Starting phenix.real_space_refine on Wed Jul 1 22:11:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp2_32667/07_2026/7wp2_32667.cif" } resolution = 3.52 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 14 5.16 5 C 2090 2.51 5 N 554 2.21 5 O 641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3299 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} 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: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1458 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.85, per 1000 atoms: 0.26 Number of scatterers: 3299 At special positions: 0 Unit cell: (76.244, 79.356, 80.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 641 8.00 N 554 7.00 C 2090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 147.3 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.905A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.037A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.520A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 89 " --> pdb=" O TYR L 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.785A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.880A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER F 399 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454 69 hydrogen bonds defined for protein. 159 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: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1049 1.34 - 1.46: 843 1.46 - 1.57: 1473 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3383 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C LYS F 462 " pdb=" N PRO F 463 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 3.02e+00 bond pdb=" CB CYS L 90 " pdb=" SG CYS L 90 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" C ASN L 55 " pdb=" N ARG L 56 " ideal model delta sigma weight residual 1.332 1.271 0.060 3.60e-02 7.72e+02 2.81e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 3378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 4496 2.54 - 5.07: 85 5.07 - 7.61: 9 7.61 - 10.15: 3 10.15 - 12.69: 1 Bond angle restraints: 4594 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 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CA LEU F 387 " pdb=" CB LEU F 387 " pdb=" CG LEU F 387 " ideal model delta sigma weight residual 116.30 128.99 -12.69 3.50e+00 8.16e-02 1.31e+01 angle pdb=" C TYR F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 122.07 127.10 -5.03 1.43e+00 4.89e-01 1.24e+01 angle pdb=" C ASP F 364 " pdb=" N TYR F 365 " pdb=" CA TYR F 365 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.58e+00 angle pdb=" C SER H 52 " pdb=" N PHE H 53 " pdb=" CA PHE H 53 " ideal model delta sigma weight residual 120.44 124.43 -3.99 1.30e+00 5.92e-01 9.40e+00 ... (remaining 4589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1741 17.78 - 35.55: 171 35.55 - 53.33: 25 53.33 - 71.11: 3 71.11 - 88.88: 3 Dihedral angle restraints: 1943 sinusoidal: 738 harmonic: 1205 Sorted by residual: dihedral pdb=" CA ASP H 113 " pdb=" C ASP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PHE F 338 " pdb=" C PHE F 338 " pdb=" N GLY F 339 " pdb=" CA GLY F 339 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE F 472 " pdb=" C ILE F 472 " pdb=" N TYR F 473 " pdb=" CA TYR F 473 " ideal model delta harmonic sigma weight residual 180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 1940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 306 0.047 - 0.094: 137 0.094 - 0.141: 34 0.141 - 0.188: 7 0.188 - 0.235: 5 Chirality restraints: 489 Sorted by residual: chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL H 100 " pdb=" CA VAL H 100 " pdb=" CG1 VAL H 100 " pdb=" CG2 VAL H 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 486 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 498 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO F 499 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 499 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 499 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 13 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO L 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO F 463 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " -0.027 5.00e-02 4.00e+02 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 909 2.79 - 3.32: 2630 3.32 - 3.85: 5262 3.85 - 4.37: 5959 4.37 - 4.90: 10778 Nonbonded