Starting phenix.real_space_refine on Tue Mar 11 18:44:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x94_33066/03_2025/7x94_33066_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x94_33066/03_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_33066/03_2025/7x94_33066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x94_33066/03_2025/7x94_33066.map" model { file = "/net/cci-nas-00/data/ceres_data/7x94_33066/03_2025/7x94_33066_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x94_33066/03_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-5624/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: 3.18, per 1000 atoms: 0.48 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: 1.47 Conformation dependent library (CDL) restraints added in 564.4 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: 0.45 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: 1.83 Time building geometry restraints manager: 1.82 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: 0.240 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: 0.100 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.980 Find NCS groups from input model: 0.050 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- 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 : 0.489 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: 0.4320 time to fit residues: 59.0700 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 : 0.569 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.046759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.036391 restraints weight = 50165.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.038919 restraints weight = 20233.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.040732 restraints weight = 10690.734| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.528 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: 0.9035 (m-80) cc_final: 0.8751 (m-80) REVERT: H 43 GLN cc_start: 0.9568 (mm110) cc_final: 0.9291 (mp10) REVERT: H 48 MET cc_start: 0.7583 (mmm) cc_final: 0.7359 (mmm) REVERT: H 104 TYR cc_start: 0.8537 (m-80) cc_final: 0.8253 (m-80) REVERT: H 117 TYR cc_start: 0.8752 (m-80) cc_final: 0.8275 (m-80) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.3958 time to fit residues: 33.7908 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 : 0.509 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 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 = 0.2928 r_free = 0.2928 target = 0.045309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.035174 restraints weight = 51534.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.037659 restraints weight = 20720.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.039434 restraints weight = 10942.828| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3582 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= 0.283 Angle : 0.602 4.361 4762 Z= 0.319 Chirality : 0.043 0.157 519 Planarity : 0.004 0.047 616 Dihedral : 6.034 32.694 541 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.74 % Allowed : 12.33 % Favored : 84.93 % 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: -2.47 (0.40), residues: 428 helix: -3.86 (0.61), residues: 32 sheet: 0.14 (0.46), residues: 128 loop : -2.42 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 34 HIS 0.006 0.002 HIS H 32 PHE 0.011 0.001 PHE A 347 TYR 0.023 0.002 TYR L 85 ARG 0.004 0.001 ARG L 28 *********************** 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 : 0.588 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: 0.9084 (m-80) cc_final: 0.8701 (m-80) REVERT: H 117 TYR cc_start: 0.8794 (m-80) cc_final: 0.8321 (m-80) REVERT: L 36 GLN cc_start: 0.9032 (pp30) cc_final: 0.8817 (pp30) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.4278 time to fit residues: 36.8324 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 : 0.721 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.2919 r_free = 0.2919 target = 0.044688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.034568 restraints weight = 52387.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037001 restraints weight = 21212.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.038728 restraints weight = 11291.917| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3497 Z= 0.246 Angle : 0.572 4.503 4762 Z= 0.301 Chirality : 0.042 0.161 519 Planarity : 0.004 0.045 616 Dihedral : 5.302 32.515 541 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 2.47 % Allowed : 13.70 % 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: -2.45 (0.40), residues: 428 helix: -3.78 (0.62), residues: 32 sheet: 0.15 (0.46), residues: 129 loop : -2.42 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 34 HIS 0.004 0.001 HIS H 32 PHE 0.009 0.001 PHE A 347 TYR 0.011 0.001 TYR L 85 ARG 0.003 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 : 0.496 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: 0.9068 (m-80) cc_final: 0.8635 (m-80) REVERT: H 117 TYR cc_start: 0.8802 (m-80) cc_final: 0.8358 (m-80) REVERT: L 36 GLN cc_start: 0.9089 (pp30) cc_final: 0.8876 (pp30) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.3980 time to fit residues: 33.3160 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 : 0.502 ------------------------------------------------------------------------------- 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 L residue 3 GLU 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: 10.0000 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 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 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 = 0.2901 r_free = 0.2901 target = 0.043741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033869 restraints weight = 51863.