Starting phenix.real_space_refine on Thu Mar 6 04:19:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x26_32959/03_2025/7x26_32959_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x26_32959/03_2025/7x26_32959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.685 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2025/7x26_32959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2025/7x26_32959.map" model { file = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2025/7x26_32959_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2025/7x26_32959_neut.cif" } resolution = 3.685 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= 0.001 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3040 2.51 5 N 803 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4828 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1594 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 191} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.51, per 1000 atoms: 0.93 Number of scatterers: 4828 At special positions: 0 Unit cell: (79.0225, 83.3525, 130.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 964 8.00 N 803 7.00 C 3040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS I 383 " - pdb=" SG CYS I 407 " distance=2.02 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS I 437 " - pdb=" SG CYS I 585 " distance=2.06 Simple disulfide: pdb=" SG CYS I 503 " - pdb=" SG CYS I 526 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 761.9 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 7.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 161 through 165 Processing helix chain 'I' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER I 390 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 399 Processing helix chain 'I' and resid 411 through 416 Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.705A pdb=" N SER I 435 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 453 removed outlier: 3.637A pdb=" N MET I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 528 removed outlier: 4.085A pdb=" N SER I 528 " --> pdb=" O PRO I 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.651A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.644A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'H' and resid 148 through 152 removed outlier: 4.636A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 152 " --> pdb=" O TYR H 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'I' and resid 400 through 404 removed outlier: 3.754A pdb=" N LYS I 400 " --> pdb=" O TYR I 445 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 445 " --> pdb=" O LYS I 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 408 through 409 Processing sheet with id=AA8, first strand: chain 'I' and resid 513 through 515 removed outlier: 3.699A pdb=" N TYR I 497 " --> pdb=" O VAL I 561 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER I 557 " --> pdb=" O ASN I 501 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 13 removed outlier: 5.677A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.795A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AB3, first strand: chain 'K' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 154 through 155 113 hydrogen bonds defined for protein. 233 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: 1.40 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1055 1.33 - 1.45: 1105 1.45 - 1.57: 2753 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4939 Sorted by residual: bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.362 -0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.234 1.358 -0.124 1.22e-02 6.72e+03 1.03e+02 bond pdb=" N VAL H 191 " pdb=" CA VAL H 191 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.58e+01 bond pdb=" N VAL K 192 " pdb=" CA VAL K 192 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.30e+01 bond pdb=" N ILE K 59 " pdb=" CA ILE K 59 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.20e+01 ... (remaining 4934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 6135 2.47 - 4.94: 563 4.94 - 7.41: 15 7.41 - 9.88: 9 9.88 - 12.34: 10 Bond angle restraints: 6732 Sorted by residual: angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.17 -11.79 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.13 -11.75 1.09e+00 8.42e-01 1.16e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA ASER H 160 " ideal model delta sigma weight residual 120.92 133.26 -12.34 1.15e+00 7.56e-01 1.15e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA BSER H 160 " ideal model delta sigma weight residual 120.92 133.26 -12.34 1.15e+00 7.56e-01 1.15e+02 angle pdb=" CA ASER H 160 " pdb=" C SER H 160 " pdb=" N TRP H 161 " ideal model delta sigma weight residual 115.86 104.32 11.54 1.24e+00 6.50e-01 8.66e+01 ... (remaining 6727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2626 16.15 - 