Starting phenix.real_space_refine on Sun Mar 10 19:48:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oot_17028/03_2024/8oot_17028_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oot_17028/03_2024/8oot_17028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oot_17028/03_2024/8oot_17028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oot_17028/03_2024/8oot_17028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oot_17028/03_2024/8oot_17028_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oot_17028/03_2024/8oot_17028_updated.pdb" } resolution = 2.85 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= 0.009 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 Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4479 Number of models: 1 Model: "" Number of chains: 2 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: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3606 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 447, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 418, None: 2} Not linked: pdbres="ALA J 767 " pdbres="ATP J 801 " Not linked: pdbres="ATP J 801 " pdbres=" MG J 802 " Chain breaks: 3 Time building chain proxies: 3.15, per 1000 atoms: 0.70 Number of scatterers: 4479 At special positions: 0 Unit cell: (87.954, 87.132, 84.666, 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 - 3.50 Amino acid : False - 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: 1.67 Conformation dependent library (CDL) restraints added in 808.8 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... running ksdssp... Secondary structure from input PDB file: 28 helices and 4 sheets defined 37.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'I' and resid 8 through 20 Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 44 through 51 removed outlier: 3.705A pdb=" N SER I 51 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 199 Processing helix chain 'I' and resid 204 through 211 Processing helix chain 'J' and resid 18 through 21 No H-bonds generated for 'chain 'J' and resid 18 through 21' Processing helix chain 'J' and resid 43 through 51 Processing helix chain 'J' and resid 129 through 142 Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 225 through 227 No H-bonds generated for 'chain 'J' and resid 225 through 227' Processing helix chain 'J' and resid 235 through 249 Processing helix chain 'J' and resid 260 through 270 removed outlier: 3.715A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 Processing helix chain 'J' and resid 290 through 293 No H-bonds generated for 'chain 'J' and resid 290 through 293' Processing helix chain 'J' and resid 604 through 606 No H-bonds generated for 'chain 'J' and resid 604 through 606' Processing helix chain 'J' and resid 608 through 614 Processing helix chain 'J' and resid 633 through 638 removed outlier: 3.859A pdb=" N ARG J 638 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing helix chain 'J' and resid 646 through 650 Processing helix chain 'J' and resid 657 through 666 Processing helix chain 'J' and resid 668 through 671 No H-bonds generated for 'chain 'J' and resid 668 through 671' Processing helix chain 'J' and resid 680 through 685 removed outlier: 4.454A pdb=" N ASP J 685 " --> pdb=" O ALA J 681 " (cutoff:3.500A) Processing helix chain 'J' and resid 691 through 693 No H-bonds generated for 'chain 'J' and resid 691 through 693' Processing helix chain 'J' and resid 698 through 709 removed outlier: 3.834A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 735 removed outlier: 3.525A pdb=" N GLY J 731 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 744 Processing helix chain 'J' and resid 748 through 754 Processing sheet with id= A, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.612A pdb=" N ILE J 296 " --> pdb=" O TYR J 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 185 through 189 removed outlier: 6.887A pdb=" N ILE J 156 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLY J 188 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET J 158 " --> pdb=" O GLY J 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE J 59 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR J 159 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE J 61 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 115 through 117 removed outlier: 3.937A pdb=" N LYS J 96 " --> pdb=" O ASP J 91 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 213 through 218 128 hydrogen bonds defined for protein. 351 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: 1.10 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1486 1.34 - 1.46: 822 1.46 - 1.58: 2247 1.58 - 1.69: 5 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 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" N ASN J 232 " pdb=" CA ASN J 232 " ideal model delta sigma weight residual 1.461 1.473 -0.012 1.49e-02 4.50e+03 6.03e-01 bond pdb=" CB CYS J 105 " pdb=" SG CYS J 105 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.23e-01 bond pdb=" CB GLU J 635 " pdb=" CG GLU J 635 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.19e-01 bond pdb=" C GLN J 298 " pdb=" N TYR J 299 " ideal model delta sigma weight residual 1.331 1.312 0.019 2.83e-02 1.25e+03 4.31e-01 ... (remaining 4589 not shown) Histogram of bond angle deviations from ideal: 100.02 - 108.01: 253 108.01 - 115.99: 2764 115.99 - 123.98: 