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.036243 restraints weight = 21025.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.037935 restraints weight = 11202.774| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4120 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= 0.273 Angle : 0.580 4.404 4762 Z= 0.306 Chirality : 0.041 0.154 519 Planarity : 0.005 0.056 616 Dihedral : 5.087 32.104 541 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.19 % Allowed : 14.52 % 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: -2.53 (0.39), residues: 428 helix: -3.78 (0.64), residues: 32 sheet: 0.06 (0.45), residues: 134 loop : -2.50 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 34 HIS 0.004 0.002 HIS H 32 PHE 0.011 0.001 PHE H 68 TYR 0.012 0.001 TYR H 112 ARG 0.007 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 68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 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: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9096 (m-80) cc_final: 0.8622 (m-80) REVERT: H 117 TYR cc_start: 0.8809 (m-80) cc_final: 0.8364 (m-80) outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.3770 time to fit residues: 30.5777 Evaluate side-chains 66 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 H residue 99 ILE Chi-restraints excluded: chain L residue 3 GLU 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 38 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.044322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.034417 restraints weight = 51068.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.036848 restraints weight = 20571.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.038573 restraints weight = 10881.968| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3497 Z= 0.192 Angle : 0.552 4.407 4762 Z= 0.290 Chirality : 0.042 0.167 519 Planarity : 0.004 0.042 616 Dihedral : 4.795 32.580 541 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 2.19 % Allowed : 15.07 % 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 (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: -2.38 (0.40), residues: 428 helix: -3.71 (0.66), residues: 32 sheet: 0.11 (0.45), residues: 134 loop : -2.37 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 34 HIS 0.002 0.001 HIS H 32 PHE 0.008 0.001 PHE A 377 TYR 0.010 0.001 TYR H 106 ARG 0.003 0.000 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 : 0.513 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: 0.9120 (m-80) cc_final: 0.8658 (m-80) REVERT: A 414 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8388 (mp10) REVERT: H 43 GLN cc_start: 0.9485 (mm110) cc_final: 0.9212 (mm-40) REVERT: H 104 TYR cc_start: 0.8466 (m-80) cc_final: 0.8185 (m-10) REVERT: H 117 TYR cc_start: 0.8753 (m-80) cc_final: 0.8285 (m-80) outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.3603 time to fit residues: 29.8939 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 : 0.505 ------------------------------------------------------------------------------- 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 99 ILE 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: 8.9990 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.2900 r_free = 0.2900 target = 0.043700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.034043 restraints weight = 52610.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.036408 restraints weight = 21356.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.038059 restraints weight = 11330.705| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4383 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= 0.258 Angle : 0.575 4.434 4762 Z= 0.303 Chirality : 0.041 0.144 519 Planarity : 0.004 0.043 616 Dihedral : 4.840 32.121 541 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.19 % Allowed : 14.52 % 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: -2.52 (0.39), residues: 428 helix: -3.76 (0.65), residues: 32 sheet: 0.04 (0.45), residues: 134 loop : -2.48 (0.37), 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 0.008 0.001 PHE A 377 TYR 0.011 0.001 TYR L 35 ARG 0.003 0.001 ARG H 38 *********************** 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 : 0.569 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: 0.9168 (m-80) cc_final: 0.8730 (m-80) REVERT: A 414 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8505 (mp10) REVERT: H 117 TYR cc_start: 0.8829 (m-80) cc_final: 0.8368 (m-80) outliers start: 8 outliers final: 8 residues processed: 68 average time/residue: 0.3723 time to fit residues: 30.4472 Evaluate side-chains 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 H residue 99 ILE 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: 9.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 0.0020 chunk 1 optimal weight: 3.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- 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 = 0.2903 r_free = 0.2903 target = 0.043929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.034211 restraints weight = 52010.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.036614 restraints weight = 20866.