 360 ASN Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 6 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 overall best weight: 0.3888 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137435 restraints weight = 4670.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140895 restraints weight = 2901.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143500 restraints weight = 2071.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145152 restraints weight = 1606.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146436 restraints weight = 1325.608| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3097 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= 0.135 Angle : 0.608 6.984 4423 Z= 0.320 Chirality : 0.044 0.152 468 Planarity : 0.005 0.037 573 Dihedral : 5.480 44.621 478 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.40 % Allowed : 24.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.40), residues: 399 helix: -4.81 (0.41), residues: 27 sheet: -0.78 (0.46), residues: 135 loop : -1.96 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.015 0.001 TYR F 369 PHE 0.010 0.001 PHE H 68 TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3252) covalent geometry : angle 0.60861 ( 4414) SS BOND : bond 0.00249 ( 3) SS BOND : angle 0.35752 ( 6) hydrogen bonds : bond 0.02663 ( 64) hydrogen bonds : angle 5.23999 ( 165) link_NAG-ASN : bond 0.00403 ( 1) link_NAG-ASN : angle 0.48727 ( 3) ********************** 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 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.114 Fit side-chains REVERT: H 57 ILE cc_start: 0.8168 (mt) cc_final: 0.7940 (mt) REVERT: F 408 ARG cc_start: 0.7972 (mpt-90) cc_final: 0.7610 (mmt90) REVERT: F 452 ARG cc_start: 0.8731 (mtp85) cc_final: 0.8318 (mtm110) REVERT: F 511 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8517 (m) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.0790 time to fit residues: 6.5857 Evaluate side-chains 71 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 53 ASN 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 F residue 358 ILE Chi-restraints excluded: chain F residue 360 ASN Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136310 restraints weight = 4744.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139956 restraints weight = 2876.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142608 restraints weight = 2045.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144379 restraints weight = 1573.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145809 restraints weight = 1290.791| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3256 Z= 0.149 Angle : 0.627 6.905 4423 Z= 0.330 Chirality : 0.045 0.174 468 Planarity : 0.004 0.039 573 Dihedral : 5.552 45.072 478 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.40 % Allowed : 25.51 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.40), residues: 399 helix: -4.63 (0.53), residues: 21 sheet: -0.79 (0.46), residues: 135 loop : -2.03 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.015 0.001 TYR F 369 PHE 0.011 0.001 PHE H 68 TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3252) covalent geometry : angle 0.62760 ( 4414) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.43662 ( 6) hydrogen bonds : bond 0.02643 ( 64) hydrogen bonds : angle 5.31576 ( 165) link_NAG-ASN : bond 0.00415 ( 1) link_NAG-ASN : angle 0.54240 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1010.12 seconds wall clock time: 18 minutes 0.21 seconds (1080.21 seconds total)