Starting phenix.real_space_refine on Thu Mar 6 02:54:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oof_17012/03_2025/8oof_17012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oof_17012/03_2025/8oof_17012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oof_17012/03_2025/8oof_17012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oof_17012/03_2025/8oof_17012.map" model { file = "/net/cci-nas-00/data/ceres_data/8oof_17012/03_2025/8oof_17012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oof_17012/03_2025/8oof_17012.cif" } resolution = 2.9 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= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 2837 2.51 5 N 799 2.21 5 O 819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 4479 Number of models: 1 Model: "" Number of chains: 3 Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3574 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 418} Chain breaks: 3 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.85, per 1000 atoms: 0.86 Number of scatterers: 4479 At special positions: 0 Unit cell: (89.598, 87.132, 85.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 3 15.00 Mg 1 11.99 O 819 8.00 N 799 7.00 C 2837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 511.1 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 41.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'I' and resid 7 through 21 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 203 through 211 removed outlier: 3.931A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.743A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 228 Processing helix chain 'J' and resid 234 through 250 Processing helix chain 'J' and resid 259 through 271 Processing helix chain 'J' and resid 276 through 283 removed outlier: 4.193A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 Processing helix chain 'J' and resid 603 through 606 Processing helix chain 'J' and resid 607 through 615 removed outlier: 3.597A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 639 Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 650 Processing helix chain 'J' and resid 656 through 667 Processing helix chain 'J' and resid 679 through 684 Processing helix chain 'J' and resid 690 through 694 Processing helix chain 'J' and resid 697 through 708 removed outlier: 3.648A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 Processing helix chain 'J' and resid 738 through 743 Processing helix chain 'J' and resid 748 through 755 removed outlier: 3.610A pdb=" N GLU J 753 " --> pdb=" O GLU J 749 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.791A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AA3, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.598A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'J' and resid 222 through 223 Processing sheet with id=AA6, first strand: chain 'J' and resid 222 through 223 removed outlier: 6.269A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1484 1.34 - 1.46: 727 1.46 - 1.57: 2346 1.57 - 1.69: 3 1.69 - 1.81: 34 Bond restraints: 4594 Sorted by residual: bond pdb=" CB THR J 689 " pdb=" CG2 THR J 689 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB LEU J 683 " pdb=" CG LEU J 683 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" N ALA I 160 " pdb=" CA ALA I 160 " ideal model delta sigma weight residual 1.455 1.477 -0.022 2.40e-02 1.74e+03 8.12e-01 bond pdb=" CG ARG J 636 " pdb=" CD ARG J 636 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.03e-01 bond pdb=" O3B ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 1.592 1.566 0.026 3.00e-02 1.11e+03 7.49e-01 ... (remaining 4589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5833 1.35 - 2.70: 339 2.70 - 4.05: 49 4.05 - 5.39: 10 5.39 - 6.74: 2 Bond angle restraints: 6233 Sorted by residual: angle pdb=" CA GLU J 17 " pdb=" C GLU J 17 " pdb=" N PRO J 18 " ideal model delta sigma weight residual 116.90 121.49 -4.59 1.50e+00 4.44e-01 9.35e+00 angle pdb=" N THR J 627 " pdb=" CA THR J 627 " pdb=" C THR J 627 " ideal model delta sigma weight residual 110.19 107.25 2.94 1.24e+00 6.50e-01 5.61e+00 angle pdb=" N VAL J 634 " pdb=" CA VAL J 634 " pdb=" C VAL J 634 " ideal model delta sigma weight residual 111.05 113.96 -2.91 1.25e+00 6.40e-01 5.41e+00 angle pdb=" N ALA I 160 " pdb=" CA ALA I 160 " pdb=" C ALA I 160 " ideal model delta sigma weight residual 107.37 114.11 -6.74 2.96e+00 1.14e-01 5.19e+00 angle pdb=" CA ARG J 295 " pdb=" CB ARG J 295 " pdb=" CG ARG J 295 " ideal model delta sigma weight residual 114.10 109.68 4.42 2.00e+00 2.50e-01 4.88e+00 ... (remaining 6228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 2518 16.44 - 32.88: 187 32.88 - 49.32: 51 49.32 - 65.76: 8 65.76 - 82.20: 6 Dihedral angle restraints: 2770 sinusoidal: 1160 harmonic: 1610 Sorted by residual: dihedral pdb=" CA GLU J 626 " pdb=" C GLU J 626 " pdb=" N THR J 627 " pdb=" CA THR J 627 " ideal model