Starting phenix.real_space_refine on Tue Mar 3 15:13:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x94_33066/03_2026/7x94_33066_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x94_33066/03_2026/7x94_33066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x94_33066/03_2026/7x94_33066_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x94_33066/03_2026/7x94_33066_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x94_33066/03_2026/7x94_33066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x94_33066/03_2026/7x94_33066.map" } resolution = 4.0 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= 0.002 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: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 2162 2.51 5 N 568 2.21 5 O 666 1.98 5 H 3208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3057 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1945 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1576 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.29, per 1000 atoms: 0.19 Number of scatterers: 6617 At special positions: 0 Unit cell: (67.978, 67.978, 109.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 O 666 8.00 N 568 7.00 C 2162 6.00 H 3208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 299.1 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 7.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.549A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.131A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 5.238A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.799A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.894A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.644A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER L 89 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL L 99 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 85 88 hydrogen bonds defined for protein. 189 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: 1.30 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3206 1.03 - 1.23: 41 1.23 - 1.43: 1520 1.43 - 1.62: 1924 1.62 - 1.82: 14 Bond restraints: 6705 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N SER L 1 " pdb=" CA SER L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" N SER L 1 " pdb=" H SER L 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 6700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 11681 1.43 - 2.85: 279 2.85 - 4.28: 29 4.28 - 5.70: 5 5.70 - 7.13: 3 Bond angle restraints: 11997 Sorted by residual: angle pdb=" N VAL L 46 " pdb=" CA VAL L 46 " pdb=" C VAL L 46 " ideal model delta sigma weight residual 113.71 110.53 3.18 9.50e-01 1.11e+00 1.12e+01 angle pdb=" CB LYS A 386 " pdb=" CG LYS A 386 " pdb=" CD LYS A 386 " ideal model delta sigma weight residual 111.30 118.43 -7.13 2.30e+00 1.89e-01 9.61e+00 angle pdb=" N ASN A 450 " pdb=" CA ASN A 450 " pdb=" C ASN A 450 " ideal model delta sigma weight residual 113.18 110.48 2.70 1.33e+00 5.65e-01 4.13e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 107.01 5.94 3.00e+00 1.11e-01 3.92e+00 angle pdb=" CG LYS A 386 " pdb=" CD LYS A 386 " pdb=" CE LYS A 386 " ideal model delta sigma weight residual 111.30 115.80 -4.50 2.30e+00 1.89e-01 3.82e+00 ... (remaining 11992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 3017 21.06 - 42.12: 198 42.12 - 63.18: 55 63.18 - 84.24: 12 84.24 - 105.30: 4 Dihedral angle restraints: 3286 sinusoidal: 1756 harmonic: 1530 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -131.64 45.64 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CA ARG A 346 " pdb=" C ARG A 346 " pdb=" N PHE A 347 " pdb=" CA PHE A 347 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual -73.00 -0.49 -72.51 1 2.00e+01 2.50e-03 1.68e+01 ... (remaining 3283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 434 0.057 - 0.114: 70 0.114 - 0.171: 13 0.171 - 0.228: 0 0.228 - 0.285: 2 Chirality restraints: 519 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2 BMA B 3 " pdb=" C1 BMA B 3 " pdb=" C3 BMA B 3 " pdb=" O2 BMA B 3 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 516 not shown) Planarity restraints: 1026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.031 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO H 14 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 463 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 99 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO H 100 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.017 5.00e-02 4.00e+02 ... (remaining 1023 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 635 2.21 - 2.81: 13624 2.81 - 3.41: 16452 3.41 - 4.00: 22579 4.00 - 4.60: 33440 