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.038289 restraints weight = 10991.953| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4380 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= 0.203 Angle : 0.564 4.827 4762 Z= 0.295 Chirality : 0.042 0.153 519 Planarity : 0.004 0.041 616 Dihedral : 4.724 32.953 541 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.19 % Allowed : 15.07 % 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 (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: -2.42 (0.40), residues: 428 helix: -3.70 (0.67), residues: 32 sheet: 0.02 (0.44), residues: 134 loop : -2.36 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 34 HIS 0.002 0.001 HIS H 32 PHE 0.009 0.001 PHE A 377 TYR 0.016 0.001 TYR L 35 ARG 0.002 0.001 ARG A 457 *********************** 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 68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.578 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: 0.9153 (m-80) cc_final: 0.8666 (m-80) REVERT: A 414 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8444 (mp10) REVERT: H 117 TYR cc_start: 0.8799 (m-80) cc_final: 0.8312 (m-80) outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.3570 time to fit residues: 29.2541 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 : 0.545 ------------------------------------------------------------------------------- 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 H residue 99 ILE 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: 3.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.2891 r_free = 0.2891 target = 0.043390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.033669 restraints weight = 53287.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.036062 restraints weight = 21316.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.037726 restraints weight = 11219.289| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3497 Z= 0.265 Angle : 0.582 5.282 4762 Z= 0.306 Chirality : 0.041 0.134 519 Planarity : 0.004 0.042 616 Dihedral : 4.814 32.207 541 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.19 % Allowed : 15.62 % Favored : 82.19 % 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: -2.59 (0.39), residues: 428 helix: -3.76 (0.64), residues: 32 sheet: -0.10 (0.43), residues: 134 loop : -2.48 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.003 0.001 HIS L 96 PHE 0.010 0.001 PHE A 515 TYR 0.012 0.001 TYR H 80 ARG 0.002 0.001 ARG A 457 *********************** 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 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.564 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: 0.9214 (m-80) cc_final: 0.8742 (m-80) REVERT: A 414 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8518 (mp10) outliers start: 8 outliers final: 8 residues processed: 66 average time/residue: 0.3539 time to fit residues: 28.3289 Evaluate side-chains 64 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 H residue 99 ILE 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: 6.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.044198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.034428 restraints weight = 52182.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.036846 restraints weight = 20983.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.038564 restraints weight = 11001.448| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4624 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= 0.185 Angle : 0.575 5.986 4762 Z= 0.300 Chirality : 0.042 0.158 519 Planarity : 0.004 0.041 616 Dihedral : 4.711 33.599 541 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 1.92 % Allowed : 15.62 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.39), residues: 428 helix: -3.67 (0.67), residues: 32 sheet: -0.04 (0.43), residues: 134 loop : -2.31 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 34 HIS 0.002 0.001 HIS H 32 PHE 0.009 0.001 PHE A 377 TYR 0.011 0.001 TYR H 106 ARG 0.002 0.000 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 65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.496 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: 0.9151 (m-80) cc_final: 0.8673 (m-80) REVERT: A 414 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8459 (mp10) REVERT: H 117 TYR cc_start: 0.8749 (m-80) cc_final: 0.8346 (m-80) outliers start: 7 outliers final: 7 residues processed: 64 average time/residue: 0.3747 time to fit residues: 29.2738 Evaluate side-chains 60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 H residue 99 ILE 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: 9.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.2916 r_free = 0.2916 target = 0.044404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.034611 restraints weight = 51681.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.037066 restraints weight = 20647.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.038792 restraints weight = 10820.822| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3497 Z= 0.185 Angle : 0.565 5.864 4762 Z= 0.295 Chirality : 0.042 0.158 519 Planarity : 0.004 0.042 616 Dihedral : 4.622 33.407 541 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.92 % Allowed : 15.07 % 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 (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: -2.33 (0.40), residues: 428 helix: -3.60 (0.68), residues: 32 sheet: -0.03 (0.43), residues: 134 loop : -2.23 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 34 HIS 0.002 0.001 HIS H 32 PHE 0.008 0.001 PHE A 377 TYR 0.010 0.001 TYR H 112 ARG 0.002 0.000 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.60 seconds wall clock time: 50 minutes 56.76 seconds (3056.76 seconds total)