Starting phenix.real_space_refine on Tue Feb 11 17:33:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x92_33064/02_2025/7x92_33064_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x92_33064/02_2025/7x92_33064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x92_33064/02_2025/7x92_33064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x92_33064/02_2025/7x92_33064.map" model { file = "/net/cci-nas-00/data/ceres_data/7x92_33064/02_2025/7x92_33064_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x92_33064/02_2025/7x92_33064_trim.cif" } resolution = 4.1 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 15 5.16 5 C 2134 2.51 5 N 557 2.21 5 O 652 1.98 5 H 3171 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6529 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "H" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1896 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1617 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.74, per 1000 atoms: 0.57 Number of scatterers: 6529 At special positions: 0 Unit cell: (69.636, 61.346, 101.967, 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 15 16.00 O 652 8.00 N 557 7.00 C 2134 6.00 H 3171 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 611.8 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.923A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.240A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.872A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.712A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.520A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 33 through 38 removed outlier: 3.639A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.582A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 84 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: 2.41 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3171 1.04 - 1.24: 413 1.24 - 1.44: 1160 1.44 - 1.63: 1853 1.63 - 1.83: 18 Bond restraints: 6615 Sorted by residual: bond pdb=" CG PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 1.503 1.281 0.222 3.40e-02 8.65e+02 4.25e+01 bond pdb=" N PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.42e+00 bond pdb=" CB PRO A 507 " pdb=" CG PRO A 507 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.28e+00 bond pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 1.466 1.445 0.021 1.17e-02 7.31e+03 3.28e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 6610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.24: 11837 6.24 - 12.49: 3 12.49 - 18.73: 2 18.73 - 24.98: 0 24.98 - 31.22: 3 Bond angle restraints: 11845 Sorted by residual: angle pdb=" CA PRO A 507 " pdb=" N PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 112.00 94.57 17.43 1.40e+00 5.10e-01 1.55e+02 angle pdb=" CB TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 109.00 77.78 31.22 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 109.00 77.92 31.08 3.00e+00 1.11e-01 1.07e+02 angle pdb=" N TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 110.00 82.48 27.52 3.00e+00 1.11e-01 8.41e+01 angle pdb=" N PRO A 507 " pdb=" CD PRO A 507 " pdb=" CG PRO A 507 " ideal model delta sigma weight residual 103.20 90.05 13.15 1.50e+00 4.44e-01 7.68e+01 ... (remaining 11840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 2933 21.81 - 43.63: 227 43.63 - 65.44: 54 65.44 - 87.26: 4 87.26 - 109.07: 9 Dihedral angle restraints: 3227 sinusoidal: 1718 harmonic: 1509 Sorted by residual: dihedral pdb=" C TYR L 96 " pdb=" N TYR L 96 " pdb=" CA TYR L 96 " pdb=" CB TYR L 96 " ideal model delta harmonic sigma weight residual -122.60 -145.46 22.86 0 2.50e+00 1.60e-01 8.36e+01 dihedral pdb=" N TYR L 96 " pdb=" C TYR L 96 " pdb=" CA TYR L 96 " pdb=" CB TYR L 96 " ideal model delta harmonic sigma weight residual 122.80 143.62 -20.82 0 2.50e+00 1.60e-01 6.93e+01 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 93.00 43.61 49.39 1 1.00e+01 1.00e-02 3.35e+01 ... (remaining 3224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 506 0.183 - 0.366: 0 0.366 - 0.549: 0 0.549 - 0.732: 0 0.732 - 0.916: 1 Chirality restraints: 507 Sorted by residual: chirality pdb=" CA TYR L 96 " pdb=" N TYR L 96 " pdb=" C TYR L 96 " pdb=" CB TYR L 96 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 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 -2.22 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 504 not shown) Planarity restraints: 1010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 506 " 0.100 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO A 507 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 94 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO L 95 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO L 59 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.022 5.00e-02 4.00e+02 ... (remaining 1007 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 847 2.24 - 2.83: 13998 2.83 - 3.42: 15813 3.42 - 4.01: 21902 4.01 - 4.60: 32318 Nonbonded interactions: 84878 Sorted by model distance: nonbonded pdb=" OG SER H 30 " pdb="HD21 ASN H 74 " model vdw 1.650 2.450 nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 101 " model vdw 1.667 2.450 nonbonded pdb=" OD1 ASN A 448 " pdb=" H ASN A 450 " model vdw 1.679 