Starting phenix.real_space_refine on Thu Oct 22 18:02:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wp0_32665/10_2026/7wp0_32665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp0_32665/10_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_32665/10_2026/7wp0_32665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp0_32665/10_2026/7wp0_32665.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wp0_32665/10_2026/7wp0_32665.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wp0_32665/10_2026/7wp0_32665.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wp0_32665/10_2026/7wp0_32665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp0_32665/10_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-2.3rc1-6221/lib/python3.11/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 chiralities: 1 Time building chain proxies: 0.92, per 1000 atoms: 0.29 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: 0.24 Conformation dependent library (CDL) restraints added in 117.3 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: 0.09 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: 0.31 Time building geometry restraints manager: 0.34 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: 1660 16.84 - 33.68: 185 33.68 - 50.52: 31 50.52 - 67.36: 6 67.36 - 84.20: 3 Dihedral angle restraints: 1885 sinusoidal: 722 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 1882 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: 7.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.600 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 14.487 84.198 1146 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/Z covalent geometry : bond 0.00691 / 0.31 ( 3252) covalent geometry : angle 0.94376 / 0.55 ( 4414) SS BOND : bond 0.00595 / 0.30 ( 3) SS BOND : angle 1.05123 / 0.79 ( 6) hydrogen bonds : bond 0.29981 / 21.60 ( 64) hydrogen bonds : angle 13.58468 / 9.84 ( 165) link_NAG-ASN : bond 0.01246 / 0.66 ( 1) link_NAG-ASN : angle 3.50911 / 1.87 ( 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 : 0.111 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: 0.0575 time to fit residues: 5.6483 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 : 0.134 ------------------------------------------------------------------------------- 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: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] 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: 0.5980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135430 restraints weight = 4773.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139296 restraints weight = 2899.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142026 restraints weight = 2051.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143888 restraints weight = 1585.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145333 restraints weight = 1303.815| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 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 = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3256 Z= 0.163 Angle : 0.647 6.839 4423 Z= 0.345 Chirality : 0.047 0.161 468 Planarity : 0.005 0.046 573 Dihedral : 6.088 46.384 457 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.93 % Allowed : 17.60 % Favored : 79.47 % 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: -3.92 (0.36), residues: 399 helix: -5.04 (0.23), residues: 27 sheet: -1.70 (0.41), residues: 141 loop : -2.99 (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 H 59 PHE 0.010 0.001 PHE F 338 TRP 0.010 0.002 TRP F 436 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 3252) covalent geometry : angle 0.64659 / 0.34 ( 4414) SS BOND : bond 0.00333 / 0.16 ( 3) SS BOND : angle 0.67164 / 0.41 ( 6) hydrogen bonds : bond 0.03869 / 2.49 ( 64) hydrogen bonds : angle 7.10386 / 5.20 ( 165) link_NAG-ASN : bond 0.00458 / 0.24 ( 1) link_NAG-ASN : angle 1.37208 / 0.72 ( 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 83 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.073 Fit side-chains REVERT: F 516 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6928 (pm20) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.0743 time to fit residues: 6.7207 Evaluate side-chains 73 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [9, 2, 24, 36, 7, 4, 33, 17, 19, 22, 30] chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 36 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136879 restraints weight = 4729.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140498 restraints weight = 2928.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142999 restraints weight = 2099.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144880 restraints weight = 1646.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146218 restraints weight = 1351.605| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- 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: 4 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3256 Z= 0.133 Angle : 0.602 5.721 4423 Z= 0.320 Chirality : 0.046 0.186 468 Planarity : 0.005 0.042 573 Dihedral : 5.672 43.306 457 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.11 % Allowed : 22.87 % Favored : 73.02 % 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: -3.27 (0.38), residues: 399 helix: -4.92 (0.30), residues: 27 sheet: -1.09 (0.41), residues: 152 loop : -2.67 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 17 TYR 0.016 0.001 TYR F 369 PHE 0.014 0.001 PHE H 29 TRP 0.008 0.001 TRP F 436 HIS 0.001 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 3252) covalent geometry : angle 0.60185 / 0.32 ( 4414) SS BOND : bond 0.00233 / 0.12 ( 3) SS BOND : angle 0.37922 / 0.25 ( 6) hydrogen bonds : bond 0.03130 / 1.98 ( 64) hydrogen bonds : angle 6.04679 / 4.47 ( 165) link_NAG-ASN : bond 0.00550 / 0.29 ( 1) link_NAG-ASN : angle 1.03415 / 0.55 ( 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 : 0.121 Fit side-chains revert: symmetry clash REVERT: L 80 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8405 (pp) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.0611 time to fit residues: 5.8206 Evaluate side-chains 73 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 80 LEU 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 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [30, 29, 38, 26, 21, 34, 14, 4, 19, 32, 15] chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 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: 0.6980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 360 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 = 0.154999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135255 restraints weight = 4590.