interactions: 25538 Sorted by model distance: nonbonded pdb=" OH TYR L 93 " pdb=" OD1 ASP H 113 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR F 415 " pdb=" OD1 ASP F 420 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR L 51 " pdb=" O THR F 415 " model vdw 2.280 3.040 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.288 3.120 ... (remaining 25533 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: 13.120 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 0.060 3387 Z= 0.304 Angle : 0.911 12.687 4604 Z= 0.500 Chirality : 0.056 0.235 489 Planarity : 0.007 0.070 594 Dihedral : 13.802 88.882 1183 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.28 % Allowed : 9.66 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.60 (0.34), residues: 416 helix: -5.07 (0.26), residues: 20 sheet: -2.60 (0.38), residues: 162 loop : -3.28 (0.31), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 408 TYR 0.028 0.003 TYR H 103 PHE 0.018 0.002 PHE F 490 TRP 0.021 0.002 TRP F 353 HIS 0.004 0.002 HIS F 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.30 ( 3383) covalent geometry : angle 0.90724 / 0.50 ( 4594) SS BOND : bond 0.00311 / 0.16 ( 2) SS BOND : angle 1.70877 / 0.98 ( 4) hydrogen bonds : bond 0.26493 / 20.07 ( 69) hydrogen bonds : angle 10.34313 / 7.30 ( 159) link_BETA1-4 : bond 0.00720 / 0.38 ( 1) link_BETA1-4 : angle 1.70846 / 0.88 ( 3) link_NAG-ASN : bond 0.00247 / 0.13 ( 1) link_NAG-ASN : angle 2.65504 / 1.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.144 Fit side-chains REVERT: L 93 TYR cc_start: 0.8650 (t80) cc_final: 0.8437 (t80) REVERT: H 19 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6860 (ttp80) REVERT: H 29 PHE cc_start: 0.9274 (t80) cc_final: 0.9067 (t80) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.0815 time to fit residues: 7.4923 Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 55 ASN F 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138435 restraints weight = 4590.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141749 restraints weight = 2404.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143966 restraints weight = 1563.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145315 restraints weight = 1146.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146401 restraints weight = 925.798| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 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 = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3387 Z= 0.152 Angle : 0.601 7.693 4604 Z= 0.312 Chirality : 0.044 0.140 489 Planarity : 0.005 0.046 594 Dihedral : 6.036 50.508 474 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.99 % Allowed : 14.77 % Favored : 83.24 % 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: -3.96 (0.35), residues: 416 helix: -4.81 (0.44), residues: 20 sheet: -1.92 (0.40), residues: 151 loop : -3.02 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 56 TYR 0.012 0.001 TYR H 103 PHE 0.013 0.001 PHE F 338 TRP 0.011 0.002 TRP F 353 HIS 0.002 0.001 HIS F 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 3383) covalent geometry : angle 0.59852 / 0.31 ( 4594) SS BOND : bond 0.00243 / 0.13 ( 2) SS BOND : angle 1.24132 / 0.71 ( 4) hydrogen bonds : bond 0.04206 / 3.68 ( 69) hydrogen bonds : angle 7.32953 / 5.44 ( 159) link_BETA1-4 : bond 0.00283 / 0.15 ( 1) link_BETA1-4 : angle 1.08767 / 0.55 ( 3) link_NAG-ASN : bond 0.00383 / 0.20 ( 1) link_NAG-ASN : angle 1.39822 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.124 Fit side-chains REVERT: L 93 TYR cc_start: 0.8662 (t80) cc_final: 0.8385 (t80) REVERT: H 19 ARG cc_start: 0.7594 (ttm170) cc_final: 0.6983 (ttp80) REVERT: F 417 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7625 (ttmm) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.0773 time to fit residues: 5.9715 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139559 restraints weight = 4572.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142962 restraints weight = 2394.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145111 restraints weight = 1544.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.146681 restraints weight = 1135.