Starting phenix.real_space_refine on Tue Mar 11 17:03:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x92_33064/03_2025/7x92_33064_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x92_33064/03_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_33064/03_2025/7x92_33064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x92_33064/03_2025/7x92_33064.map" model { file = "/net/cci-nas-00/data/ceres_data/7x92_33064/03_2025/7x92_33064_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x92_33064/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.94, per 1000 atoms: 0.60 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: 1.58 Conformation dependent library (CDL) restraints added in 651.7 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: 0.51 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: 2.87 Time building geometry restraints manager: 1.96 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: 0.180 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: 0.120 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- 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 : 0.565 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: 0.4457 time to fit residues: 70.3040 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 : 0.649 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041340 restraints weight = 44326.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044270 restraints weight = 19706.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046436 restraints weight = 10918.029| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 76.886 512 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 : 0.468 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: 0.7667 (m-30) cc_final: 0.7108 (m-30) REVERT: A 405 ASP cc_start: 0.9022 (t70) cc_final: 0.8818 (t0) REVERT: A 442 ASP cc_start: 0.9207 (m-30) cc_final: 0.8838 (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: 0.3766 time to fit residues: 47.1823 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 : 0.559 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3061 r_free = 0.3061 target = 0.053416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.042477 restraints weight = 44375.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045509 restraints weight = 19303.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.047671 restraints weight = 10533.358| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3444 Z= 0.216 Angle : 0.635 7.900 4685 Z= 0.326 Chirality : 0.047 0.323 507 Planarity : 0.004 0.042 607 Dihedral : 8.573 49.520 512 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % 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: -2.92 (0.39), residues: 420 helix: -4.61 (0.38), residues: 24 sheet: -0.72 (0.48), residues: 134 loop : -2.47 (0.35), residues: 262 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 0.009 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 108 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.554 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: 0.7598 (m-30) cc_final: 0.7225 (m-30) REVERT: A 405 ASP cc_start: 0.8886 (t70) cc_final: 0.8648 (t0) REVERT: A 442 ASP cc_start: 0.9123 (m-30) cc_final: 0.8758 (m-30) REVERT: H 35 HIS cc_start: 0.9244 (m90) cc_final: 0.8830 (m90) REVERT: H 73 ASP cc_start: 0.8234 (t0) cc_final: 0.7995 (t0) REVERT: H 114 TYR cc_start: 0.9512 (m-80) cc_final: 0.9198 (m-10) REVERT: L 97 THR cc_start: 0.8792 (t) cc_final: 0.8575 (t) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.3597 time to fit residues: 46.1605 Evaluate side-chains 93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3100 r_free = 0.3100 target = 0.054231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.043308 restraints weight = 45687.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046305 restraints weight = 19445.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.048439 restraints weight = 10537.547| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3682 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= 0.211 Angle : 0.632 6.961 4685 Z= 0.326 Chirality : 0.047 0.320 507 Planarity : 0.003 0.042 607 Dihedral : 7.135 47.202 512 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % 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: -2.85 (0.40), residues: 420 helix: -4.65 (0.36), residues: 24 sheet: -0.57 (0.49), residues: 136 loop : -2.49 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.018 0.002 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 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.485 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: 0.7636 (m-30) cc_final: 0.7209 (m-30) REVERT: A 442 ASP cc_start: 0.9076 (m-30) cc_final: 0.8702 (m-30) REVERT: H 34 MET cc_start: 0.7649 (pmm) cc_final: 0.7433 (pmm) REVERT: H 35 HIS cc_start: 0.9121 (m90) cc_final: 0.8730 (m90) REVERT: H 73 ASP cc_start: 0.8223 (t0) cc_final: 0.7965 (t0) REVERT: H 114 TYR cc_start: 0.9530 (m-80) cc_final: 0.9191 (m-10) REVERT: L 97 THR cc_start: 0.8754 (t) cc_final: 0.8528 (t) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3481 time to fit residues: 41.1218 Evaluate side-chains 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 10.0000 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043407 restraints weight = 46424.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046375 restraints weight = 19807.