delta harmonic sigma weight residual 180.00 150.59 29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASP J 104 " pdb=" C ASP J 104 " pdb=" N CYS J 105 " pdb=" CA CYS J 105 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ARG J 90 " pdb=" C ARG J 90 " pdb=" N ASP J 91 " pdb=" CA ASP J 91 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 2767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 417 0.041 - 0.083: 170 0.083 - 0.124: 62 0.124 - 0.165: 2 0.165 - 0.206: 3 Chirality restraints: 654 Sorted by residual: chirality pdb=" CB ILE J 39 " pdb=" CA ILE J 39 " pdb=" CG1 ILE J 39 " pdb=" CG2 ILE J 39 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU J 635 " pdb=" N GLU J 635 " pdb=" C GLU J 635 " pdb=" CB GLU J 635 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ARG I 185 " pdb=" N ARG I 185 " pdb=" C ARG I 185 " pdb=" CB ARG I 185 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 651 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 293 " -0.210 9.50e-02 1.11e+02 9.48e-02 6.86e+00 pdb=" NE ARG J 293 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG J 293 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG J 293 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 293 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 284 " -0.007 2.00e-02 2.50e+03 1.46e-02 4.28e+00 pdb=" CG TYR J 284 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR J 284 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR J 284 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 284 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR J 284 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 284 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR J 284 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 636 " 0.165 9.50e-02 1.11e+02 7.45e-02 4.03e+00 pdb=" NE ARG J 636 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG J 636 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG J 636 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG J 636 " 0.001 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 35 2.61 - 3.19: 3966 3.19 - 3.76: 6776 3.76 - 4.33: 10095 4.33 - 4.90: 16176 Nonbonded interactions: 37048 Sorted by model distance: nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 2.087 2.170 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 2.096 2.170 nonbonded pdb=" OE2 GLU J 264 " pdb=" NH2 ARG J 268 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS I 42 " pdb=" OE1 GLU I 50 " model vdw 2.305 3.120 ... (remaining 37043 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 individual isotropic 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: 2.660 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.150 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.004 0.043 4594 Z= 0.273 Angle : 0.706 6.743 6233 Z= 0.407 Chirality : 0.049 0.206 654 Planarity : 0.009 0.095 811 Dihedral : 13.651 82.195 1734 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.80 (0.34), residues: 544 helix: -1.27 (0.33), residues: 197 sheet: 0.92 (0.80), residues: 46 loop : -0.10 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 735 HIS 0.008 0.002 HIS J 197 PHE 0.019 0.002 PHE J 612 TYR 0.023 0.004 TYR J 284 ARG 0.021 0.003 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.8993 (mt) cc_final: 0.8675 (mt) REVERT: I 191 LYS cc_start: 0.8398 (pttt) cc_final: 0.7010 (mmtt) REVERT: J 677 ASP cc_start: 0.7923 (t0) cc_final: 0.7552 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.5301 time to fit residues: 155.8350 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 52 GLN J 628 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073511 restraints weight = 7429.634| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.79 r_work: 0.3000 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4594 Z= 0.263 Angle : 0.614 5.786 6233 Z= 0.327 Chirality : 0.045 0.147 654 Planarity : 0.005 0.045 811 Dihedral : 8.112 81.955 649 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.14 % Allowed : 11.56 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.28 (0.35), residues: 544 helix: 0.01 (0.34), residues: 217 sheet: 0.73 (0.82), residues: 46 loop : 0.44 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 129 HIS 0.004 0.001 HIS I 189 PHE 0.014 0.002 PHE J 612 TYR 0.014 0.002 TYR J 180 ARG 0.005 0.001 ARG J 748 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.506 Fit side-chains REVERT: I 48 LEU cc_start: 0.9130 (mt) cc_final: 0.8872 (mt) REVERT: I 158 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6475 (mt-10) REVERT: I 191 LYS cc_start: 0.8333 (pttt) cc_final: 0.6915 (mmtt) REVERT: J 242 MET cc_start: 0.8761 (tpp) cc_final: 0.8547 (tpp) REVERT: J 635 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: J 677 ASP cc_start: 0.8105 (t0) cc_final: 0.7893 (t0) outliers start: 10 outliers final: 2 residues processed: 80 average time/residue: 1.6006 time to