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138989 restraints weight = 2803.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141536 restraints weight = 1978.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143216 restraints weight = 1530.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144597 restraints weight = 1266.079| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3256 Z= 0.200 Angle : 0.658 5.907 4423 Z= 0.348 Chirality : 0.047 0.158 468 Planarity : 0.005 0.055 573 Dihedral : 5.959 47.065 457 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.99 % Allowed : 22.87 % Favored : 72.14 % 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: -3.15 (0.39), residues: 399 helix: -4.83 (0.39), residues: 27 sheet: -1.12 (0.42), residues: 144 loop : -2.47 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 17 TYR 0.015 0.001 TYR F 369 PHE 0.013 0.002 PHE F 377 TRP 0.012 0.002 TRP F 436 HIS 0.001 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 3252) covalent geometry : angle 0.65766 / 0.35 ( 4414) SS BOND : bond 0.00345 / 0.17 ( 3) SS BOND : angle 0.49994 / 0.36 ( 6) hydrogen bonds : bond 0.03198 / 2.00 ( 64) hydrogen bonds : angle 5.89469 / 4.34 ( 165) link_NAG-ASN : bond 0.00629 / 0.33 ( 1) link_NAG-ASN : angle 1.13634 / 0.60 ( 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 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: H 53 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7563 (t80) outliers start: 17 outliers final: 13 residues processed: 78 average time/residue: 0.0605 time to fit residues: 5.7500 Evaluate side-chains 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 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 405 ASP 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: [37, 6, 24, 17, 20, 25, 21, 22, 12, 33, 19] chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.0470 chunk 33 optimal weight: 0.0670 chunk 19 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136924 restraints weight = 4636.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140485 restraints weight = 2900.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142980 restraints weight = 2080.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144828 restraints weight = 1621.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146074 restraints weight = 1328.785| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 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 = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2671 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= 0.135 Angle : 0.613 6.016 4423 Z= 0.323 Chirality : 0.045 0.177 468 Planarity : 0.005 0.045 573 Dihedral : 5.578 44.632 457 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.57 % Allowed : 23.17 % 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: -2.98 (0.39), residues: 399 helix: -4.81 (0.42), residues: 27 sheet: -1.07 (0.44), residues: 136 loop : -2.26 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 17 TYR 0.017 0.001 TYR H 59 PHE 0.014 0.001 PHE H 29 TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3252) covalent geometry : angle 0.61348 / 0.32 ( 4414) SS BOND : bond 0.00219 / 0.11 ( 3) SS BOND : angle 0.30330 / 0.20 ( 6) hydrogen bonds : bond 0.02944 / 1.87 ( 64) hydrogen bonds : angle 5.46354 / 4.03 ( 165) link_NAG-ASN : bond 0.00507 / 0.27 ( 1) link_NAG-ASN : angle 0.62870 / 0.33 ( 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 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.114 Fit side-chains REVERT: H 51 MET cc_start: 0.7570 (tpt) cc_final: 0.7251 (tpp) REVERT: H 53 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7568 (t80) REVERT: F 452 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8403 (mtm-85) REVERT: F 511 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8637 (m) outliers start: 19 outliers final: 13 residues processed: 76 average time/residue: 0.0536 time to fit residues: 5.0355 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 : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 80 LEU 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 360 ASN Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 433 VAL 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: [38, 15, 22, 1, 8, 13, 4, 27, 10, 12, 5] chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135794 restraints weight = 4673.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139218 restraints weight = 2941.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141731 restraints weight = 2125.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143335 restraints weight = 1658.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144641 restraints weight = 1378.048| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 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 = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2802 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= 0.154 Angle : 0.642 10.873 4423 Z= 0.329 Chirality : 0.045 0.158 468 Planarity : 0.005 0.042 573 Dihedral : 5.549 44.629 457 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.57 % Allowed : 24.63 % 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: -2.94 (0.39), residues: 399 helix: -4.61 (0.54), residues: 21 sheet: -1.17 (0.47), residues: 124 loop : -2.22 (0.36), residues: 254 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 0.012 0.001 PHE H 68 TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 3252) covalent geometry : angle 0.64200 / 0.33 ( 4414) SS BOND : bond 0.00255 / 0.13 ( 3) SS BOND : angle 0.39902 / 0.30 ( 6) hydrogen bonds : bond 0.02933 / 1.85 ( 64) hydrogen bonds : angle 5.42458 / 4.00 ( 165) link_NAG-ASN : bond 0.00525 / 0.28 ( 1) link_NAG-ASN : angle 0.69628 / 0.37 ( 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 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.120 Fit side-chains REVERT: H 51 MET cc_start: 0.7573 (tpt) cc_final: 0.7341 (tpp) REVERT: H 53 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7566 (t80) REVERT: F 452 ARG cc_start: 0.8801 (mtp85) cc_final: 0.8441 (mtm-85) REVERT: F 511 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8598 (m) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.0607 time to fit residues: 5.3604 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 : 0.097 ------------------------------------------------------------------------------- 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 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 402 ILE Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 433 VAL 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: [26, 21, 13, 35, 17, 23, 32, 20, 36, 28, 11] chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136772 restraints weight = 4714.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140238 restraints weight = 2941.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142739 restraints weight = 2107.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144488 restraints weight = 1640.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145688 restraints weight = 1348.613| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 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 = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2917 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= 0.138 Angle : 0.599 6.460 4423 Z= 0.314 Chirality : 0.045 0.156 468 Planarity : 0.004 0.039 573 Dihedral : 5.416 43.737 457 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.99 % Allowed : 24.63 % Favored : 70.38 % 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: -2.81 (0.40), residues: 399 helix: -4.62 (0.55), residues: 21 sheet: -1.03 (0.45), residues: 135 loop : -2.18 (0.37), residues: 243 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 0.011 0.001 PHE H 68 TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3252) covalent geometry : angle 0.59914 / 0.31 ( 4414) SS BOND : bond 0.00227 / 0.11 ( 3) SS BOND : angle 0.32178 / 0.25 ( 6) hydrogen bonds : bond 0.02798 / 1.77 ( 64) hydrogen bonds : angle 5.29703 / 3.91 ( 165) link_NAG-ASN : bond 0.00497 / 0.26 ( 1) link_NAG-ASN : angle 0.58835 / 0.31 ( 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 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.093 Fit side-chains REVERT: H 51 MET cc_start: 0.7548 (tpt) cc_final: 0.7333 (tpp) REVERT: H 53 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7569 (t80) REVERT: F 452 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8296 (mtm110) REVERT: F 511 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8605 (m) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.0627 time to fit residues: 5.6067 Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 118 MET Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 360 ASN Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 415 THR 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: [3, 1, 11, 2, 6, 28, 23, 0, 17, 24, 10] chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134873 restraints weight = 4736.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138588 restraints weight = 2886.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141234 restraints weight = 2038.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143050 restraints weight = 1570.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144345 restraints weight = 1284.417| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 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 = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2957 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= 0.155 Angle : 0.612 6.539 4423 Z= 0.322 Chirality : 0.045 0.177 468 Planarity : 0.004 0.037 573 Dihedral : 5.417 44.422 457 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.99 % Allowed : 24.93 % 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: -2.75 (0.40), residues: 399 helix: -4.63 (0.53), residues: 21 sheet: -0.99 (0.45), residues: 135 loop : -2.14 (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 0.012 0.001 PHE H 68 TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 3252) covalent geometry : angle 0.61255 / 0.32 ( 4414) SS BOND : bond 0.00275 / 0.14 ( 3) SS BOND : angle 0.39712 / 0.31 ( 6) hydrogen bonds : bond 0.02799 / 1.75 ( 64) hydrogen bonds : angle 5.30848 / 3.93 ( 165) link_NAG-ASN : bond 0.00499 / 0.26 ( 1) link_NAG-ASN : angle 0.63446 / 0.33 ( 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 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.125 Fit side-chains REVERT: H 53 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7599 (t80) REVERT: H 116 TYR cc_start: 0.8469 (m-80) cc_final: 0.8246 (m-80) REVERT: F 408 ARG cc_start: 0.8069 (mpt-90) cc_final: 0.7767 (mpt-90) REVERT: F 452 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8276 (mtm110) REVERT: F 511 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8529 (m) outliers start: 17 outliers final: 14 residues processed: 70 average time/residue: 0.0689 time to fit residues: 5.7885 Evaluate side-chains 75 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.077 ------------------------------------------------------------------------------- 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 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 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 415 THR 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: [32, 17, 15, 30, 9, 4, 16, 38, 7, 11, 2] chunk 32 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3790 r_free = 0.3790 target = 0.156342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136686 restraints weight = 4700.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140351 restraints weight = 2829.