3054 123.98 - 131.97: 148 131.97 - 139.96: 14 Bond angle restraints: 6233 Sorted by residual: angle pdb=" N VAL J 634 " pdb=" CA VAL J 634 " pdb=" C VAL J 634 " ideal model delta sigma weight residual 110.62 113.19 -2.57 1.02e+00 9.61e-01 6.33e+00 angle pdb=" N ALA J 736 " pdb=" CA ALA J 736 " pdb=" C ALA J 736 " ideal model delta sigma weight residual 111.37 115.31 -3.94 1.65e+00 3.67e-01 5.69e+00 angle pdb=" N ARG J 221 " pdb=" CA ARG J 221 " pdb=" C ARG J 221 " ideal model delta sigma weight residual 110.80 115.68 -4.88 2.13e+00 2.20e-01 5.26e+00 angle pdb=" C TRP J 735 " pdb=" N ALA J 736 " pdb=" CA ALA J 736 " ideal model delta sigma weight residual 120.82 124.19 -3.37 1.50e+00 4.44e-01 5.05e+00 angle pdb=" C LEU J 290 " pdb=" N GLU J 291 " pdb=" CA GLU J 291 " ideal model delta sigma weight residual 120.38 123.38 -3.00 1.46e+00 4.69e-01 4.22e+00 ... (remaining 6228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2497 15.24 - 30.48: 197 30.48 - 45.71: 44 45.71 - 60.95: 23 60.95 - 76.19: 9 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 180.00 149.95 30.05 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA CYS J 105 " pdb=" C CYS J 105 " pdb=" N TYR J 106 " pdb=" CA TYR J 106 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP J 292 " pdb=" C ASP J 292 " pdb=" N ARG J 293 " pdb=" CA ARG J 293 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 2767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 404 0.037 - 0.075: 176 0.075 - 0.112: 58 0.112 - 0.149: 15 0.149 - 0.186: 1 Chirality restraints: 654 Sorted by residual: 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 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CA ARG J 221 " pdb=" N ARG J 221 " pdb=" C ARG J 221 " pdb=" CB ARG J 221 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 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 2.51 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 651 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 720 " -0.213 9.50e-02 1.11e+02 9.61e-02 7.07e+00 pdb=" NE ARG J 720 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG J 720 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG J 720 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 720 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 293 " -0.168 9.50e-02 1.11e+02 7.58e-02 4.73e+00 pdb=" NE ARG J 293 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG J 293 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG J 293 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 293 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 284 " -0.003 2.00e-02 2.50e+03 1.52e-02 4.65e+00 pdb=" CG TYR J 284 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR J 284 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR J 284 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR J 284 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR J 284 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR J 284 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR J 284 " -0.023 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 7 2.37 - 3.01: 2451 3.01 - 3.64: 6708 3.64 - 4.27: 10714 4.27 - 4.90: 17569 Nonbonded interactions: 37449 Sorted by model distance: nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 1.743 2.170 nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 1.886 2.170 nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.170 2.170 nonbonded pdb=" OD1 ASP I 171 " pdb=" NH1 ARG I 212 " model vdw 2.223 2.520 nonbonded pdb=" OE1 GLN J 42 " pdb=" NH1 ARG J 79 " model vdw 2.291 2.520 ... (remaining 37444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.120 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: 0.000 Extract box with map and model: 9.320 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.980 Find NCS groups from input model: 0.120 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:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4594 Z= 0.211 Angle : 0.645 4.958 6233 Z= 0.375 Chirality : 0.046 0.186 654 Planarity : 0.009 0.096 811 Dihedral : 13.623 76.185 1734 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.61 (0.34), residues: 544 helix: -0.91 (0.33), residues: 196 sheet: 0.52 (0.72), residues: 51 loop : -0.07 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 129 HIS 0.003 0.001 HIS I 189 PHE 0.015 0.002 PHE J 687 TYR 0.023 0.004 TYR J 284 ARG 0.021 0.003 ARG J 720 *********************** 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 84 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 16 LEU cc_start: 0.9200 (tp) cc_final: 0.8956 (tp) REVERT: I 191 LYS cc_start: 0.8519 (ptmm) cc_final: 0.8296 (tptt) REVERT: J 106 TYR cc_start: 0.7549 (m-80) cc_final: 0.7131 (m-80) REVERT: J 238 MET cc_start: 0.8849 (mtt) cc_final: 0.8515 (mtm) REVERT: J 707 MET cc_start: 0.9280 (ttp) cc_final: 0.9079 (ttp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 1.8093 time to fit residues: 156.0520 Evaluate side-chains 55 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 8.9990 chunk 40 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.0070 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 42 GLN J 63 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 HIS ** J 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 692 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4594 Z= 0.179 Angle : 0.571 5.164 