Nonbonded interactions: 86730 Sorted by model distance: nonbonded pdb=" OD1 ASP H 116 " pdb=" H TYR H 117 " model vdw 1.616 2.450 nonbonded pdb=" OD2 ASP A 398 " pdb=" HH TYR A 423 " model vdw 1.618 2.450 nonbonded pdb="HH22 ARG A 454 " pdb=" O SER A 469 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLU A 471 " pdb=" H GLU A 471 " model vdw 1.645 2.450 nonbonded pdb="HH21 ARG H 98 " pdb=" OD2 ASP H 116 " model vdw 1.651 2.450 ... (remaining 86725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.380 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: 0.030 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 : 0.003 0.033 3505 Z= 0.149 Angle : 0.636 7.130 4781 Z= 0.333 Chirality : 0.047 0.285 519 Planarity : 0.004 0.048 616 Dihedral : 15.697 105.302 1279 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.27 (0.41), residues: 428 helix: -4.13 (0.55), residues: 32 sheet: -0.01 (0.45), residues: 130 loop : -2.06 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.018 0.001 TYR H 60 PHE 0.020 0.001 PHE A 347 TRP 0.016 0.001 TRP L 34 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3497) covalent geometry : angle 0.61963 ( 4762) SS BOND : bond 0.00197 ( 5) SS BOND : angle 1.45154 ( 10) hydrogen bonds : bond 0.14462 ( 88) hydrogen bonds : angle 5.80480 ( 189) link_BETA1-4 : bond 0.00569 ( 2) link_BETA1-4 : angle 2.13419 ( 6) link_NAG-ASN : bond 0.01270 ( 1) link_NAG-ASN : angle 4.36631 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1916 time to fit residues: 25.8903 Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.036957 restraints weight = 50647.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.039511 restraints weight = 20180.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.041302 restraints weight = 10654.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.042522 restraints weight = 6580.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043303 restraints weight = 4480.705| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3505 Z= 0.191 Angle : 0.659 5.601 4781 Z= 0.339 Chirality : 0.044 0.171 519 Planarity : 0.005 0.049 616 Dihedral : 8.726 60.813 541 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 1.37 % Allowed : 12.60 % Favored : 86.03 % 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: -2.37 (0.41), residues: 428 helix: -3.91 (0.66), residues: 32 sheet: 0.06 (0.46), residues: 135 loop : -2.29 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 28 TYR 0.018 0.001 TYR L 85 PHE 0.014 0.001 PHE A 347 TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3497) covalent geometry : angle 0.64602 ( 4762) SS BOND : bond 0.00936 ( 5) SS BOND : angle 1.65015 ( 10) hydrogen bonds : bond 0.04136 ( 88) hydrogen bonds : angle 5.72466 ( 189) link_BETA1-4 : bond 0.00467 ( 2) link_BETA1-4 : angle 2.32010 ( 6) link_NAG-ASN : bond 0.00706 ( 1) link_NAG-ASN : angle 3.13095 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.9557 (mm110) cc_final: 0.9292 (mp10) REVERT: H 48 MET cc_start: 0.7632 (mmm) cc_final: 0.7412 (mmm) REVERT: H 104 TYR cc_start: 0.8519 (m-80) cc_final: 0.8237 (m-80) REVERT: H 117 TYR cc_start: 0.8717 (m-80) cc_final: 0.8242 (m-80) outliers start: 5 outliers final: 5 residues processed: 73 average time/residue: 0.1830 time to fit residues: 15.6412 Evaluate side-chains 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 88 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.036852 restraints weight = 49222.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.039478 restraints weight = 19687.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041342 restraints weight = 10393.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042616 restraints weight = 6308.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043414 restraints weight = 4240.787| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3505 Z= 0.120 Angle : 0.593 4.740 4781 Z= 0.307 Chirality : 0.044 0.190 519 Planarity : 0.004 0.044 616 Dihedral : 5.934 32.265 541 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.37 % Allowed : 13.15 % Favored : 85.48 % 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: -2.20 (0.41), residues: 428 helix: -3.71 (0.69), residues: 32 sheet: 0.17 (0.47), residues: 130 loop : -2.15 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 28 TYR 0.020 0.001 TYR L 85 PHE 0.010 0.001 PHE A 347 TRP 0.004 0.001 TRP L 34 HIS 0.005 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3497) covalent geometry : angle 0.58142 ( 4762) SS BOND : bond 0.00501 ( 5) SS BOND : angle 1.51869 ( 10) hydrogen bonds : bond 0.03649 ( 88) hydrogen bonds : angle 5.59691 ( 189) link_BETA1-4 : bond 0.00419 ( 2) link_BETA1-4 : angle 1.88493 ( 6) link_NAG-ASN : bond 0.00780 ( 1) link_NAG-ASN : angle 2.96066 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.9556 (mm110) cc_final: 0.9309 (mp10) REVERT: H 117 TYR cc_start: 0.8688 (m-80) cc_final: 0.8261 (m-80) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.2009 time to fit residues: 17.0777 Evaluate side-chains 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 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 = 0.2923 r_free = 0.2923 target = 0.044793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.034739 restraints weight = 51626.