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142896 restraints weight = 1980.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144806 restraints weight = 1534.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146045 restraints weight = 1246.024| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 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 = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3018 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= 0.131 Angle : 0.622 8.144 4423 Z= 0.326 Chirality : 0.045 0.155 468 Planarity : 0.004 0.038 573 Dihedral : 5.304 44.198 457 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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: -2.62 (0.40), residues: 399 helix: -4.63 (0.53), residues: 21 sheet: -0.84 (0.46), residues: 135 loop : -2.08 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 17 TYR 0.015 0.001 TYR F 369 PHE 0.011 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/Z covalent geometry : bond 0.00308 / 0.13 ( 3252) covalent geometry : angle 0.62207 / 0.33 ( 4414) SS BOND : bond 0.00225 / 0.11 ( 3) SS BOND : angle 0.31037 / 0.23 ( 6) hydrogen bonds : bond 0.02702 / 1.72 ( 64) hydrogen bonds : angle 5.22692 / 3.87 ( 165) link_NAG-ASN : bond 0.00460 / 0.24 ( 1) link_NAG-ASN : angle 0.49380 / 0.26 ( 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 : 0.118 Fit side-chains REVERT: F 408 ARG cc_start: 0.8016 (mpt-90) cc_final: 0.7771 (mpt-90) REVERT: F 452 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8271 (mtm110) REVERT: F 511 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8497 (m) outliers start: 18 outliers final: 14 residues processed: 73 average time/residue: 0.0591 time to fit residues: 5.3096 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 : 0.121 ------------------------------------------------------------------------------- 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 118 MET Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 415 THR 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: [39, 1, 3, 5, 2, 25, 17, 33, 38, 6, 21] chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.0170 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3782 r_free = 0.3782 target = 0.155457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136638 restraints weight = 4677.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140132 restraints weight = 2909.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142424 restraints weight = 2075.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144220 restraints weight = 1624.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145278 restraints weight = 1335.580| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 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 = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3080 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= 0.150 Angle : 0.636 7.131 4423 Z= 0.333 Chirality : 0.045 0.156 468 Planarity : 0.004 0.035 573 Dihedral : 5.441 45.390 457 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.40 % Allowed : 25.22 % Favored : 70.38 % 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: -4.63 (0.54), residues: 21 sheet: -0.79 (0.46), residues: 135 loop : -2.08 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 17 TYR 0.015 0.001 TYR F 369 PHE 0.011 0.001 PHE H 68 TRP 0.008 0.001 TRP F 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 3252) covalent geometry : angle 0.63619 / 0.33 ( 4414) SS BOND : bond 0.00274 / 0.14 ( 3) SS BOND : angle 0.38530 / 0.29 ( 6) hydrogen bonds : bond 0.02779 / 1.81 ( 64) hydrogen bonds : angle 5.36046 / 3.96 ( 165) link_NAG-ASN : bond 0.00474 / 0.25 ( 1) link_NAG-ASN : angle 0.56807 / 0.30 ( 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 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.095 Fit side-chains REVERT: F 408 ARG cc_start: 0.8050 (mpt-90) cc_final: 0.7797 (mpt-90) REVERT: F 452 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8312 (mtm110) REVERT: F 511 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8532 (m) outliers start: 15 outliers final: 13 residues processed: 71 average time/residue: 0.0610 time to fit residues: 5.2342 Evaluate side-chains 75 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 118 MET Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 415 THR 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: [17, 22, 13, 26, 36, 12, 7, 20, 23, 38, 3] chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 12 optimal weight: 0.0670 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 38 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139126 restraints weight = 4736.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142596 restraints weight = 2917.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145107 restraints weight = 2076.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146863 restraints weight = 1609.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148161 restraints weight = 1319.887| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 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 = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3256 Z= 0.126 Angle : 0.611 7.349 4423 Z= 0.321 Chirality : 0.045 0.172 468 Planarity : 0.004 0.038 573 Dihedral : 5.305 42.966 457 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.40 % Allowed : 25.22 % Favored : 70.38 % 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: -2.52 (0.40), residues: 399 helix: -4.65 (0.52), residues: 21 sheet: -0.74 (0.47), residues: 130 loop : -2.01 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 17 TYR 0.015 0.001 TYR F 369 PHE 0.010 0.001 PHE H 68 TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3252) covalent geometry : angle 0.61187 / 0.32 ( 4414) SS BOND : bond 0.00211 / 0.11 ( 3) SS BOND : angle 0.26634 / 0.23 ( 6) hydrogen bonds : bond 0.02622 / 1.75 ( 64) hydrogen bonds : angle 5.26181 / 3.90 ( 165) link_NAG-ASN : bond 0.00428 / 0.23 ( 1) link_NAG-ASN : angle 0.43539 / 0.23 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 915.06 seconds wall clock time: 16 minutes 21.04 seconds (981.04 seconds total)