Starting phenix.real_space_refine on Tue Feb 11 08:30:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x26_32959/02_2025/7x26_32959_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x26_32959/02_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_32959/02_2025/7x26_32959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x26_32959/02_2025/7x26_32959.map" model { file = "/net/cci-nas-00/data/ceres_data/7x26_32959/02_2025/7x26_32959_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x26_32959/02_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-5592/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: 4.28, per 1000 atoms: 0.89 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: 1.09 Conformation dependent library (CDL) restraints added in 862.4 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: 0.67 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: 1.30 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: 1.540 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.050 Find NCS groups from input model: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- 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 : 0.563 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: 0.1904 time to fit residues: 40.9045 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 : 0.520 ------------------------------------------------------------------------------- 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 = 0.175609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157576 restraints weight = 13298.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161716 restraints weight = 8590.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.162517 restraints weight = 4139.078| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 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 = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3999 ------------------------------------------------------------------------------- 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 55.602 715 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 : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 157 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (p) REVERT: K 13 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6280 (mt) REVERT: K 75 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6934 (p) REVERT: K 76 ILE cc_start: 0.7122 (mt) cc_final: 0.6767 (mt) outliers start: 32 outliers final: 15 residues processed: 113 average time/residue: 0.1968 time to fit residues: 27.9471 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 : 0.552 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** 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 = 0.3996 r_free = 0.3996 target = 0.162202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143999 restraints weight = 15111.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147882 restraints weight = 7321.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.148429 restraints weight = 4405.292| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3082 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= 0.246 Angle : 0.711 11.657 6732 Z= 0.364 Chirality : 0.047 0.234 774 Planarity : 0.005 0.034 861 Dihedral : 7.025 50.654 704 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.87 % Favored : 88.66 % Rotamer: Outliers : 5.09 % Allowed : 16.91 % 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: -2.50 (0.32), residues: 637 helix: -4.33 (0.73), residues: 18 sheet: -0.81 (0.35), residues: 244 loop : -2.19 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 161 HIS 0.003 0.001 HIS H 207 PHE 0.016 0.002 PHE I 423 TYR 0.020 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 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 157 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8649 (p) REVERT: H 214 VAL cc_start: 0.8038 (t) cc_final: 0.7780 (m) REVERT: K 13 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6420 (mt) REVERT: K 75 THR cc_start: 0.7273 (OUTLIER) cc_final: 0.6921 (p) REVERT: K 76 ILE cc_start: 0.6824 (mt) cc_final: 0.6443 (mt) REVERT: K 143 ARG cc_start: 0.6408 (mtp85) cc_final: 0.5856 (ttm-80) outliers start: 28 outliers final: 20 residues processed: 109 average time/residue: 0.1777 time to fit residues: 24.7589 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 62 GLN 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 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 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 90 GLN 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 197 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: 0.6980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144104 restraints weight = 23883.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.148728 restraints weight = 13646.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151749 restraints weight = 5334.174| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4939 Z= 0.174 Angle : 0.666 10.860 6732 Z= 0.338 Chirality : 0.045 0.228 774 Planarity : 0.004 0.037 861 Dihedral : 6.732 52.335 704 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.72 % Favored : 91.81 % Rotamer: Outliers : 4.55 % Allowed : 18.73 % Favored : 76.73 % 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: -2.46 (0.33), residues: 637 helix: -3.62 (0.81), residues: 24 sheet: -0.85 (0.34), residues: 254 loop : -2.12 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.001 0.000 HIS H 207 PHE 0.011 0.001 PHE I 423 TYR 0.014 0.002 TYR H 183 ARG 0.003 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 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6362 (mt) REVERT: K 75 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6928 (p) REVERT: K 76 ILE cc_start: 0.6815 (mt) cc_final: 0.6514 (mt) REVERT: K 143 ARG cc_start: 0.6256 (mtp85) cc_final: 0.5806 (ttm-80) outliers start: 25 outliers final: 19 residues processed: 103 average time/residue: 0.1793 time to fit residues: 23.6190 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 126 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 206 ASN I 486 HIS ** K 148 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 = 0.3973 r_free = 0.3973 target = 0.160585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142929 restraints weight = 18690.