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147697 restraints weight = 904.223| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3387 Z= 0.116 Angle : 0.550 7.199 4604 Z= 0.284 Chirality : 0.042 0.135 489 Planarity : 0.004 0.035 594 Dihedral : 5.440 45.522 474 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.98 % Allowed : 14.77 % Favored : 81.25 % 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: -3.61 (0.36), residues: 416 helix: -4.70 (0.51), residues: 20 sheet: -1.71 (0.41), residues: 148 loop : -2.74 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 454 TYR 0.010 0.001 TYR F 369 PHE 0.009 0.001 PHE F 338 TRP 0.009 0.001 TRP F 353 HIS 0.002 0.001 HIS F 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 3383) covalent geometry : angle 0.54830 / 0.28 ( 4594) SS BOND : bond 0.00160 / 0.08 ( 2) SS BOND : angle 1.15401 / 0.65 ( 4) hydrogen bonds : bond 0.03262 / 2.66 ( 69) hydrogen bonds : angle 6.43928 / 4.94 ( 159) link_BETA1-4 : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : angle 1.03911 / 0.53 ( 3) link_NAG-ASN : bond 0.00280 / 0.15 ( 1) link_NAG-ASN : angle 1.04229 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.127 Fit side-chains REVERT: L 93 TYR cc_start: 0.8640 (t80) cc_final: 0.8398 (t80) REVERT: H 19 ARG cc_start: 0.7594 (ttm170) cc_final: 0.7287 (ttp-170) REVERT: H 94 TYR cc_start: 0.8079 (m-80) cc_final: 0.7483 (m-80) REVERT: F 338 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6648 (p90) REVERT: F 417 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7600 (ttmm) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.0800 time to fit residues: 6.7257 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132124 restraints weight = 4630.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135398 restraints weight = 2442.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137619 restraints weight = 1595.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139101 restraints weight = 1178.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139947 restraints weight = 945.404| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3387 Z= 0.171 Angle : 0.576 7.650 4604 Z= 0.295 Chirality : 0.043 0.140 489 Planarity : 0.004 0.033 594 Dihedral : 5.536 43.439 474 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.68 % Allowed : 14.20 % Favored : 80.11 % 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: -3.45 (0.37), residues: 416 helix: -4.69 (0.50), residues: 20 sheet: -1.61 (0.39), residues: 167 loop : -2.64 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 454 TYR 0.011 0.001 TYR F 453 PHE 0.014 0.001 PHE F 338 TRP 0.011 0.001 TRP F 353 HIS 0.003 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 ( 3383) covalent geometry : angle 0.57409 / 0.29 ( 4594) SS BOND : bond 0.00265 / 0.14 ( 2) SS BOND : angle 1.09022 / 0.60 ( 4) hydrogen bonds : bond 0.03376 / 2.90 ( 69) hydrogen bonds : angle 6.17136 / 4.65 ( 159) link_BETA1-4 : bond 0.00242 / 0.13 ( 1) link_BETA1-4 : angle 1.04060 / 0.53 ( 3) link_NAG-ASN : bond 0.00338 / 0.18 ( 1) link_NAG-ASN : angle 1.32428 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.119 Fit side-chains REVERT: L 93 TYR cc_start: 0.8715 (t80) cc_final: 0.8434 (t80) REVERT: H 13 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5997 (tt0) REVERT: H 19 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7266 (ttp-170) REVERT: H 94 TYR cc_start: 0.8213 (m-80) cc_final: 0.7433 (m-80) REVERT: F 338 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6599 (p90) REVERT: F 417 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7667 (ttmm) outliers start: 20 outliers final: 11 residues processed: 69 average time/residue: 0.0623 time to fit residues: 5.2904 Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 0.0040 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.150308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133611 restraints weight = 4643.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136882 restraints weight = 2464.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139023 restraints weight = 1611.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140492 restraints weight = 1197.