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.037181 restraints weight = 20918.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.038938 restraints weight = 11139.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.040117 restraints weight = 6819.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.040919 restraints weight = 4642.383| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3505 Z= 0.213 Angle : 0.611 4.434 4781 Z= 0.317 Chirality : 0.042 0.179 519 Planarity : 0.004 0.046 616 Dihedral : 5.250 31.875 541 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.19 % Allowed : 14.25 % Favored : 83.56 % 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: -2.44 (0.40), residues: 428 helix: -3.78 (0.64), residues: 32 sheet: 0.14 (0.46), residues: 128 loop : -2.39 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.009 0.001 TYR H 27 PHE 0.007 0.001 PHE A 515 TRP 0.004 0.001 TRP L 34 HIS 0.006 0.002 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 3497) covalent geometry : angle 0.60274 ( 4762) SS BOND : bond 0.00734 ( 5) SS BOND : angle 1.22749 ( 10) hydrogen bonds : bond 0.03744 ( 88) hydrogen bonds : angle 5.68591 ( 189) link_BETA1-4 : bond 0.00687 ( 2) link_BETA1-4 : angle 2.05863 ( 6) link_NAG-ASN : bond 0.00359 ( 1) link_NAG-ASN : angle 2.26447 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 117 TYR cc_start: 0.8808 (m-80) cc_final: 0.8331 (m-80) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.1748 time to fit residues: 14.3617 Evaluate side-chains 65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN L 52 ASN L 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.033615 restraints weight = 53960.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.035977 restraints weight = 21703.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.037645 restraints weight = 11552.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.038795 restraints weight = 7134.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.039539 restraints weight = 4888.821| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3505 Z= 0.249 Angle : 0.620 4.979 4781 Z= 0.327 Chirality : 0.042 0.144 519 Planarity : 0.004 0.046 616 Dihedral : 5.186 32.350 541 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.47 % Allowed : 14.52 % Favored : 83.01 % 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: -2.74 (0.38), residues: 428 helix: -3.87 (0.62), residues: 32 sheet: -0.11 (0.44), residues: 134 loop : -2.65 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.011 0.001 TYR A 365 PHE 0.011 0.002 PHE L 100 TRP 0.005 0.001 TRP A 353 HIS 0.005 0.002 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 3497) covalent geometry : angle 0.61264 ( 4762) SS BOND : bond 0.00661 ( 5) SS BOND : angle 1.29089 ( 10) hydrogen bonds : bond 0.03777 ( 88) hydrogen bonds : angle 5.75540 ( 189) link_BETA1-4 : bond 0.00772 ( 2) link_BETA1-4 : angle 2.06392 ( 6) link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 1.73646 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 TYR cc_start: 0.8997 (m-10) cc_final: 0.8784 (m-10) REVERT: H 117 TYR cc_start: 0.8754 (m-80) cc_final: 0.8337 (m-80) outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 0.1790 time to fit residues: 13.7954 Evaluate side-chains 64 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 overall best weight: 2.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.044667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.034753 restraints weight = 51637.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.037195 restraints weight = 20995.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.038906 restraints weight = 11130.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040099 restraints weight = 6864.