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145993 restraints weight = 10419.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146699 restraints weight = 5960.709| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4939 Z= 0.280 Angle : 0.723 11.838 6732 Z= 0.367 Chirality : 0.047 0.233 774 Planarity : 0.005 0.058 861 Dihedral : 6.792 50.451 703 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.87 % Favored : 88.66 % Rotamer: Outliers : 6.00 % Allowed : 18.18 % 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: -2.41 (0.32), residues: 637 helix: -4.39 (0.60), residues: 24 sheet: -0.79 (0.33), residues: 262 loop : -2.07 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 97 HIS 0.002 0.001 HIS I 486 PHE 0.016 0.002 PHE I 423 TYR 0.019 0.002 TYR H 183 ARG 0.002 0.000 ARG H 98 *********************** 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: 33 poor density : 77 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 171 HIS cc_start: 0.7566 (m170) cc_final: 0.7342 (m170) REVERT: K 13 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6800 (mt) REVERT: K 75 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6866 (p) REVERT: K 76 ILE cc_start: 0.7004 (mt) cc_final: 0.6631 (mt) REVERT: K 124 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6666 (tm-30) REVERT: K 143 ARG cc_start: 0.6526 (mtp85) cc_final: 0.6201 (ttm-80) outliers start: 33 outliers final: 22 residues processed: 104 average time/residue: 0.1833 time to fit residues: 24.4668 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 90 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 0.0040 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.162408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.142728 restraints weight = 22740.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148039 restraints weight = 13516.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149755 restraints weight = 4751.838| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3964 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= 0.210 Angle : 0.679 10.963 6732 Z= 0.341 Chirality : 0.045 0.230 774 Planarity : 0.004 0.034 861 Dihedral : 6.604 51.518 703 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.82 % Favored : 90.71 % Rotamer: Outliers : 4.91 % Allowed : 19.09 % Favored : 76.00 % 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: -2.32 (0.32), residues: 637 helix: -3.89 (0.75), residues: 24 sheet: -0.73 (0.33), residues: 260 loop : -2.04 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 97 HIS 0.001 0.000 HIS H 207 PHE 0.015 0.002 PHE H 107 TYR 0.014 0.002 TYR H 183 ARG 0.002 0.000 ARG K 62 *********************** 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 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 171 HIS cc_start: 0.7547 (m170) cc_final: 0.7313 (m170) REVERT: H 211 ASN cc_start: 0.6757 (m-40) cc_final: 0.6547 (t0) REVERT: K 75 THR cc_start: 0.7050 (OUTLIER) cc_final: 0.6661 (p) REVERT: K 76 ILE cc_start: 0.6934 (mt) cc_final: 0.6601 (mt) REVERT: K 124 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6662 (tm-30) REVERT: K 143 ARG cc_start: 0.6452 (mtp85) cc_final: 0.6139 (ttm-80) outliers start: 27 outliers final: 24 residues processed: 98 average time/residue: 0.1910 time to fit residues: 23.4138 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 67 ARG 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 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 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 90 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 22 optimal weight: 0.0170 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.162955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143445 restraints weight = 20441.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148407 restraints weight = 12675.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150400 restraints weight = 4715.284| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4939 Z= 0.202 Angle : 0.681 10.996 6732 Z= 0.341 Chirality : 0.045 0.219 774 Planarity : 0.004 0.039 861 Dihedral : 6.304 51.312 701 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.24 % Favored : 89.29 % Rotamer: Outliers : 5.09 % Allowed : 19.64 % 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: -2.29 (0.32), residues: 637 helix: -3.89 (0.74), residues: 24 sheet: -0.65 (0.32), residues: 269 loop : -2.11 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 97 HIS 0.001 0.001 HIS H 207 PHE 0.014 0.001 PHE H 107 TYR 0.018 0.002 TYR H 32 ARG 0.003 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7600 (t80) REVERT: H 171 HIS cc_start: 0.7529 (m170) cc_final: 0.7302 (m170) REVERT: H 211 ASN cc_start: 0.6834 (m-40) cc_final: 0.6622 (t0) REVERT: K 75 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6708 (p) REVERT: K 76 ILE cc_start: 0.6916 (mt) cc_final: 0.6679 (mt) REVERT: K 124 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6903 (tm-30) REVERT: K 143 ARG cc_start: 0.6445 (mtp85) cc_final: 0.6106 (ttm-80) outliers start: 28 outliers final: 21 residues processed: 94 average time/residue: 0.1818 time to fit residues: 21.8347 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 67 ARG 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 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 90 GLN 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 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: 0.1980 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** 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 = 0.3979 r_free = 0.3979 target = 0.160946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.141350 restraints weight = 25801.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146120 restraints weight = 16431.