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141355 restraints weight = 962.511| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3387 Z= 0.112 Angle : 0.556 9.028 4604 Z= 0.282 Chirality : 0.042 0.134 489 Planarity : 0.003 0.031 594 Dihedral : 5.177 39.557 474 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.12 % Allowed : 16.76 % Favored : 80.11 % 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: -3.18 (0.38), residues: 416 helix: -4.65 (0.50), residues: 20 sheet: -1.41 (0.41), residues: 165 loop : -2.44 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.011 0.001 TYR F 369 PHE 0.015 0.001 PHE H 53 TRP 0.010 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 3383) covalent geometry : angle 0.55423 / 0.28 ( 4594) SS BOND : bond 0.00425 / 0.21 ( 2) SS BOND : angle 1.18148 / 0.69 ( 4) hydrogen bonds : bond 0.03066 / 2.65 ( 69) hydrogen bonds : angle 6.12822 / 4.58 ( 159) link_BETA1-4 : bond 0.00338 / 0.18 ( 1) link_BETA1-4 : angle 1.00772 / 0.51 ( 3) link_NAG-ASN : bond 0.00382 / 0.20 ( 1) link_NAG-ASN : angle 0.88759 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.122 Fit side-chains REVERT: L 93 TYR cc_start: 0.8659 (t80) cc_final: 0.8440 (t80) REVERT: H 19 ARG cc_start: 0.7635 (ttm170) cc_final: 0.6956 (ttp80) REVERT: H 38 ARG cc_start: 0.7545 (ptm-80) cc_final: 0.7139 (ptt90) REVERT: H 51 MET cc_start: 0.7299 (tpt) cc_final: 0.6928 (tpt) REVERT: H 94 TYR cc_start: 0.8143 (m-80) cc_final: 0.7434 (m-80) REVERT: F 417 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7628 (ttmm) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.0756 time to fit residues: 5.7659 Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130194 restraints weight = 4606.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133492 restraints weight = 2444.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135628 restraints weight = 1600.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137107 restraints weight = 1190.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138003 restraints weight = 962.018| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 3387 Z= 0.249 Angle : 0.650 7.591 4604 Z= 0.334 Chirality : 0.045 0.164 489 Planarity : 0.004 0.033 594 Dihedral : 5.816 41.013 474 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.83 % Allowed : 16.76 % Favored : 78.41 % 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: -3.21 (0.38), residues: 416 helix: -4.71 (0.45), residues: 20 sheet: -1.42 (0.44), residues: 144 loop : -2.44 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 454 TYR 0.014 0.002 TYR H 94 PHE 0.021 0.002 PHE F 338 TRP 0.012 0.002 TRP F 353 HIS 0.004 0.002 HIS F 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.25 ( 3383) covalent geometry : angle 0.64757 / 0.33 ( 4594) SS BOND : bond 0.00456 / 0.24 ( 2) SS BOND : angle 1.48863 / 0.87 ( 4) hydrogen bonds : bond 0.03615 / 3.12 ( 69) hydrogen bonds : angle 6.09199 / 4.48 ( 159) link_BETA1-4 : bond 0.00168 / 0.09 ( 1) link_BETA1-4 : angle 1.04256 / 0.53 ( 3) link_NAG-ASN : bond 0.00355 / 0.19 ( 1) link_NAG-ASN : angle 1.65801 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.114 Fit side-chains REVERT: L 93 TYR cc_start: 0.8762 (t80) cc_final: 0.8559 (t80) REVERT: H 13 GLN cc_start: 0.6131 (OUTLIER) cc_final: 0.5809 (tt0) REVERT: H 19 ARG cc_start: 0.7669 (ttm170) cc_final: 0.6976 (ttp80) REVERT: H 94 TYR cc_start: 0.8333 (m-80) cc_final: 0.7493 (m-80) REVERT: F 338 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7052 (p90) outliers start: 17 outliers final: 13 residues processed: 71 average time/residue: 0.0676 time to fit residues: 5.8764 Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 29 optimal weight: 0.3980 chunk 5 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.0050 overall best weight: 0.2594 ------------------------------------------------------------------------------- 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 = 0.156042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139044 restraints weight = 4581.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142398 restraints weight = 2403.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144656 restraints weight = 1559.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145958 restraints weight = 1150.