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.040867 restraints weight = 4654.242| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3505 Z= 0.122 Angle : 0.570 4.276 4781 Z= 0.296 Chirality : 0.042 0.168 519 Planarity : 0.004 0.043 616 Dihedral : 4.790 33.126 541 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 1.64 % Allowed : 15.07 % Favored : 83.29 % 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: -2.55 (0.39), residues: 428 helix: -3.71 (0.66), residues: 32 sheet: -0.05 (0.44), residues: 134 loop : -2.47 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 90 TYR 0.013 0.001 TYR L 35 PHE 0.009 0.001 PHE A 377 TRP 0.005 0.001 TRP L 34 HIS 0.003 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3497) covalent geometry : angle 0.56253 ( 4762) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.12969 ( 10) hydrogen bonds : bond 0.03318 ( 88) hydrogen bonds : angle 5.56149 ( 189) link_BETA1-4 : bond 0.00462 ( 2) link_BETA1-4 : angle 1.87413 ( 6) link_NAG-ASN : bond 0.00571 ( 1) link_NAG-ASN : angle 2.05512 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8379 (mp10) REVERT: H 43 GLN cc_start: 0.9476 (mm110) cc_final: 0.9199 (mm-40) REVERT: H 117 TYR cc_start: 0.8750 (m-80) cc_final: 0.8326 (m-80) outliers start: 6 outliers final: 6 residues processed: 65 average time/residue: 0.1540 time to fit residues: 12.0812 Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.034360 restraints weight = 51699.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.036781 restraints weight = 20996.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.038476 restraints weight = 11146.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.039638 restraints weight = 6846.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.040379 restraints weight = 4664.669| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3505 Z= 0.153 Angle : 0.569 4.488 4781 Z= 0.296 Chirality : 0.041 0.153 519 Planarity : 0.004 0.042 616 Dihedral : 4.718 32.541 541 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 1.64 % Allowed : 15.62 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.39), residues: 428 helix: -3.69 (0.67), residues: 32 sheet: -0.09 (0.43), residues: 134 loop : -2.46 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 90 TYR 0.016 0.001 TYR H 80 PHE 0.008 0.001 PHE A 377 TRP 0.005 0.001 TRP L 34 HIS 0.003 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3497) covalent geometry : angle 0.56121 ( 4762) SS BOND : bond 0.00521 ( 5) SS BOND : angle 1.18845 ( 10) hydrogen bonds : bond 0.03293 ( 88) hydrogen bonds : angle 5.52323 ( 189) link_BETA1-4 : bond 0.00522 ( 2) link_BETA1-4 : angle 1.89756 ( 6) link_NAG-ASN : bond 0.00466 ( 1) link_NAG-ASN : angle 1.94366 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8433 (mp10) REVERT: H 117 TYR cc_start: 0.8788 (m-80) cc_final: 0.8348 (m-80) outliers start: 6 outliers final: 6 residues processed: 62 average time/residue: 0.1489 time to fit residues: 11.1620 Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.034851 restraints weight = 51022.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.037334 restraints weight = 20633.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.039075 restraints weight = 10937.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.040257 restraints weight = 6685.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.041021 restraints weight = 4538.215| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3505 Z= 0.111 Angle : 0.559 4.876 4781 Z= 0.290 Chirality : 0.042 0.169 519 Planarity : 0.004 0.040 616 Dihedral : 4.566 33.447 541 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 1.64 % Allowed : 15.07 % Favored : 83.29 % 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: -2.35 (0.40), residues: 428 helix: -3.57 (0.70), residues: 32 sheet: -0.02 (0.43), residues: 134 loop : -2.26 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 90 TYR 0.013 0.001 TYR L 35 PHE 0.009 0.001 PHE A 377 TRP 0.004 0.001 TRP L 34 HIS 0.002 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3497) covalent geometry : angle 0.55160 ( 4762) SS BOND : bond 0.00385 ( 5) SS BOND : angle 1.13513 ( 10) hydrogen bonds : bond 0.03067 ( 88) hydrogen bonds : angle 5.41487 ( 189) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 1.83140 ( 6) link_NAG-ASN : bond 0.00692 ( 1) link_NAG-ASN : angle 2.17321 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8386 (mp10) REVERT: H 43 GLN cc_start: 0.9461 (mm110) cc_final: 0.9190 (mm-40) REVERT: H 117 TYR cc_start: 0.8763 (m-80) cc_final: 0.8296 (m-80) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.1654 time to fit residues: 12.7007 Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.034160 restraints weight = 52269.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.036561 restraints weight = 21107.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.038256 restraints weight = 11148.