6233 Z= 0.302 Chirality : 0.042 0.127 654 Planarity : 0.004 0.043 811 Dihedral : 8.579 71.539 649 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.36 % Allowed : 8.99 % Favored : 88.65 % 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: 0.62 (0.35), residues: 544 helix: 0.66 (0.37), residues: 200 sheet: 0.35 (0.64), residues: 59 loop : 0.41 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 129 HIS 0.003 0.001 HIS J 610 PHE 0.010 0.001 PHE J 612 TYR 0.011 0.001 TYR J 210 ARG 0.007 0.001 ARG J 279 *********************** 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 71 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 14 GLN cc_start: 0.8660 (tm-30) cc_final: 0.7936 (tp-100) REVERT: I 167 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8044 (mtpp) REVERT: J 94 MET cc_start: 0.7874 (mtm) cc_final: 0.7674 (ttp) REVERT: J 106 TYR cc_start: 0.7372 (m-80) cc_final: 0.7080 (m-80) outliers start: 11 outliers final: 2 residues processed: 63 average time/residue: 1.6124 time to fit residues: 104.7688 Evaluate side-chains 56 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 73 ASN ** J 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2595 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= 0.163 Angle : 0.518 5.819 6233 Z= 0.269 Chirality : 0.041 0.125 654 Planarity : 0.004 0.041 811 Dihedral : 7.358 68.986 649 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.93 % Allowed : 10.06 % Favored : 88.01 % 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: 0.81 (0.35), residues: 544 helix: 0.82 (0.36), residues: 200 sheet: 0.51 (0.66), residues: 53 loop : 0.51 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.003 0.001 HIS J 610 PHE 0.008 0.001 PHE J 612 TYR 0.011 0.001 TYR J 251 ARG 0.007 0.000 ARG J 116 *********************** 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 65 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: I 167 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8055 (mtpp) REVERT: J 154 MET cc_start: 0.8946 (tpp) cc_final: 0.8384 (mtm) outliers start: 9 outliers final: 2 residues processed: 60 average time/residue: 1.5795 time to fit residues: 97.7950 Evaluate side-chains 54 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4594 Z= 0.253 Angle : 0.552 8.487 6233 Z= 0.289 Chirality : 0.042 0.126 654 Planarity : 0.005 0.044 811 Dihedral : 7.372 70.154 649 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.64 % Allowed : 10.71 % Favored : 85.65 % 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 (0.35), residues: 544 helix: 0.73 (0.35), residues: 205 sheet: 0.18 (0.61), residues: 67 loop : 0.37 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.003 0.001 HIS I 189 PHE 0.009 0.001 PHE J 612 TYR 0.011 0.001 TYR J 180 ARG 0.009 0.001 ARG J 748 *********************** 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 70 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8615 (mp) REVERT: I 167 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8079 (mtpp) REVERT: J 94 MET cc_start: 0.8779 (ttp) cc_final: 0.8422 (mtp) REVERT: J 154 MET cc_start: 0.8962 (tpp) cc_final: 0.8438 (mtm) outliers start: 17 outliers final: 6 residues processed: 60 average time/residue: 1.5318 time to fit residues: 94.8935 Evaluate side-chains 59 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 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 ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4594 Z= 0.207 Angle : 0.521 6.970 6233 Z= 0.270 Chirality : 0.042 0.131 654 Planarity : 0.004 0.037 811 Dihedral : 7.168 68.899 649 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 12.63 % Favored : 85.22 % 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: 0.70 (0.35), residues: 544 helix: 0.86 (0.36), residues: 200 sheet: 0.05 (0.60), residues: 67 loop : 0.44 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.002 0.001 HIS I 189 PHE 0.007 0.001 PHE J 612 TYR 0.010 0.001 TYR J 210 ARG 0.008 0.001 ARG J 748 *********************** 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 63 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8998 (mp) cc_final: 0.8624 (mp) REVERT: I 39 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7984 (mtt-85) REVERT: I 167 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8065 (mtpp) REVERT: J 154 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8465 (mtm) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 1.6589 time to fit residues: 95.7459 Evaluate side-chains 58 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0170 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4594 Z= 0.183 Angle : 0.524 7.716 6233 Z= 0.273 Chirality : 0.041 0.122 654 Planarity : 0.004 0.034 811 Dihedral : 6.936 68.051 649 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.36 % Allowed : 13.28 % Favored : 84.37 % 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: 0.67 (0.36), residues: 544 helix: 0.89 (0.36), residues: 200 sheet: -0.03 (0.60), residues: 67 loop : 0.40 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 PHE 0.007 0.001 PHE J 35 TYR 0.010 0.001 TYR J 251 ARG 0.008 0.001 ARG J 279 *********************** 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 67 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8630 (mp) REVERT: I 167 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8049 (mtpp) REVERT: J 154 