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147080 restraints weight = 937.230| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3387 Z= 0.109 Angle : 0.542 6.880 4604 Z= 0.279 Chirality : 0.042 0.159 489 Planarity : 0.004 0.040 594 Dihedral : 5.214 37.763 474 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.12 % Allowed : 18.75 % Favored : 78.12 % 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: 416 helix: -4.71 (0.44), residues: 20 sheet: -1.31 (0.44), residues: 146 loop : -2.23 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.016 0.001 TYR F 369 PHE 0.017 0.001 PHE H 53 TRP 0.011 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 3383) covalent geometry : angle 0.54005 / 0.28 ( 4594) SS BOND : bond 0.00206 / 0.11 ( 2) SS BOND : angle 1.15806 / 0.68 ( 4) hydrogen bonds : bond 0.03025 / 2.59 ( 69) hydrogen bonds : angle 6.01888 / 4.47 ( 159) link_BETA1-4 : bond 0.00373 / 0.20 ( 1) link_BETA1-4 : angle 0.99615 / 0.50 ( 3) link_NAG-ASN : bond 0.00301 / 0.16 ( 1) link_NAG-ASN : angle 0.84537 / 0.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.120 Fit side-chains REVERT: H 19 ARG cc_start: 0.7636 (ttm170) cc_final: 0.6908 (ttp80) REVERT: H 94 TYR cc_start: 0.8145 (m-80) cc_final: 0.7362 (m-80) REVERT: F 338 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6700 (p90) REVERT: F 417 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7615 (ttmm) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.0739 time to fit residues: 5.9771 Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.154268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136849 restraints weight = 4639.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140187 restraints weight = 2475.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142386 restraints weight = 1630.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143915 restraints weight = 1216.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144860 restraints weight = 984.869| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3387 Z= 0.149 Angle : 0.570 7.298 4604 Z= 0.292 Chirality : 0.043 0.151 489 Planarity : 0.004 0.034 594 Dihedral : 5.235 36.218 474 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.41 % Allowed : 18.75 % Favored : 77.84 % 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: -2.78 (0.39), residues: 416 helix: -4.69 (0.44), residues: 20 sheet: -1.13 (0.45), residues: 144 loop : -2.10 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.013 0.001 TYR F 369 PHE 0.016 0.001 PHE H 53 TRP 0.009 0.001 TRP F 353 HIS 0.002 0.001 HIS F 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 3383) covalent geometry : angle 0.56856 / 0.29 ( 4594) SS BOND : bond 0.00305 / 0.16 ( 2) SS BOND : angle 1.11445 / 0.66 ( 4) hydrogen bonds : bond 0.03166 / 2.75 ( 69) hydrogen bonds : angle 5.87955 / 4.33 ( 159) link_BETA1-4 : bond 0.00289 / 0.15 ( 1) link_BETA1-4 : angle 0.97545 / 0.49 ( 3) link_NAG-ASN : bond 0.00338 / 0.18 ( 1) link_NAG-ASN : angle 1.11661 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.085 Fit side-chains REVERT: H 19 ARG cc_start: 0.7517 (ttm170) cc_final: 0.6816 (ttp80) REVERT: H 94 TYR cc_start: 0.8182 (m-80) cc_final: 0.7417 (m-80) REVERT: F 338 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.6839 (p90) REVERT: F 417 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7624 (ttmm) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.0594 time to fit residues: 4.7197 Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 0.0770 chunk 29 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 0.0970 overall best weight: 0.1936 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.156359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139857 restraints weight = 4560.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143245 restraints weight = 2381.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145479 restraints weight = 1524.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146903 restraints weight = 1114.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148023 restraints weight = 890.179| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3387 Z= 0.099 Angle : 0.548 6.855 4604 Z= 0.277 Chirality : 0.042 0.179 489 Planarity : 0.003 0.032 594 Dihedral : 4.845 34.606 474 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.56 % Allowed : 20.17 % Favored : 77.27 % 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: -2.64 (0.40), residues: 416 helix: -4.58 (0.50), residues: 20 sheet: -1.03 (0.45), residues: 157 loop : -2.04 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.013 0.001 TYR F 369 PHE 0.018 0.001 PHE H 53 TRP 0.009 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 3383) covalent geometry : angle 0.54751 / 0.28 ( 4594) SS BOND : bond 0.00224 / 0.12 ( 2) SS BOND : angle 0.94273 / 0.55 ( 