2.450 nonbonded pdb=" H TYR L 96 " pdb=" HA TYR L 96 " model vdw 1.695 1.816 nonbonded pdb=" OH TYR A 449 " pdb="HD21 ASN H 31 " model vdw 1.697 2.450 ... (remaining 84873 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: 0.230 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.910 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.005 0.222 3444 Z= 0.416 Angle : 0.745 17.433 4685 Z= 0.430 Chirality : 0.061 0.916 507 Planarity : 0.007 0.136 607 Dihedral : 17.172 109.073 1252 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % Cbeta Deviations : 0.26 % 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 (0.41), residues: 420 helix: -2.72 (1.22), residues: 20 sheet: -0.96 (0.47), residues: 143 loop : -2.10 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 PHE 0.012 0.001 PHE A 377 TYR 0.007 0.001 TYR L 96 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.530 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8126 (pp) cc_final: 0.7842 (pp) REVERT: L 34 ASN cc_start: 0.7531 (m-40) cc_final: 0.7317 (m-40) REVERT: L 46 LEU cc_start: 0.8679 (tp) cc_final: 0.8435 (tp) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.4225 time to fit residues: 65.9516 Evaluate side-chains 106 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.052672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041339 restraints weight = 44326.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044279 restraints weight = 19708.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.046441 restraints weight = 10894.890| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3444 Z= 0.326 Angle : 0.667 6.829 4685 Z= 0.345 Chirality : 0.047 0.372 507 Planarity : 0.005 0.049 607 Dihedral : 11.101 76.887 512 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -2.80 (0.40), residues: 420 helix: -4.53 (0.46), residues: 24 sheet: -0.92 (0.47), residues: 143 loop : -2.23 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.001 PHE A 377 TYR 0.015 0.002 TYR L 96 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7668 (m-30) cc_final: 0.7109 (m-30) REVERT: A 405 ASP cc_start: 0.9021 (t70) cc_final: 0.8817 (t0) REVERT: A 442 ASP cc_start: 0.9207 (m-30) cc_final: 0.8839 (m-30) REVERT: H 114 TYR cc_start: 0.9551 (m-80) cc_final: 0.9169 (m-10) REVERT: L 4 LEU cc_start: 0.9083 (mm) cc_final: 0.8792 (tt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3783 time to fit residues: 47.1796 Evaluate side-chains 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.041587 restraints weight = 44700.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.044567 restraints weight = 19431.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046704 restraints weight = 10605.275| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3444 Z= 0.247 Angle : 0.643 7.746 4685 Z= 0.331 Chirality : 0.047 0.324 507 Planarity : 0.004 0.042 607 Dihedral : 8.527 48.411 512 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 0.27 % Allowed : 1.65 % Favored : 98.08 % 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: -2.88 (0.39), residues: 420 helix: -4.62 (0.38), residues: 24 sheet: -0.47 (0.49), residues: 128 loop : -2.54 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE A 377 TYR 0.013 0.001 TYR H 53 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.510 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 REVERT: A 398 ASP cc_start: 0.7559 (m-30) cc_final: 0.7191 (m-30) REVERT: A 405 ASP cc_start: 0.8901 (t70) cc_final: 0.8410 (t0) REVERT: A 442 ASP cc_start: 0.9111 (m-30) cc_final: 0.8742 (m-30) REVERT: H 35 HIS cc_start: 0.9262 (m90) cc_final: 0.8965 (m90) REVERT: H 73 ASP cc_start: 0.8209 (t0) cc_final: 0.7975 (t0) REVERT: H 114 TYR cc_start: 0.9531 (m-80) cc_final: 0.9201 (m-10) REVERT: L 49 TYR cc_start: 0.9586 (p90) cc_final: 0.9274 (p90) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.3795 time to fit residues: 46.6418 Evaluate side-chains 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.043014 restraints weight = 44631.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046012 restraints weight = 19153.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048195 restraints weight = 10443.335| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3444 Z= 0.178 Angle : 0.605 6.908 4685 Z= 0.311 Chirality : 0.046 0.313 507 Planarity : 0.003 0.041 607 Dihedral : 6.820 46.824 512 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -2.93 (0.39), residues: 420 helix: -4.62 (0.37), residues: 24 sheet: -0.79 (0.47), residues: 136 loop : -2.45 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.020 0.001 TYR H 53 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.501 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 revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7616 (m-30) cc_final: 0.7172 (m-30) REVERT: A 405 ASP cc_start: 0.8735 (t70) cc_final: 0.8252 (t0) REVERT: A 442 ASP cc_start: 0.9040 (m-30) cc_final: 0.8651 (m-30) REVERT: H 73 ASP cc_start: 0.8169 (t0) cc_final: 0.7967 (t0) REVERT: H 114 TYR cc_start: 0.9504 (m-80) cc_final: 0.8513 (m-10) REVERT: L 49 TYR cc_start: 0.9568 (p90) cc_final: 0.9214 (p90) REVERT: L 97 THR cc_start: 0.8748 (t) cc_final: 0.8528 (t) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3064 time to fit residues: 38.0312 Evaluate side-chains 88 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 = 0.3096 r_free = 0.3096 target = 0.053793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043172 restraints weight = 46676.