fit residues: 131.8616 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.070601 restraints weight = 7635.577| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.77 r_work: 0.2938 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4594 Z= 0.324 Angle : 0.617 6.336 6233 Z= 0.327 Chirality : 0.046 0.140 654 Planarity : 0.005 0.049 811 Dihedral : 7.980 80.765 649 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.00 % Allowed : 12.21 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.24 (0.35), residues: 544 helix: 0.18 (0.35), residues: 217 sheet: -0.03 (0.77), residues: 45 loop : 0.36 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 287 HIS 0.004 0.001 HIS I 189 PHE 0.016 0.002 PHE J 612 TYR 0.015 0.002 TYR J 180 ARG 0.003 0.000 ARG J 602 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9130 (mt) cc_final: 0.8854 (mt) REVERT: I 191 LYS cc_start: 0.8354 (pttt) cc_final: 0.6945 (mmtt) REVERT: J 174 GLU cc_start: 0.7686 (tt0) cc_final: 0.7485 (tt0) REVERT: J 626 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8248 (mt-10) outliers start: 14 outliers final: 5 residues processed: 72 average time/residue: 1.4591 time to fit residues: 108.4985 Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 12 optimal weight: 0.0070 chunk 40 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 128 ASN J 259 ASN J 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072892 restraints weight = 7679.182| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.84 r_work: 0.2980 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4594 Z= 0.171 Angle : 0.531 5.578 6233 Z= 0.280 Chirality : 0.042 0.134 654 Planarity : 0.004 0.044 811 Dihedral : 7.309 84.121 649 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.57 % Allowed : 13.28 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.58 (0.36), residues: 544 helix: 0.61 (0.35), residues: 223 sheet: -0.13 (0.76), residues: 45 loop : 0.47 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.005 0.001 HIS J 628 PHE 0.008 0.001 PHE J 193 TYR 0.013 0.001 TYR J 167 ARG 0.001 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9068 (mt) cc_final: 0.8790 (mt) REVERT: I 191 LYS cc_start: 0.8293 (pttt) cc_final: 0.6877 (mmtt) REVERT: J 174 GLU cc_start: 0.7763 (tt0) cc_final: 0.7556 (tt0) outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 1.3813 time to fit residues: 98.6934 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 237 HIS J 633 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070884 restraints weight = 7804.752| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.78 r_work: 0.2944 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4594 Z= 0.303 Angle : 0.594 5.921 6233 Z= 0.311 Chirality : 0.044 0.132 654 Planarity : 0.005 0.047 811 Dihedral : 7.665 81.234 649 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.78 % Allowed : 14.35 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.41 (0.36), residues: 544 helix: 0.50 (0.35), residues: 223 sheet: -0.29 (0.73), residues: 45 loop : 0.36 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 287 HIS 0.004 0.001 HIS I 189 PHE 0.014 0.002 PHE J 612 TYR 0.010 0.001 TYR J 180 ARG 0.002 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9115 (mt) cc_final: 0.8858 (mt) REVERT: I 191 LYS cc_start: 0.8333 (pttt) cc_final: 0.6983 (mmtt) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 1.4309 time to fit residues: 97.6912 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073208 restraints weight = 7672.871| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.81 r_work: 0.2987 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4594 Z= 0.211 Angle : 0.539 5.728 6233 Z= 0.284 Chirality : 0.043 0.140 654 Planarity : 0.004 0.043 811 Dihedral : 7.316 84.595 649 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.00 % Allowed : 15.20 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.55 (0.36), residues: 544 helix: 0.67 (0.36), residues: 223 sheet: -0.34 (0.73), residues: 45 loop : 0.41 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.010 0.001 PHE J 612 TYR 0.008 0.001 TYR J 180 ARG 0.002 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9068 (mt) cc_final: 0.8792 (mt) REVERT: I 167 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7809 (mmmm) REVERT: I 191 LYS cc_start: 0.8324 (pttt) cc_final: 0.6954 (mmtt) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 1.3624 time to fit residues: 96.0643 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072695 restraints weight = 7671.484| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.82 r_work: 0.2975 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4594 Z= 0.239 Angle : 0.564 5.985 6233 Z= 0.296 Chirality : 0.043 0.130 654 Planarity : 0.004 0.043 811 Dihedral : 7.345 83.850 649 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.78 % Allowed : 15.63 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.52 (0.36), residues: 544 helix: 0.68 (0.36), residues: 223 sheet: -0.38 (0.73), residues: 45 loop : 0.36 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 287 HIS 0.003 0.001 HIS J 628 PHE 0.012 0.001 PHE J 612 TYR 0.008 0.001 TYR J 106 ARG 0.002 0.000 ARG J 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9078 (mt) cc_final: 0.8809 (mt) REVERT: I 191 LYS cc_start: 0.8334 (pttt) cc_final: 0.6961 (mmtt) REVERT: I 206 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8171 (mm-30) outliers start: 13 outliers final: 9 residues processed: 65 average time/residue: 1.3807 time to fit residues: 92.9853 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.0370 chunk 18 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.073788 restraints weight = 7582.670| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.81 r_work: 0.2998 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4594 Z= 0.192 Angle : 0.534 6.545 6233 Z= 0.280 Chirality : 0.042 0.137 654 Planarity : 0.004 0.040 811 Dihedral : 7.106 85.647 649 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.57 % Allowed : 16.70 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.60 (0.37), residues: 544 helix: 0.80 (0.36), residues: 223 sheet: -0.31 (0.73), residues: 45 loop : 0.35 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.009 0.001 PHE J 612 TYR 0.022 0.001 TYR J 167 ARG 0.002 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9069 (mt) cc_final: 0.8792 (mt) REVERT: I 167 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7850 (mmmm) REVERT: I 191 LYS cc_start: 0.8320 (pttt) cc_final: 0.6952 (mmtt) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 1.4450 time to fit residues: 100.1663 Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.0970 chunk 53 optimal weight: 0.2980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.073899 restraints weight = 7633.233| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.81 r_work: 0.3004 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4594 Z= 0.193 Angle : 0.531 6.502 6233 Z= 0.278 Chirality : 0.042 0.130 654 Planarity : 0.004 0.040 811 Dihedral : 7.065 85.263 649 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.57 % Allowed : 17.13 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.63 (0.37), residues: 544 helix: 0.80 (0.36), residues: 223 sheet: -0.09 (0.74), residues: 45 loop : 0.35 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.008 0.001 PHE J 612 TYR 0.008 0.001 TYR J 167 ARG 0.002 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9102 (mt) cc_final: 0.8856 (mt) REVERT: I 167 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7866 (mmmm) REVERT: I 191 LYS cc_start: 0.8323 (pttt) cc_final: 0.6987 (mmtt) REVERT: J 48 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7582 (mtp180) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 1.3977 time to fit residues: 88.4347 Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.091277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074187 restraints weight = 7609.205| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.81 r_work: 0.3008 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4594 Z= 0.193 Angle : 0.544 9.046 6233 Z= 0.283 Chirality : 0.042 0.130 654 Planarity : 0.004 0.039 811 Dihedral : 7.022 85.551 649 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.14 % Allowed : 17.77 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.66 (0.37), residues: 544 helix: 0.82 (0.36), residues: 223 sheet: -0.11 (0.74), residues: 45 loop : 0.38 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.008 0.001 PHE J 612 TYR 0.008 0.001 TYR J 210 ARG 0.002 0.000 ARG J 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9095 (mt) cc_final: 0.8845 (mt) REVERT: I 167 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7865 (mmmm) REVERT: I 191 LYS cc_start: 0.8315 (pttt) cc_final: 0.6989 (mmtt) REVERT: J 48 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7572 (mtp180) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 1.3509 time to fit residues: 85.4516 Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072927 restraints weight = 7614.634| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.76 r_work: 0.2990 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4594 Z= 0.262 Angle : 0.587 11.031 6233 Z= 0.303 Chirality : 0.044 0.133 654 Planarity : 0.004 0.043 811 Dihedral : 7.297 83.644 649 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.57 % Allowed : 17.77 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.50 (0.37), residues: 544 helix: 0.65 (0.36), residues: 223 sheet: -0.13 (0.73), residues: 45 loop : 0.31 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 287 HIS 0.004 0.001 HIS I 189 PHE 0.013 0.001 PHE J 612 TYR 0.009 0.001 TYR J 210 ARG 0.002 0.000 ARG J 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4497.62 seconds wall clock time: 77 minutes 15.93 seconds (4635.93 seconds total)