4) hydrogen bonds : bond 0.02972 / 2.52 ( 69) hydrogen bonds : angle 5.81808 / 4.32 ( 159) link_BETA1-4 : bond 0.00439 / 0.23 ( 1) link_BETA1-4 : angle 0.97841 / 0.49 ( 3) link_NAG-ASN : bond 0.00337 / 0.18 ( 1) link_NAG-ASN : angle 0.69809 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.138 Fit side-chains REVERT: H 19 ARG cc_start: 0.7415 (ttm170) cc_final: 0.6949 (ttp-170) REVERT: H 94 TYR cc_start: 0.7965 (m-80) cc_final: 0.7490 (m-80) REVERT: F 417 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7502 (ttmm) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.0531 time to fit residues: 4.0970 Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.152998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136322 restraints weight = 4577.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139660 restraints weight = 2411.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141856 restraints weight = 1564.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143205 restraints weight = 1152.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144177 restraints weight = 930.758| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3387 Z= 0.156 Angle : 0.577 7.222 4604 Z= 0.295 Chirality : 0.043 0.177 489 Planarity : 0.003 0.033 594 Dihedral : 5.087 36.487 474 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.84 % Allowed : 20.17 % Favored : 76.99 % 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: -2.58 (0.41), residues: 416 helix: -4.68 (0.43), residues: 20 sheet: -0.96 (0.44), residues: 158 loop : -2.01 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 67 TYR 0.014 0.001 TYR F 369 PHE 0.018 0.002 PHE H 53 TRP 0.010 0.001 TRP F 353 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 3383) covalent geometry : angle 0.57542 / 0.30 ( 4594) SS BOND : bond 0.00304 / 0.16 ( 2) SS BOND : angle 1.05754 / 0.62 ( 4) hydrogen bonds : bond 0.03185 / 2.74 ( 69) hydrogen bonds : angle 5.77766 / 4.25 ( 159) link_BETA1-4 : bond 0.00276 / 0.15 ( 1) link_BETA1-4 : angle 0.95698 / 0.49 ( 3) link_NAG-ASN : bond 0.00326 / 0.17 ( 1) link_NAG-ASN : angle 1.15677 / 0.64 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.120 Fit side-chains REVERT: H 19 ARG cc_start: 0.7373 (ttm170) cc_final: 0.6551 (ttp80) REVERT: H 94 TYR cc_start: 0.8152 (m-80) cc_final: 0.7487 (m-80) REVERT: F 386 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7589 (mttp) REVERT: F 417 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7539 (ttmm) outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.0519 time to fit residues: 4.0634 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.0370 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 27 optimal weight: 0.0030 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.2066 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.157299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140163 restraints weight = 4635.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143531 restraints weight = 2540.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145744 restraints weight = 1677.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147192 restraints weight = 1247.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148057 restraints weight = 1008.397| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3387 Z= 0.102 Angle : 0.537 6.877 4604 Z= 0.274 Chirality : 0.042 0.178 489 Planarity : 0.003 0.032 594 Dihedral : 4.809 35.128 474 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.84 % Allowed : 20.17 % Favored : 76.99 % 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: -2.48 (0.41), residues: 416 helix: -4.59 (0.48), residues: 20 sheet: -0.93 (0.45), residues: 155 loop : -1.90 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.013 0.001 TYR F 369 PHE 0.020 0.001 PHE H 53 TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 ( 3383) covalent geometry : angle 0.53573 / 0.27 ( 4594) SS BOND : bond 0.00217 / 0.11 ( 2) SS BOND : angle 0.96766 / 0.57 ( 4) hydrogen bonds : bond 0.02938 / 2.48 ( 69) hydrogen bonds : angle 5.76988 / 4.27 ( 159) link_BETA1-4 : bond 0.00334 / 0.18 ( 1) link_BETA1-4 : angle 0.93941 / 0.47 ( 3) link_NAG-ASN : bond 0.00322 / 0.17 ( 1) link_NAG-ASN : angle 0.74629 / 0.43 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1039.39 seconds wall clock time: 18 minutes 37.27 seconds (1117.27 seconds total)