32.30: 263 32.30 - 48.44: 69 48.44 - 64.59: 13 64.59 - 80.74: 9 Dihedral angle restraints: 2980 sinusoidal: 1121 harmonic: 1859 Sorted by residual: dihedral pdb=" CA GLU H 155 " pdb=" C GLU H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta harmonic sigma weight residual 0.00 40.97 -40.97 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CA ASN I 521 " pdb=" C ASN I 521 " pdb=" N GLN I 522 " pdb=" CA GLN I 522 " ideal model delta harmonic sigma weight residual 180.00 149.27 30.73 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA ASP K 61 " pdb=" C ASP K 61 " pdb=" N ARG K 62 " pdb=" CA ARG K 62 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 539 0.085 - 0.169: 186 0.169 - 0.254: 44 0.254 - 0.339: 2 0.339 - 0.423: 3 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA GLN H 199 " pdb=" N GLN H 199 " pdb=" C GLN H 199 " pdb=" CB GLN H 199 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA BSER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB BSER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ASER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB ASER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 771 not shown) Planarity restraints: 861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 91 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C GLN K 91 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN K 91 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR K 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 160 " -0.039 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" O SER H 160 " 0.016 2.00e-02 2.50e+03 pdb=" CA ASER H 160 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP H 161 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 160 " -0.039 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" O SER H 160 " 0.016 2.00e-02 2.50e+03 pdb=" CA BSER H 160 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP H 161 " 0.012 2.00e-02 2.50e+03 ... (remaining 858 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 334 2.73 - 3.27: 4653 3.27 - 3.81: 7236 3.81 - 4.36: 9557 4.36 - 4.90: 15675 Nonbonded interactions: 37455 Sorted by model distance: nonbonded pdb=" O ASN I 521 " pdb=" N TYR I 523 " model vdw 2.186 3.120 nonbonded pdb=" O ALA H 121 " pdb=" OG SER H 122 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN I 436 " pdb=" OH TYR I 438 " model vdw 2.268 3.040 nonbonded pdb=" O PRO I 463 " pdb=" ND2 ASN I 468 " model vdw 2.269 3.120 nonbonded pdb=" O LEU I 456 " pdb=" OG SER I 457 " model vdw 2.355 3.040 ... (remaining 37450 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.011 0.126 4939 Z= 0.764 Angle : 1.460 12.344 6732 Z= 1.021 Chirality : 0.087 0.423 774 Planarity : 0.005 0.048 861 Dihedral : 14.527 80.739 1768 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 2.68 % Allowed : 16.22 % Favored : 81.10 % Rotamer: Outliers : 9.27 % Allowed : 6.18 % Favored : 84.55 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.33 % Twisted Proline : 2.63 % Twisted General : 0.33 % 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: -3.21 (0.32), residues: 637 helix: -3.94 (0.94), residues: 12 sheet: -1.45 (0.34), residues: 249 loop : -2.65 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 36 HIS 0.004 0.001 HIS K 199 PHE 0.013 0.002 PHE I 467 TYR 0.031 0.002 TYR I 438 ARG 0.005 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7955 (m) REVERT: H 38 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8024 (ttm-80) REVERT: H 157 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8560 (p) REVERT: H 189 VAL cc_start: 0.5888 (OUTLIER) cc_final: 0.5675 (p) REVERT: I 438 TYR cc_start: 0.8187 (m-80) cc_final: 0.7809 (m-80) REVERT: I 502 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7376 (mttp) REVERT: K 13 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6634 (mt) REVERT: K 75 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.6908 (p) REVERT: K 97 TRP cc_start: 0.7650 (m-10) cc_final: 0.7191 (m-10) REVERT: K 136 LEU cc_start: 0.8169 (tp) cc_final: 0.7959 (tt) outliers start: 51 outliers final: 14 residues processed: 174 average time/residue: 0.1868 time to fit residues: 40.1154 Evaluate side-chains 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 GLN Chi-restraints excluded: chain K residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0070 chunk 36 optimal weight: 0.0000 chunk 57 optimal weight: 0.0980 overall best weight: 0.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS I 519 ASN I 582 ASN K 6 GLN K 90 GLN K 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.175608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157575 restraints weight = 13298.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161726 restraints weight = 8624.