Starting phenix.real_space_refine on Tue Feb 11 19:13:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x94_33066/02_2025/7x94_33066_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x94_33066/02_2025/7x94_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x94_33066/02_2025/7x94_33066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x94_33066/02_2025/7x94_33066.map" model { file = "/net/cci-nas-00/data/ceres_data/7x94_33066/02_2025/7x94_33066_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x94_33066/02_2025/7x94_33066_trim.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.76, per 1000 atoms: 0.57 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: 1.94 Conformation dependent library (CDL) restraints added in 612.7 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: 0.57 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: 2.23 Time building geometry restraints manager: 2.28 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: 0.150 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: 0.110 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- 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 3497 Z= 0.199 Angle : 0.620 7.130 4762 Z= 0.329 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (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 TRP 0.016 0.001 TRP L 34 HIS 0.003 0.001 HIS A 519 PHE 0.020 0.001 PHE A 347 TYR 0.018 0.001 TYR H 60 ARG 0.004 0.000 ARG A 457 *********************** 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 : 0.515 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: 0.4198 time to fit residues: 56.9879 Evaluate side-chains 68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN L 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.036478 restraints weight = 50079.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.039008 restraints weight = 20170.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.040802 restraints weight = 10719.262| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3497 Z= 0.285 Angle : 0.637 5.634 4762 Z= 0.333 Chirality : 0.044 0.165 519 Planarity : 0.005 0.049 616 Dihedral : 8.632 60.093 541 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 1.64 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.41), residues: 428 helix: -3.93 (0.64), residues: 32 sheet: 0.02 (0.45), residues: 140 loop : -2.36 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS A 519 PHE 0.014 0.002 PHE A 347 TYR 0.016 0.001 TYR L 85 ARG 0.007 0.001 ARG L 28 *********************** 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 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.542 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 365 TYR cc_start: 0.9033 (m-80) cc_final: 0.8749 (m-80) REVERT: H 43 GLN cc_start: 0.9568 (mm110) cc_final: 0.9291 (mp10) REVERT: H 48 MET cc_start: 0.7586 (mmm) cc_final: 0.7361 (mmm) REVERT: H 104 TYR cc_start: 0.8534 (m-80) cc_final: 0.8250 (m-80) REVERT: H 117 TYR cc_start: 0.8751 (m-80) cc_final: 0.8275 (m-80) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.3888 time to fit residues: 33.0664 Evaluate side-chains 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 4 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.2932 r_free = 0.2932 target = 0.045476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.035347 restraints weight = 51539.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.037818 restraints weight = 20633.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.039573 restraints weight = 10972.485| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3497 Z= 0.285 Angle : 0.602 4.355 4762 Z= 0.319 Chirality : 0.043 0.157 519 Planarity : 0.004 0.047 616 Dihedral : 6.132 32.683 541 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.74 % Allowed : 12.05 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.40), residues: 428 helix: -3.86 (0.62), residues: 32 sheet: 0.16 (0.46), residues: 128 loop : -2.41 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 34 HIS 0.008 0.002 HIS H 32 PHE 0.011 0.001 PHE A 347 TYR 0.019 0.002 TYR L 85 ARG 0.004 0.001 ARG A 457 *********************** 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 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.607 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 365 TYR cc_start: 0.9082 (m-80) cc_final: 0.8697 (m-80) REVERT: L 36 GLN cc_start: 0.9021 (pp30) cc_final: 0.8808 (pp30) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.4252 time to fit residues: 36.2277 Evaluate side-chains 72 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 3 GLU Chi-restraints excluded: chain L residue 75 THR 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 31 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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** L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.044192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.034156 restraints weight = 52566.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.036558 restraints weight = 21301.