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046155 restraints weight = 19952.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048258 restraints weight = 10731.516| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3444 Z= 0.213 Angle : 0.611 6.783 4685 Z= 0.316 Chirality : 0.046 0.317 507 Planarity : 0.003 0.042 607 Dihedral : 6.460 44.271 512 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.76 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -2.78 (0.39), residues: 420 helix: -3.46 (0.84), residues: 26 sheet: -0.60 (0.48), residues: 130 loop : -2.46 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.005 0.002 HIS H 35 PHE 0.009 0.001 PHE A 377 TYR 0.017 0.001 TYR H 53 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.567 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: A 398 ASP cc_start: 0.7566 (m-30) cc_final: 0.7164 (m-30) REVERT: A 405 ASP cc_start: 0.8686 (t70) cc_final: 0.8261 (t0) REVERT: A 442 ASP cc_start: 0.9068 (m-30) cc_final: 0.8696 (m-30) REVERT: H 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7994 (t0) REVERT: H 114 TYR cc_start: 0.9532 (m-80) cc_final: 0.8512 (m-10) REVERT: L 49 TYR cc_start: 0.9561 (p90) cc_final: 0.9187 (p90) REVERT: L 97 THR cc_start: 0.8882 (t) cc_final: 0.8653 (t) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3187 time to fit residues: 37.6862 Evaluate side-chains 86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.3115 r_free = 0.3115 target = 0.054527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.043572 restraints weight = 45603.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046608 restraints weight = 19451.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048758 restraints weight = 10503.585| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3444 Z= 0.167 Angle : 0.593 7.457 4685 Z= 0.304 Chirality : 0.047 0.326 507 Planarity : 0.003 0.042 607 Dihedral : 6.175 42.922 512 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.81 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.84 (0.39), residues: 420 helix: -3.71 (0.75), residues: 26 sheet: -0.88 (0.47), residues: 136 loop : -2.37 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.005 0.002 HIS H 35 PHE 0.009 0.001 PHE A 377 TYR 0.016 0.001 TYR H 53 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.570 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: A 398 ASP cc_start: 0.7546 (m-30) cc_final: 0.7118 (m-30) REVERT: A 405 ASP cc_start: 0.8656 (t70) cc_final: 0.8175 (t0) REVERT: A 442 ASP cc_start: 0.8978 (m-30) cc_final: 0.8592 (m-30) REVERT: H 35 HIS cc_start: 0.9117 (m-70) cc_final: 0.8881 (m90) REVERT: H 114 TYR cc_start: 0.9494 (m-80) cc_final: 0.8544 (m-10) REVERT: L 49 TYR cc_start: 0.9583 (p90) cc_final: 0.9212 (p90) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3184 time to fit residues: 38.3541 Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.0470 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.3139 r_free = 0.3139 target = 0.055542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.044627 restraints weight = 45513.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047734 restraints weight = 19436.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049897 restraints weight = 10441.007| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3444 Z= 0.163 Angle : 0.575 6.215 4685 Z= 0.295 Chirality : 0.047 0.330 507 Planarity : 0.003 0.042 607 Dihedral : 5.883 39.190 512 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.33 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -2.85 (0.39), residues: 420 helix: -3.82 (0.69), residues: 26 sheet: -0.88 (0.47), residues: 136 loop : -2.36 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 35 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE A 377 TYR 0.013 0.001 TYR H 53 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.518 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: A 386 LYS cc_start: 0.9642 (mttp) cc_final: 0.9424 (mttm) REVERT: A 398 ASP cc_start: 0.7543 (m-30) cc_final: 0.7115 (m-30) REVERT: A 405 ASP cc_start: 0.8637 (t70) cc_final: 0.8280 (t0) REVERT: A 442 ASP cc_start: 0.8963 (m-30) cc_final: 0.8565 (m-30) REVERT: H 35 HIS cc_start: 0.9015 (m-70) cc_final: 0.8646 (m90) REVERT: H 45 LEU cc_start: 0.8911 (pp) cc_final: 0.8595 (pp) REVERT: H 114 TYR cc_start: 0.9459 (m-80) cc_final: 0.8549 (m-10) REVERT: L 49 TYR cc_start: 0.9589 (p90) cc_final: 0.9341 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3068 time to fit residues: 38.4373 Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 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 = 0.3114 r_free = 0.3114 target = 0.054114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042987 restraints weight = 44557.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.045965 restraints weight = 18959.