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.162486 restraints weight = 4183.030| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4939 Z= 0.202 Angle : 0.730 11.011 6732 Z= 0.376 Chirality : 0.047 0.243 774 Planarity : 0.005 0.037 861 Dihedral : 8.470 55.603 715 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.61 % Favored : 89.92 % Rotamer: Outliers : 5.82 % Allowed : 12.91 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.32), residues: 637 helix: -3.44 (0.95), residues: 18 sheet: -1.34 (0.32), residues: 265 loop : -2.32 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS H 207 PHE 0.014 0.001 PHE I 423 TYR 0.019 0.002 TYR I 445 ARG 0.007 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 157 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (p) REVERT: K 13 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6280 (mt) REVERT: K 75 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6935 (p) REVERT: K 76 ILE cc_start: 0.7122 (mt) cc_final: 0.6768 (mt) outliers start: 32 outliers final: 15 residues processed: 113 average time/residue: 0.1880 time to fit residues: 26.4883 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 24 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS K 90 GLN K 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.165494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147776 restraints weight = 15043.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150772 restraints weight = 6985.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151643 restraints weight = 4557.040| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4939 Z= 0.189 Angle : 0.672 11.081 6732 Z= 0.343 Chirality : 0.045 0.223 774 Planarity : 0.004 0.034 861 Dihedral : 6.783 49.944 704 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.92 % Favored : 89.61 % Rotamer: Outliers : 4.91 % Allowed : 17.09 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.32), residues: 637 helix: -3.80 (0.78), residues: 24 sheet: -0.67 (0.35), residues: 238 loop : -2.25 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 161 HIS 0.002 0.001 HIS H 207 PHE 0.013 0.001 PHE I 423 TYR 0.016 0.002 TYR H 183 ARG 0.007 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6392 (mt) REVERT: K 75 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6982 (p) REVERT: K 76 ILE cc_start: 0.6900 (mt) cc_final: 0.6595 (mt) REVERT: K 143 ARG cc_start: 0.6278 (mtp85) cc_final: 0.5749 (ttm-80) outliers start: 27 outliers final: 17 residues processed: 108 average time/residue: 0.1673 time to fit residues: 23.0240 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS H 206 ASN K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142961 restraints weight = 24070.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.147734 restraints weight = 12218.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.148362 restraints weight = 5621.988| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4939 Z= 0.235 Angle : 0.696 11.304 6732 Z= 0.356 Chirality : 0.047 0.230 774 Planarity : 0.005 0.039 861 Dihedral : 6.730 49.359 703 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.82 % Favored : 90.71 % Rotamer: Outliers : 4.73 % Allowed : 17.27 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.33), residues: 637 helix: -4.15 (0.81), residues: 18 sheet: -0.77 (0.33), residues: 262 loop : -2.00 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 97 HIS 0.001 0.001 HIS H 207 PHE 0.014 0.002 PHE I 423 TYR 0.023 0.002 TYR H 183 ARG 0.002 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 214 VAL cc_start: 0.8062 (t) cc_final: 0.7734 (m) REVERT: K 13 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6450 (mt) REVERT: K 75 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6855 (p) REVERT: K 76 ILE cc_start: 0.6864 (mt) cc_final: 0.6546 (mt) REVERT: K 124 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6558 (tm-30) REVERT: K 143 ARG cc_start: 0.6411 (mtp85) cc_final: 0.6003 (ttm-80) outliers start: 26 outliers final: 19 residues processed: 103 average time/residue: 0.1827 time to fit residues: 23.9299 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.159597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140817 restraints weight = 18702.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144970 restraints weight = 12045.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146503 restraints weight = 5182.033| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4939 Z= 0.298 Angle : 0.744 11.942 6732 Z= 0.377 Chirality : 0.048 0.253 774 Planarity : 0.005 0.042 861 Dihedral : 6.918 49.737 703 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.02 % Favored : 88.50 % Rotamer: Outliers : 5.64 % Allowed : 18.18 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.32), residues: 637 helix: -4.34 (0.76), residues: 18 sheet: -0.76 (0.33), residues: 257 loop : -2.