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8490 (mtm) outliers start: 11 outliers final: 2 residues processed: 59 average time/residue: 1.5918 time to fit residues: 96.8935 Evaluate side-chains 57 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3290 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= 0.223 Angle : 0.536 7.581 6233 Z= 0.275 Chirality : 0.042 0.127 654 Planarity : 0.004 0.032 811 Dihedral : 6.962 68.762 649 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.58 % 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: 0.59 (0.35), residues: 544 helix: 0.83 (0.36), residues: 205 sheet: 0.34 (0.64), residues: 61 loop : 0.21 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.002 0.001 HIS I 189 PHE 0.007 0.001 PHE J 612 TYR 0.009 0.001 TYR I 188 ARG 0.008 0.001 ARG J 279 *********************** 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 60 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8616 (mp) REVERT: I 167 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8053 (mtpp) REVERT: J 154 MET cc_start: 0.8940 (tpp) cc_final: 0.8500 (mtm) outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 1.6992 time to fit residues: 98.1602 Evaluate side-chains 56 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3394 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= 0.205 Angle : 0.555 9.101 6233 Z= 0.287 Chirality : 0.041 0.123 654 Planarity : 0.004 0.032 811 Dihedral : 6.869 67.673 649 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.50 % Allowed : 14.13 % Favored : 84.37 % 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: 0.67 (0.36), residues: 544 helix: 0.89 (0.36), residues: 200 sheet: 0.34 (0.64), residues: 61 loop : 0.28 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 PHE 0.008 0.001 PHE J 695 TYR 0.009 0.001 TYR I 188 ARG 0.009 0.001 ARG J 279 *********************** 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 59 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8981 (mp) cc_final: 0.8616 (mp) REVERT: I 167 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8041 (mtpp) REVERT: J 154 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8721 (mmm) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 1.8046 time to fit residues: 100.3156 Evaluate side-chains 56 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.0270 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3495 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= 0.188 Angle : 0.540 8.209 6233 Z= 0.277 Chirality : 0.041 0.124 654 Planarity : 0.004 0.033 811 Dihedral : 6.705 67.677 649 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.86 % Allowed : 14.78 % Favored : 84.37 % 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: 0.72 (0.36), residues: 544 helix: 0.96 (0.37), residues: 201 sheet: 0.34 (0.64), residues: 61 loop : 0.30 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 PHE 0.008 0.001 PHE J 695 TYR 0.009 0.001 TYR J 210 ARG 0.010 0.001 ARG J 279 *********************** 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 60 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8976 (mp) cc_final: 0.8576 (mp) REVERT: I 167 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8029 (mtpp) REVERT: I 206 GLU cc_start: 0.8133 (pm20) cc_final: 0.7374 (tp30) REVERT: J 154 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8496 (mtm) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 1.7854 time to fit residues: 104.7082 Evaluate side-chains 55 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 13 optimal weight: 0.0050 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4594 Z= 0.179 Angle : 0.555 8.082 6233 Z= 0.288 Chirality : 0.040 0.123 654 Planarity : 0.004 0.039 811 Dihedral : 6.550 68.108 649 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.71 % Allowed : 13.92 % Favored : 84.37 % 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: 0.69 (0.36), residues: 544 helix: 0.88 (0.36), residues: 204 sheet: 0.28 (0.64), residues: 61 loop : 0.33 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 PHE 0.008 0.001 PHE J 695 TYR 0.009 0.001 TYR J 210 ARG 0.011 0.001 ARG J 279 ********************** 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 64 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8963 (mp) cc_final: 0.8559 (mp) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 1.5523 time to fit residues: 94.4728 Evaluate side-chains 56 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 707 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.058566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.047406 restraints weight = 13169.619| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.77 r_work: 0.2740 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4594 Z= 0.199 Angle : 0.559 8.077 6233 Z= 0.289 Chirality : 0.041 0.171 654 Planarity : 0.004 0.042 811 Dihedral : 6.629 67.392 649 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.86 % Allowed : 15.20 % Favored : 83.94 % 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: 0.59 (0.36), residues: 544 helix: 0.72 (0.36), residues: 213 sheet: 0.42 (0.65), residues: 60 loop : 0.28 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 PHE 0.007 0.001 PHE J 695 TYR 0.009 0.001 TYR J 250 ARG 0.011 0.001 ARG J 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.70 seconds wall clock time: 44 minutes 25.48 seconds (2665.48 seconds total)