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.048113 restraints weight = 10290.774| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3444 Z= 0.231 Angle : 0.618 7.583 4685 Z= 0.323 Chirality : 0.047 0.339 507 Planarity : 0.004 0.042 607 Dihedral : 5.822 37.769 512 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.76 % Favored : 84.76 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.89 (0.39), residues: 420 helix: -3.76 (0.75), residues: 26 sheet: -0.85 (0.46), residues: 142 loop : -2.46 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.029 0.002 PHE A 392 TYR 0.020 0.002 TYR L 91 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.526 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: A 398 ASP cc_start: 0.7422 (m-30) cc_final: 0.7007 (m-30) REVERT: A 405 ASP cc_start: 0.8769 (t70) cc_final: 0.8451 (t0) REVERT: A 442 ASP cc_start: 0.8984 (m-30) cc_final: 0.8599 (m-30) REVERT: H 34 MET cc_start: 0.8064 (pmm) cc_final: 0.7853 (pmm) REVERT: H 114 TYR cc_start: 0.9464 (m-80) cc_final: 0.8560 (m-10) REVERT: L 49 TYR cc_start: 0.9582 (p90) cc_final: 0.9360 (p90) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3077 time to fit residues: 37.3189 Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 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 = 0.3082 r_free = 0.3082 target = 0.052692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.041572 restraints weight = 46121.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044531 restraints weight = 19931.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046642 restraints weight = 10900.132| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3444 Z= 0.231 Angle : 0.604 5.194 4685 Z= 0.317 Chirality : 0.047 0.374 507 Planarity : 0.003 0.042 607 Dihedral : 5.670 35.402 512 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.52 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.26 % 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: -2.91 (0.39), residues: 420 helix: -3.75 (0.77), residues: 26 sheet: -0.96 (0.45), residues: 144 loop : -2.42 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 47 HIS 0.004 0.002 HIS H 35 PHE 0.036 0.002 PHE H 112 TYR 0.022 0.002 TYR L 91 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.502 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 REVERT: A 398 ASP cc_start: 0.7411 (m-30) cc_final: 0.7006 (m-30) REVERT: A 405 ASP cc_start: 0.8750 (t70) cc_final: 0.8485 (t0) REVERT: A 442 ASP cc_start: 0.8969 (m-30) cc_final: 0.8585 (m-30) REVERT: H 34 MET cc_start: 0.8251 (pmm) cc_final: 0.8010 (pmm) REVERT: H 114 TYR cc_start: 0.9452 (m-80) cc_final: 0.8544 (m-10) REVERT: L 49 TYR cc_start: 0.9568 (p90) cc_final: 0.9367 (p90) REVERT: L 50 ASP cc_start: 0.9618 (m-30) cc_final: 0.9413 (m-30) REVERT: L 91 TYR cc_start: 0.9423 (p90) cc_final: 0.8797 (p90) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3049 time to fit residues: 36.2545 Evaluate side-chains 82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.053978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.042744 restraints weight = 45010.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045763 restraints weight = 19389.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047942 restraints weight = 10559.075| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3444 Z= 0.181 Angle : 0.592 5.278 4685 Z= 0.304 Chirality : 0.048 0.367 507 Planarity : 0.003 0.041 607 Dihedral : 5.412 31.620 512 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.52 % Favored : 85.00 % 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: -2.88 (0.39), residues: 420 helix: -3.98 (0.68), residues: 26 sheet: -0.88 (0.46), residues: 142 loop : -2.40 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.029 0.002 PHE H 112 TYR 0.018 0.001 TYR L 91 ARG 0.002 0.000 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.540 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7513 (m-30) cc_final: 0.7072 (m-30) REVERT: A 405 ASP cc_start: 0.8721 (t70) cc_final: 0.8452 (t0) REVERT: A 442 ASP cc_start: 0.8862 (m-30) cc_final: 0.8466 (m-30) REVERT: H 34 MET cc_start: 0.8301 (pmm) cc_final: 0.8036 (pmm) REVERT: H 114 TYR cc_start: 0.9394 (m-80) cc_final: 0.9099 (m-80) REVERT: L 50 ASP cc_start: 0.9609 (m-30) cc_final: 0.9408 (m-30) REVERT: L 91 TYR cc_start: 0.9346 (p90) cc_final: 0.8750 (p90) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2989 time to fit residues: 37.7767 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.041883 restraints weight = 45691.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.044908 restraints weight = 20206.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047078 restraints weight = 11150.637| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3444 Z= 0.184 Angle : 0.583 5.268 4685 Z= 0.301 Chirality : 0.047 0.362 507 Planarity : 0.003 0.042 607 Dihedral : 5.302 29.356 512 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.76 % Favored : 84.76 % 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: -2.86 (0.39), residues: 420 helix: -4.01 (0.66), residues: 26 sheet: -0.89 (0.46), residues: 142 loop : -2.36 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.002 PHE H 112 TYR 0.024 0.002 TYR L 96 ARG 0.002 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.66 seconds wall clock time: 52 minutes 52.49 seconds (3172.49 seconds total)