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 97 HIS 0.002 0.001 HIS H 207 PHE 0.017 0.002 PHE I 423 TYR 0.019 0.002 TYR H 183 ARG 0.005 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 171 HIS cc_start: 0.7602 (m170) cc_final: 0.7379 (m170) REVERT: K 13 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6860 (mt) REVERT: K 75 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6739 (p) REVERT: K 76 ILE cc_start: 0.6846 (mt) cc_final: 0.6478 (mt) REVERT: K 124 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6701 (tm-30) REVERT: K 143 ARG cc_start: 0.6659 (mtp85) cc_final: 0.6359 (ttm-80) outliers start: 31 outliers final: 23 residues processed: 101 average time/residue: 0.1948 time to fit residues: 24.9724 Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 422 ASP Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 47 optimal weight: 0.1980 chunk 1 optimal weight: 0.4980 chunk 37 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.165249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146643 restraints weight = 22521.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149871 restraints weight = 12474.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152503 restraints weight = 6252.419| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4939 Z= 0.161 Angle : 0.663 10.536 6732 Z= 0.331 Chirality : 0.044 0.211 774 Planarity : 0.004 0.035 861 Dihedral : 6.414 52.169 703 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.72 % Favored : 91.81 % Rotamer: Outliers : 3.82 % Allowed : 19.82 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.32), residues: 637 helix: -3.98 (0.66), residues: 30 sheet: -0.66 (0.32), residues: 261 loop : -2.11 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 97 HIS 0.001 0.000 HIS H 207 PHE 0.009 0.001 PHE I 423 TYR 0.013 0.002 TYR H 183 ARG 0.003 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 171 HIS cc_start: 0.7472 (m170) cc_final: 0.7242 (m170) REVERT: H 214 VAL cc_start: 0.8113 (t) cc_final: 0.7846 (m) REVERT: K 75 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6766 (p) REVERT: K 76 ILE cc_start: 0.6750 (mt) cc_final: 0.6489 (mt) REVERT: K 124 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6860 (tm-30) REVERT: K 136 LEU cc_start: 0.8299 (tp) cc_final: 0.8086 (tt) REVERT: K 143 ARG cc_start: 0.6425 (mtp85) cc_final: 0.6099 (ttm-80) outliers start: 21 outliers final: 16 residues processed: 94 average time/residue: 0.2069 time to fit residues: 25.3621 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS I 486 HIS ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143198 restraints weight = 20477.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146320 restraints weight = 10704.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147537 restraints weight = 6261.904| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4939 Z= 0.258 Angle : 0.702 11.323 6732 Z= 0.354 Chirality : 0.046 0.219 774 Planarity : 0.005 0.040 861 Dihedral : 6.334 50.096 700 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.92 % Favored : 89.61 % Rotamer: Outliers : 4.00 % Allowed : 20.18 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.32), residues: 637 helix: -4.35 (0.74), residues: 18 sheet: -0.61 (0.32), residues: 266 loop : -2.14 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 97 HIS 0.002 0.001 HIS I 486 PHE 0.014 0.002 PHE I 423 TYR 0.017 0.002 TYR H 183 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7635 (t80) REVERT: K 75 THR cc_start: 0.7063 (OUTLIER) cc_final: 0.6714 (p) REVERT: K 76 ILE cc_start: 0.6633 (mt) cc_final: 0.6327 (mt) REVERT: K 124 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6886 (tm-30) REVERT: K 143 ARG cc_start: 0.6637 (mtp85) cc_final: 0.6227 (ttm170) outliers start: 22 outliers final: 17 residues processed: 94 average time/residue: 0.2289 time to fit residues: 27.4506 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 422 ASP Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 29 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.163435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143719 restraints weight = 25701.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148319 restraints weight = 16201.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151689 restraints weight = 5246.376| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4939 Z= 0.190 Angle : 0.676 10.638 6732 Z= 0.336 Chirality : 0.045 0.214 774 Planarity : 0.004 0.037 861 Dihedral : 6.130 51.839 700 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.35 % Favored : 91.18 % Rotamer: Outliers : 4.00 % Allowed : 20.73 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.32), residues: 637 helix: -3.68 (0.82), residues: 24 sheet: -0.60 (0.32), residues: 269 loop : -2.09 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 97 HIS 0.001 0.000 HIS K 190 PHE 0.011 0.001 PHE I 423 TYR 0.014 0.002 TYR H 183 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 536 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7526 (mt-10) REVERT: K 75 THR cc_start: 0.7070 (OUTLIER) cc_final: 0.6726 (p) REVERT: K 76 ILE cc_start: 0.6430 (mt) cc_final: 0.6130 (mt) REVERT: K 143 ARG cc_start: 0.6690 (mtp85) cc_final: 0.6211 (ttm170) outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 0.2469 time to fit residues: 30.5842 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.0070 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 204 ASN H 211 ASN I 486 HIS ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146674 restraints weight = 19818.