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.039385 restraints weight = 6797.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.040150 restraints weight = 4596.716| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3505 Z= 0.165 Angle : 0.575 5.954 4781 Z= 0.299 Chirality : 0.041 0.146 519 Planarity : 0.004 0.040 616 Dihedral : 4.628 32.526 541 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.64 % Allowed : 15.07 % Favored : 83.29 % 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: -2.46 (0.39), residues: 428 helix: -3.66 (0.68), residues: 32 sheet: -0.03 (0.43), residues: 134 loop : -2.38 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.011 0.001 TYR H 80 PHE 0.008 0.001 PHE A 515 TRP 0.003 0.001 TRP L 34 HIS 0.002 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3497) covalent geometry : angle 0.56765 ( 4762) SS BOND : bond 0.00443 ( 5) SS BOND : angle 1.13562 ( 10) hydrogen bonds : bond 0.03255 ( 88) hydrogen bonds : angle 5.47962 ( 189) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 1.93244 ( 6) link_NAG-ASN : bond 0.00440 ( 1) link_NAG-ASN : angle 1.91559 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8407 (mp10) REVERT: H 117 TYR cc_start: 0.8817 (m-80) cc_final: 0.8356 (m-80) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.1485 time to fit residues: 11.0632 Evaluate side-chains 62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 0.0570 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.034787 restraints weight = 51178.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.037251 restraints weight = 20692.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.038982 restraints weight = 10908.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.040116 restraints weight = 6638.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.040893 restraints weight = 4487.130| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3505 Z= 0.113 Angle : 0.571 6.292 4781 Z= 0.296 Chirality : 0.042 0.165 519 Planarity : 0.004 0.040 616 Dihedral : 4.535 33.528 541 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.64 % Allowed : 15.62 % Favored : 82.74 % 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: -2.29 (0.40), residues: 428 helix: -3.55 (0.71), residues: 32 sheet: 0.02 (0.43), residues: 134 loop : -2.22 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.011 0.001 TYR H 106 PHE 0.009 0.001 PHE A 377 TRP 0.004 0.001 TRP L 34 HIS 0.001 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3497) covalent geometry : angle 0.56363 ( 4762) SS BOND : bond 0.00380 ( 5) SS BOND : angle 1.09010 ( 10) hydrogen bonds : bond 0.03010 ( 88) hydrogen bonds : angle 5.35537 ( 189) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 1.90553 ( 6) link_NAG-ASN : bond 0.00670 ( 1) link_NAG-ASN : angle 2.10529 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8368 (mp10) REVERT: H 117 TYR cc_start: 0.8786 (m-80) cc_final: 0.8312 (m-80) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1516 time to fit residues: 11.5427 Evaluate side-chains 62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.044352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.034464 restraints weight = 50278.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.036885 restraints weight = 20475.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.038618 restraints weight = 10818.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.039760 restraints weight = 6573.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.040567 restraints weight = 4423.172| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3505 Z= 0.124 Angle : 0.568 5.758 4781 Z= 0.294 Chirality : 0.042 0.158 519 Planarity : 0.004 0.040 616 Dihedral : 4.513 33.249 541 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 1.37 % Allowed : 15.89 % Favored : 82.74 % 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: -2.32 (0.39), residues: 428 helix: -3.49 (0.71), residues: 32 sheet: -0.02 (0.43), residues: 134 loop : -2.24 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 90 TYR 0.013 0.001 TYR L 35 PHE 0.008 0.001 PHE A 377 TRP 0.003 0.001 TRP L 34 HIS 0.001 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3497) covalent geometry : angle 0.56072 ( 4762) SS BOND : bond 0.00390 ( 5) SS BOND : angle 1.07441 ( 10) hydrogen bonds : bond 0.03006 ( 88) hydrogen bonds : angle 5.35767 ( 189) link_BETA1-4 : bond 0.00421 ( 2) link_BETA1-4 : angle 1.88062 ( 6) link_NAG-ASN : bond 0.00602 ( 1) link_NAG-ASN : angle 2.10551 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.48 seconds wall clock time: 25 minutes 19.75 seconds (1519.75 seconds total)