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048490 restraints weight = 10673.176| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3444 Z= 0.202 Angle : 0.618 7.024 4685 Z= 0.320 Chirality : 0.046 0.321 507 Planarity : 0.003 0.042 607 Dihedral : 6.558 45.191 512 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.76 % Favored : 85.00 % 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: -2.81 (0.40), residues: 420 helix: -4.57 (0.40), residues: 24 sheet: -0.52 (0.49), residues: 134 loop : -2.47 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.001 0.000 HIS A 519 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 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.551 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: 0.7566 (m-30) cc_final: 0.7166 (m-30) REVERT: A 405 ASP cc_start: 0.8522 (t70) cc_final: 0.8169 (t0) REVERT: A 442 ASP cc_start: 0.9062 (m-30) cc_final: 0.8695 (m-30) REVERT: H 34 MET cc_start: 0.7814 (pmm) cc_final: 0.7564 (pmm) REVERT: H 35 HIS cc_start: 0.9133 (m90) cc_final: 0.8846 (m-70) REVERT: H 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7938 (t0) REVERT: H 114 TYR cc_start: 0.9534 (m-80) cc_final: 0.8517 (m-10) REVERT: L 49 TYR cc_start: 0.9433 (p90) cc_final: 0.9150 (p90) REVERT: L 97 THR cc_start: 0.8849 (t) cc_final: 0.8607 (t) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3153 time to fit residues: 37.8517 Evaluate side-chains 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3092 r_free = 0.3092 target = 0.053621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043151 restraints weight = 46348.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.046038 restraints weight = 19762.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048087 restraints weight = 10707.513| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3444 Z= 0.196 Angle : 0.620 7.257 4685 Z= 0.319 Chirality : 0.047 0.324 507 Planarity : 0.003 0.041 607 Dihedral : 6.340 43.559 512 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.48 % Allowed : 15.48 % Favored : 84.05 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -2.72 (0.40), residues: 420 helix: -3.73 (0.74), residues: 26 sheet: -0.48 (0.50), residues: 134 loop : -2.46 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.002 0.001 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 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 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.596 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: A 398 ASP cc_start: 0.7530 (m-30) cc_final: 0.7124 (m-30) REVERT: A 405 ASP cc_start: 0.8528 (t70) cc_final: 0.8245 (t0) REVERT: A 442 ASP cc_start: 0.9051 (m-30) cc_final: 0.8681 (m-30) REVERT: H 34 MET cc_start: 0.7865 (pmm) cc_final: 0.7615 (pmm) REVERT: H 35 HIS cc_start: 0.9071 (m90) cc_final: 0.8853 (m90) REVERT: H 114 TYR cc_start: 0.9530 (m-80) cc_final: 0.8538 (m-10) REVERT: L 36 TYR cc_start: 0.8854 (m-80) cc_final: 0.8348 (m-10) REVERT: L 49 TYR cc_start: 0.9441 (p90) cc_final: 0.9198 (p90) REVERT: L 97 THR cc_start: 0.8883 (t) cc_final: 0.8632 (t) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3135 time to fit residues: 37.6811 Evaluate side-chains 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3075 r_free = 0.3075 target = 0.053135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042592 restraints weight = 46647.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045572 restraints weight = 19531.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047634 restraints weight = 10410.684| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3444 Z= 0.235 Angle : 0.637 7.290 4685 Z= 0.329 Chirality : 0.046 0.323 507 Planarity : 0.003 0.041 607 Dihedral : 6.213 41.888 512 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 15.00 % Favored : 84.52 % 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: -2.69 (0.40), residues: 420 helix: -3.77 (0.75), residues: 26 sheet: -0.24 (0.50), residues: 128 loop : -2.54 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE A 377 TYR 0.017 0.002 TYR H 53 ARG 0.003 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 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.487 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: 0.7402 (m-30) cc_final: 0.6995 (m-30) REVERT: A 405 ASP cc_start: 0.8551 (t70) cc_final: 0.8328 (t0) REVERT: A 442 ASP cc_start: 0.9014 (m-30) cc_final: 0.8621 (m-30) REVERT: H 34 MET cc_start: 0.8040 (pmm) cc_final: 0.7786 (pmm) REVERT: H 73 ASP cc_start: 0.8142 (t0) cc_final: 0.7790 (t0) REVERT: H 80 TYR cc_start: 0.8717 (m-80) cc_final: 0.8482 (m-80) REVERT: H 114 TYR cc_start: 0.9513 (m-80) cc_final: 0.8560 (m-10) REVERT: L 91 TYR cc_start: 0.9305 (p90) cc_final: 0.8817 (p90) REVERT: L 97 THR cc_start: 0.8509 (t) cc_final: 0.8305 (t) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3137 time to fit residues: 37.4242 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 : 0.474 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3067 r_free = 0.3067 target = 0.052361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041431 restraints weight = 44331.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044349 restraints weight = 18752.