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.038272 restraints weight = 11344.549| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3497 Z= 0.267 Angle : 0.586 4.517 4762 Z= 0.307 Chirality : 0.042 0.172 519 Planarity : 0.004 0.046 616 Dihedral : 5.325 32.540 541 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.47 % Allowed : 13.15 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.39), residues: 428 helix: -3.78 (0.63), residues: 32 sheet: 0.12 (0.46), residues: 129 loop : -2.45 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 34 HIS 0.005 0.002 HIS H 32 PHE 0.008 0.001 PHE A 347 TYR 0.012 0.001 TYR L 85 ARG 0.004 0.001 ARG H 98 *********************** 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 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.582 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 365 TYR cc_start: 0.9073 (m-80) cc_final: 0.8650 (m-80) REVERT: H 43 GLN cc_start: 0.9508 (mm110) cc_final: 0.9255 (mm-40) REVERT: H 117 TYR cc_start: 0.8821 (m-80) cc_final: 0.8312 (m-80) outliers start: 9 outliers final: 9 residues processed: 71 average time/residue: 0.4112 time to fit residues: 34.5789 Evaluate side-chains 68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 488 CYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 3 GLU 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 27 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 32 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN L 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.044406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.034477 restraints weight = 50822.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.036907 restraints weight = 20534.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.038633 restraints weight = 10879.051| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3497 Z= 0.213 Angle : 0.565 4.324 4762 Z= 0.297 Chirality : 0.042 0.168 519 Planarity : 0.004 0.045 616 Dihedral : 4.985 32.280 541 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.74 % Allowed : 13.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.40), residues: 428 helix: -3.74 (0.65), residues: 32 sheet: 0.10 (0.45), residues: 134 loop : -2.41 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 34 HIS 0.004 0.001 HIS H 32 PHE 0.011 0.001 PHE H 68 TYR 0.010 0.001 TYR H 112 ARG 0.009 0.001 ARG H 38 *********************** 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 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.517 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 365 TYR cc_start: 0.9056 (m-80) cc_final: 0.8588 (m-80) REVERT: A 414 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8448 (mp10) REVERT: H 43 GLN cc_start: 0.9509 (mm110) cc_final: 0.9250 (mm-40) REVERT: H 117 TYR cc_start: 0.8776 (m-80) cc_final: 0.8324 (m-80) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.3483 time to fit residues: 29.1668 Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 442 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 488 CYS 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: 6.9990 chunk 38 optimal weight: 20.0000 chunk 36 optimal weight: 0.0060 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- 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 = 0.2907 r_free = 0.2907 target = 0.043820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.033975 restraints weight = 51841.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036349 restraints weight = 20876.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.038061 restraints weight = 11154.454| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3497 Z= 0.250 Angle : 0.566 4.400 4762 Z= 0.298 Chirality : 0.041 0.152 519 Planarity : 0.004 0.042 616 Dihedral : 4.876 32.019 541 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.19 % Allowed : 13.97 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.39), residues: 428 helix: -3.75 (0.65), residues: 32 sheet: 0.00 (0.44), residues: 134 loop : -2.54 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 34 HIS 0.004 0.001 HIS H 32 PHE 0.008 0.001 PHE A 377 TYR 0.009 0.001 TYR L 85 ARG 0.003 0.001 ARG L 90 *********************** 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 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.532 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 365 TYR cc_start: 0.9168 (m-80) cc_final: 0.8722 (m-80) REVERT: A 414 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8450 (mp10) REVERT: H 117 TYR cc_start: 0.8796 (m-80) cc_final: 0.8375 (m-80) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.3414 time to fit residues: 28.4897 Evaluate side-chains 68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 442 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain L residue 88 ASN 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 39 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 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 = 0.2906 r_free = 0.2906 target = 0.043899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.034124 restraints weight = 51689.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036524 restraints weight = 21054.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.038209 restraints weight = 11174.370| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3497 Z= 0.225 Angle : 0.562 4.382 4762 Z= 0.296 Chirality : 0.041 0.151 519 Planarity : 0.004 0.042 616 Dihedral : 4.800 32.541 541 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.39), residues: 428 helix: -3.73 (0.66), residues: 32 sheet: 0.01 (0.44), residues: 134 loop : -2.49 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 34 HIS 0.003 0.001 HIS H 32 PHE 0.009 0.001 PHE A 377 TYR 0.010 0.001 TYR L 85 ARG 0.002 0.000 ARG L 90 *********************** 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 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.500 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 365 TYR cc_start: 0.9165 (m-80) cc_final: 0.8725 (m-80) REVERT: A 414 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8440 (mp10) REVERT: H 117 TYR cc_start: 0.8779 (m-80) cc_final: 0.8338 (m-80) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.3832 time to fit residues: 30.7711 Evaluate side-chains 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 A residue 488 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 88 ASN 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 6 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 = 0.044317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.034361 restraints weight = 50295.