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149941 restraints weight = 5355.426| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4264 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= 0.246 Angle : 0.712 13.702 6732 Z= 0.358 Chirality : 0.047 0.212 774 Planarity : 0.005 0.038 861 Dihedral : 6.415 51.788 701 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.08 % Favored : 89.45 % Rotamer: Outliers : 5.09 % Allowed : 19.45 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.22 (0.32), residues: 637 helix: -4.41 (0.73), residues: 18 sheet: -0.63 (0.32), residues: 266 loop : -2.04 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 97 HIS 0.002 0.001 HIS I 486 PHE 0.014 0.002 PHE I 423 TYR 0.019 0.002 TYR H 32 ARG 0.004 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7607 (t80) REVERT: H 171 HIS cc_start: 0.7489 (m170) cc_final: 0.7274 (m170) REVERT: H 211 ASN cc_start: 0.6779 (m-40) cc_final: 0.6575 (t0) REVERT: I 536 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7496 (mt-10) REVERT: K 75 THR cc_start: 0.7085 (OUTLIER) cc_final: 0.6743 (p) REVERT: K 76 ILE cc_start: 0.6696 (mt) cc_final: 0.6366 (mt) REVERT: K 124 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6986 (tm-30) REVERT: K 143 ARG cc_start: 0.6525 (mtp85) cc_final: 0.6135 (ttm170) outliers start: 28 outliers final: 22 residues processed: 95 average time/residue: 0.2000 time to fit residues: 24.4813 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 67 ARG 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 422 ASP Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 90 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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** ** 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 = 0.3968 r_free = 0.3968 target = 0.159848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140577 restraints weight = 19854.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145473 restraints weight = 12943.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147318 restraints weight = 4688.891| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4939 Z= 0.275 Angle : 0.736 14.461 6732 Z= 0.371 Chirality : 0.047 0.218 774 Planarity : 0.005 0.039 861 Dihedral : 6.542 52.669 701 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.34 % Favored : 88.19 % Rotamer: Outliers : 4.18 % Allowed : 20.18 % Favored : 75.64 % 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: -2.35 (0.32), residues: 637 helix: -4.45 (0.73), residues: 18 sheet: -0.78 (0.32), residues: 266 loop : -2.06 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 97 HIS 0.002 0.001 HIS I 486 PHE 0.015 0.002 PHE I 423 TYR 0.018 0.002 TYR H 32 ARG 0.004 0.001 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7577 (t80) REVERT: I 536 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7568 (mt-10) REVERT: K 75 THR cc_start: 0.7066 (OUTLIER) cc_final: 0.6711 (p) REVERT: K 76 ILE cc_start: 0.6670 (mt) cc_final: 0.6356 (mt) REVERT: K 124 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6835 (tm-30) REVERT: K 143 ARG cc_start: 0.6617 (mtp85) cc_final: 0.6220 (ttm170) outliers start: 23 outliers final: 20 residues processed: 95 average time/residue: 0.1911 time to fit residues: 22.8518 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 : 0.545 ------------------------------------------------------------------------------- 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 67 ARG 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 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 90 GLN 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: 0.5980 chunk 36 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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** ** 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 = 0.3996 r_free = 0.3996 target = 0.162616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143095 restraints weight = 25548.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148071 restraints weight = 16724.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151231 restraints weight = 5011.517| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4939 Z= 0.192 Angle : 0.696 13.990 6732 Z= 0.347 Chirality : 0.046 0.210 774 Planarity : 0.004 0.039 861 Dihedral : 6.280 54.184 701 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.61 % Favored : 89.92 % Rotamer: Outliers : 3.64 % Allowed : 20.91 % Favored : 75.45 % 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: -3.96 (0.73), residues: 24 sheet: -0.69 (0.32), residues: 264 loop : -2.03 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 97 HIS 0.001 0.000 HIS H 207 PHE 0.012 0.001 PHE H 107 TYR 0.017 0.002 TYR H 32 ARG 0.002 0.000 ARG H 98 ********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7587 (t80) REVERT: H 171 HIS cc_start: 0.7378 (m170) cc_final: 0.7161 (m170) REVERT: I 536 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7474 (mt-10) REVERT: K 75 THR cc_start: 0.7069 (OUTLIER) cc_final: 0.6730 (p) REVERT: K 76 ILE cc_start: 0.6629 (mt) cc_final: 0.6314 (mt) REVERT: K 124 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6980 (tm-30) REVERT: K 143 ARG cc_start: 0.6728 (mtp85) cc_final: 0.6301 (ttm170) outliers start: 20 outliers final: 16 residues processed: 91 average time/residue: 0.1904 time to fit residues: 21.9908 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 67 ARG 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 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 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 34 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 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 = 0.3980 r_free = 0.3980 target = 0.161036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141499 restraints weight = 23779.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146298 restraints weight = 14911.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149042 restraints weight = 5145.250| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4939 Z= 0.231 Angle : 0.712 14.248 6732 Z= 0.358 Chirality : 0.046 0.209 774 Planarity : 0.004 0.041 861 Dihedral : 6.274 54.253 700 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.71 % Favored : 88.82 % Rotamer: Outliers : 4.00 % Allowed : 21.27 % 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: -2.30 (0.32), residues: 637 helix: -3.96 (0.72), residues: 24 sheet: -0.72 (0.32), residues: 264 loop : -2.04 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 97 HIS 0.002 0.001 HIS H 207 PHE 0.013 0.002 PHE I 423 TYR 0.018 0.002 TYR H 32 ARG 0.003 0.000 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.34 seconds wall clock time: 37 minutes 13.64 seconds (2233.64 seconds total)