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149376 restraints weight = 9865.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150187 restraints weight = 6090.054| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4939 Z= 0.210 Angle : 0.685 10.786 6732 Z= 0.343 Chirality : 0.045 0.212 774 Planarity : 0.004 0.041 861 Dihedral : 6.103 52.287 700 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.76 % Favored : 89.76 % Rotamer: Outliers : 3.82 % Allowed : 21.09 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.33), residues: 637 helix: -3.68 (0.82), residues: 24 sheet: -0.59 (0.32), residues: 269 loop : -2.01 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 97 HIS 0.001 0.000 HIS K 199 PHE 0.013 0.001 PHE I 423 TYR 0.015 0.002 TYR H 183 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7814 (t80) REVERT: I 536 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7592 (mt-10) REVERT: K 75 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6660 (p) REVERT: K 76 ILE cc_start: 0.6466 (mt) cc_final: 0.6172 (mt) REVERT: K 143 ARG cc_start: 0.6785 (mtp85) cc_final: 0.6469 (ttm170) outliers start: 21 outliers final: 17 residues processed: 92 average time/residue: 0.2885 time to fit residues: 33.7892 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 60 optimal weight: 0.0000 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 0.0370 chunk 13 optimal weight: 0.0270 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.0000 overall best weight: 0.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN I 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.169194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149730 restraints weight = 25236.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154245 restraints weight = 16305.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157101 restraints weight = 5616.332| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4939 Z= 0.161 Angle : 0.658 9.765 6732 Z= 0.328 Chirality : 0.044 0.190 774 Planarity : 0.004 0.040 861 Dihedral : 5.819 53.165 700 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.09 % Favored : 92.44 % Rotamer: Outliers : 3.09 % Allowed : 21.82 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.33), residues: 637 helix: -3.68 (0.72), residues: 30 sheet: -0.35 (0.33), residues: 268 loop : -1.97 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 97 HIS 0.007 0.001 HIS I 486 PHE 0.009 0.001 PHE I 423 TYR 0.012 0.001 TYR I 523 ARG 0.002 0.000 ARG K 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7476 (t80) REVERT: H 119 SER cc_start: 0.7244 (m) cc_final: 0.6935 (p) REVERT: H 214 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7817 (m) REVERT: I 536 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7458 (mt-10) REVERT: K 75 THR cc_start: 0.7013 (OUTLIER) cc_final: 0.6674 (p) REVERT: K 108 LYS cc_start: 0.7565 (ptpt) cc_final: 0.7349 (ptpt) REVERT: K 143 ARG cc_start: 0.6538 (mtp85) cc_final: 0.6073 (ttm170) outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 0.2091 time to fit residues: 25.2235 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.0040 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN I 486 HIS ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.164878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146245 restraints weight = 23632.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149696 restraints weight = 12871.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151500 restraints weight = 6266.286| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4939 Z= 0.202 Angle : 0.666 10.423 6732 Z= 0.333 Chirality : 0.045 0.188 774 Planarity : 0.004 0.040 861 Dihedral : 5.792 52.165 699 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.50 % Favored : 91.02 % Rotamer: Outliers : 3.45 % Allowed : 21.82 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.33), residues: 637 helix: -3.70 (0.73), residues: 30 sheet: -0.46 (0.32), residues: 269 loop : -1.90 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 97 HIS 0.002 0.001 HIS I 486 PHE 0.012 0.001 PHE I 423 TYR 0.014 0.002 TYR H 183 ARG 0.004 0.000 ARG K 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2337.96 seconds wall clock time: 43 minutes 0.63 seconds (2580.63 seconds total)