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.036815 restraints weight = 20336.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.038554 restraints weight = 10718.490| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3497 Z= 0.181 Angle : 0.561 4.589 4762 Z= 0.294 Chirality : 0.042 0.161 519 Planarity : 0.004 0.041 616 Dihedral : 4.668 33.086 541 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 1.64 % Allowed : 14.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.40), residues: 428 helix: -3.65 (0.68), residues: 32 sheet: -0.05 (0.44), residues: 134 loop : -2.34 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 34 HIS 0.003 0.001 HIS H 32 PHE 0.009 0.001 PHE A 377 TYR 0.014 0.001 TYR L 35 ARG 0.003 0.000 ARG A 357 *********************** 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 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.524 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 365 TYR cc_start: 0.9164 (m-80) cc_final: 0.8685 (m-80) REVERT: A 414 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8410 (mp10) REVERT: H 117 TYR cc_start: 0.8785 (m-80) cc_final: 0.8368 (m-80) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.3882 time to fit residues: 31.1108 Evaluate side-chains 60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 88 ASN 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 18 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.2890 r_free = 0.2890 target = 0.043170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.033469 restraints weight = 54327.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035799 restraints weight = 21994.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.037450 restraints weight = 11675.413| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3497 Z= 0.325 Angle : 0.617 4.730 4762 Z= 0.326 Chirality : 0.041 0.128 519 Planarity : 0.004 0.043 616 Dihedral : 5.011 31.462 541 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 1.92 % Allowed : 14.25 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.38), residues: 428 helix: -3.85 (0.62), residues: 32 sheet: -0.26 (0.43), residues: 134 loop : -2.62 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.002 HIS L 96 PHE 0.012 0.002 PHE A 515 TYR 0.014 0.002 TYR L 85 ARG 0.003 0.001 ARG A 466 *********************** 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 58 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.535 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: A 365 TYR cc_start: 0.9268 (m-80) cc_final: 0.8788 (m-80) REVERT: A 414 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8544 (mp10) REVERT: A 424 LYS cc_start: 0.9422 (tttp) cc_final: 0.9173 (ttpt) outliers start: 7 outliers final: 7 residues processed: 57 average time/residue: 0.3691 time to fit residues: 25.8063 Evaluate side-chains 58 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 442 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 88 ASN 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 40 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.2888 r_free = 0.2888 target = 0.043048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.033448 restraints weight = 53470.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035763 restraints weight = 21662.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.037422 restraints weight = 11399.662| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3497 Z= 0.282 Angle : 0.604 5.111 4762 Z= 0.319 Chirality : 0.042 0.134 519 Planarity : 0.004 0.043 616 Dihedral : 5.008 33.105 541 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.19 % Allowed : 13.97 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.38), residues: 428 helix: -3.78 (0.63), residues: 32 sheet: -0.32 (0.42), residues: 134 loop : -2.63 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 34 HIS 0.003 0.001 HIS H 32 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.002 TYR H 106 ARG 0.004 0.001 ARG A 457 ********************** 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 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.550 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: A 365 TYR cc_start: 0.9232 (m-80) cc_final: 0.8764 (m-80) REVERT: A 414 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8557 (mp10) REVERT: A 417 LYS cc_start: 0.9444 (ptmm) cc_final: 0.9177 (pttt) outliers start: 8 outliers final: 8 residues processed: 62 average time/residue: 0.3481 time to fit residues: 26.3371 Evaluate side-chains 62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 442 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 88 ASN 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 26 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.043324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.033720 restraints weight = 52897.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.036075 restraints weight = 21361.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.037735 restraints weight = 11229.528| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3497 Z= 0.239 Angle : 0.590 4.970 4762 Z= 0.311 Chirality : 0.042 0.138 519 Planarity : 0.004 0.043 616 Dihedral : 4.912 33.257 541 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 1.92 % Allowed : 14.25 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.38), residues: 428 helix: -3.69 (0.63), residues: 32 sheet: -0.27 (0.42), residues: 134 loop : -2.51 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 34 HIS 0.002 0.001 HIS H 32 PHE 0.009 0.001 PHE A 377 TYR 0.017 0.002 TYR H 104 ARG 0.003 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.71 seconds wall clock time: 48 minutes 20.07 seconds (2900.07 seconds total)