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046444 restraints weight = 10134.483| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3444 Z= 0.218 Angle : 0.630 7.767 4685 Z= 0.328 Chirality : 0.046 0.307 507 Planarity : 0.004 0.041 607 Dihedral : 6.009 39.209 512 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 16.19 % Favored : 83.33 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.71 (0.40), residues: 420 helix: -3.88 (0.72), residues: 26 sheet: -0.38 (0.49), residues: 140 loop : -2.54 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE A 377 TYR 0.017 0.002 TYR H 53 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 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.494 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: 0.7360 (m-30) cc_final: 0.6950 (m-30) REVERT: A 442 ASP cc_start: 0.8964 (m-30) cc_final: 0.8575 (m-30) REVERT: H 4 LEU cc_start: 0.9059 (tp) cc_final: 0.8848 (tp) REVERT: H 34 MET cc_start: 0.8197 (pmm) cc_final: 0.7935 (pmm) REVERT: H 114 TYR cc_start: 0.9496 (m-80) cc_final: 0.8584 (m-10) REVERT: L 91 TYR cc_start: 0.9333 (p90) cc_final: 0.8831 (p90) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3089 time to fit residues: 37.3789 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 : 0.483 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.041892 restraints weight = 48503.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.044797 restraints weight = 20320.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046808 restraints weight = 10906.864| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3444 Z= 0.245 Angle : 0.644 7.920 4685 Z= 0.336 Chirality : 0.046 0.319 507 Planarity : 0.003 0.041 607 Dihedral : 6.003 36.887 512 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.48 % Allowed : 15.95 % Favored : 83.57 % 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: -2.77 (0.40), residues: 420 helix: -3.92 (0.70), residues: 26 sheet: -0.49 (0.48), residues: 142 loop : -2.56 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE A 377 TYR 0.016 0.002 TYR H 53 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 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.503 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: 0.7361 (m-30) cc_final: 0.6967 (m-30) REVERT: A 405 ASP cc_start: 0.8722 (t70) cc_final: 0.8361 (t0) REVERT: A 442 ASP cc_start: 0.8989 (m-30) cc_final: 0.8611 (m-30) REVERT: H 34 MET cc_start: 0.8217 (pmm) cc_final: 0.7916 (pmm) REVERT: H 73 ASP cc_start: 0.8300 (t0) cc_final: 0.7962 (t0) REVERT: H 77 ASN cc_start: 0.9648 (p0) cc_final: 0.9435 (p0) REVERT: H 114 TYR cc_start: 0.9506 (m-80) cc_final: 0.8559 (m-10) REVERT: L 49 TYR cc_start: 0.9509 (p90) cc_final: 0.9232 (p90) REVERT: L 91 TYR cc_start: 0.9336 (p90) cc_final: 0.8867 (p90) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3195 time to fit residues: 38.7541 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 : 0.557 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042936 restraints weight = 46160.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045877 restraints weight = 19511.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047979 restraints weight = 10566.521| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3444 Z= 0.205 Angle : 0.635 7.606 4685 Z= 0.328 Chirality : 0.048 0.319 507 Planarity : 0.003 0.041 607 Dihedral : 5.736 34.209 512 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 15.24 % Favored : 84.29 % 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: -2.84 (0.40), residues: 420 helix: -3.94 (0.67), residues: 26 sheet: -0.74 (0.48), residues: 146 loop : -2.48 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE L 62 TYR 0.016 0.001 TYR H 53 ARG 0.002 0.000 ARG H 67 ********************** 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 102 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.547 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: A 398 ASP cc_start: 0.7399 (m-30) cc_final: 0.6981 (m-30) REVERT: A 405 ASP cc_start: 0.8724 (t70) cc_final: 0.8340 (t0) REVERT: A 442 ASP cc_start: 0.8875 (m-30) cc_final: 0.8479 (m-30) REVERT: H 4 LEU cc_start: 0.9017 (tp) cc_final: 0.8812 (tp) REVERT: H 34 MET cc_start: 0.8148 (pmm) cc_final: 0.7886 (pmm) REVERT: H 46 GLU cc_start: 0.9130 (pm20) cc_final: 0.8868 (pm20) REVERT: H 77 ASN cc_start: 0.9648 (p0) cc_final: 0.9404 (p0) REVERT: H 83 MET cc_start: 0.9138 (mmp) cc_final: 0.8914 (mmm) REVERT: H 108 MET cc_start: 0.9115 (mtm) cc_final: 0.8852 (mtm) REVERT: H 114 TYR cc_start: 0.9474 (m-80) cc_final: 0.9141 (m-80) REVERT: L 49 TYR cc_start: 0.9530 (p90) cc_final: 0.9255 (p90) REVERT: L 75 ILE cc_start: 0.9607 (mp) cc_final: 0.9382 (mp) REVERT: L 91 TYR cc_start: 0.9265 (p90) cc_final: 0.8639 (p90) REVERT: L 97 THR cc_start: 0.8460 (t) cc_final: 0.8225 (t) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3125 time to fit residues: 38.9723 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 : 0.545 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.053287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.042729 restraints weight = 48877.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045670 restraints weight = 20576.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047726 restraints weight = 11056.495| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4873 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= 0.200 Angle : 0.626 8.272 4685 Z= 0.325 Chirality : 0.046 0.322 507 Planarity : 0.003 0.042 607 Dihedral : 5.553 31.264 512 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 15.95 % Favored : 83.57 % 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: -2.78 (0.40), residues: 420 helix: -4.00 (0.65), residues: 26 sheet: -0.55 (0.48), residues: 140 loop : -2.50 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.005 0.002 HIS H 35 PHE 0.012 0.001 PHE H 112 TYR 0.015 0.001 TYR H 53 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: 2942.22 seconds wall clock time: 50 minutes 59.20 seconds (3059.20 seconds total)