Starting phenix.real_space_refine on Thu Jul 24 01:16:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x26_32959/07_2025/7x26_32959_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x26_32959/07_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_32959/07_2025/7x26_32959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x26_32959/07_2025/7x26_32959.map" model { file = "/net/cci-nas-00/data/ceres_data/7x26_32959/07_2025/7x26_32959_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x26_32959/07_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-5711/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: 4.54, per 1000 atoms: 0.94 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: 1.06 Conformation dependent library (CDL) restraints added in 722.8 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: 1.26 Time building geometry restraints manager: 1.31 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.800 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- 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 4947 Z= 0.824 Angle : 1.462 12.344 6748 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 : 2.52 % Allowed : 16.38 % 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 Details of bonding type rmsd hydrogen bonds : bond 0.20904 ( 113) hydrogen bonds : angle 9.01767 ( 233) SS BOND : bond 0.01373 ( 8) SS BOND : angle 2.06288 ( 16) covalent geometry : bond 0.01137 ( 4939) covalent geometry : angle 1.46038 ( 6732) *********************** 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 : 0.497 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: 0.1804 time to fit residues: 39.1927 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 : 0.496 ------------------------------------------------------------------------------- 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 4947 Z= 0.135 Angle : 0.731 11.011 6748 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 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 113) hydrogen bonds : angle 6.24041 ( 233) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.98542 ( 16) covalent geometry : bond 0.00308 ( 4939) covalent geometry : angle 0.72980 ( 6732) *********************** 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 : 0.843 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: 0.1931 time to fit residues: 27.6423 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 : 0.413 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.4936 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.162859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144245 restraints weight = 15101.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.148058 restraints weight = 7807.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148197 restraints weight = 4709.192| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 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 = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4947 Z= 0.153 Angle : 0.701 11.539 6748 Z= 0.359 Chirality : 0.046 0.230 774 Planarity : 0.005 0.035 861 Dihedral : 6.936 50.580 704 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.87 % Favored : 88.66 % Rotamer: Outliers : 5.09 % Allowed : 17.09 % Favored : 77.82 % 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: -2.43 (0.32), residues: 637 helix: -4.33 (0.74), residues: 18 sheet: -0.70 (0.35), residues: 238 loop : -2.17 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 161 HIS 0.002 0.001 HIS H 207 PHE 0.015 0.002 PHE I 423 TYR 0.019 0.002 TYR H 183 ARG 0.007 0.001 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 113) hydrogen bonds : angle 5.90636 ( 233) SS BOND : bond 0.00295 ( 8) SS BOND : angle 0.82393 ( 16) covalent geometry : bond 0.00357 ( 4939) covalent geometry : angle 0.70116 ( 6732) *********************** 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 117 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 157 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8601 (p) REVERT: H 214 VAL cc_start: 0.8013 (t) cc_final: 0.7759 (m) REVERT: K 13 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6414 (mt) REVERT: K 75 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6922 (p) REVERT: K 76 ILE cc_start: 0.6890 (mt) cc_final: 0.6535 (mt) REVERT: K 143 ARG cc_start: 0.6392 (mtp85) cc_final: 0.5844 (ttm-80) outliers start: 28 outliers final: 20 residues processed: 110 average time/residue: 0.2812 time to fit residues: 40.0167 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 90 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.162845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144305 restraints weight = 24048.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.147537 restraints weight = 13660.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149721 restraints weight = 6417.811| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- 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 = 0.38 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4947 Z= 0.149 Angle : 0.697 11.236 6748 Z= 0.355 Chirality : 0.046 0.231 774 Planarity : 0.004 0.037 861 Dihedral : 6.866 52.229 704 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.35 % Favored : 91.18 % Rotamer: Outliers : 5.09 % Allowed : 18.55 % 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: -2.44 (0.33), residues: 637 helix: -4.51 (0.58), residues: 24 sheet: -0.85 (0.33), residues: 262 loop : -2.04 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS H 207 PHE 0.013 0.002 PHE K 99 TYR 0.018 0.002 TYR H 183 ARG 0.003 0.000 ARG K 24 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 113) hydrogen bonds : angle 5.71685 ( 233) SS BOND : bond 0.00275 ( 8) SS BOND : angle 0.98021 ( 16) covalent geometry : bond 0.00345 ( 4939) covalent geometry : angle 0.69619 ( 6732) *********************** 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 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6464 (mt) REVERT: K 75 THR cc_start: 0.7223 (OUTLIER) cc_final: 0.6860 (p) REVERT: K 76 ILE cc_start: 0.6841 (mt) cc_final: 0.6530 (mt) REVERT: K 143 ARG cc_start: 0.6292 (mtp85) cc_final: 0.5910 (ttm-80) outliers start: 28 outliers final: 20 residues processed: 106 average time/residue: 0.2429 time to fit residues: 33.5134 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.161208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141879 restraints weight = 18726.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146961 restraints weight = 11930.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148252 restraints weight = 4489.611| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4947 Z= 0.167 Angle : 0.713 11.529 6748 Z= 0.362 Chirality : 0.046 0.235 774 Planarity : 0.005 0.054 861 Dihedral : 6.815 50.783 703 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.08 % Favored : 89.45 % 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: -2.34 (0.32), residues: 637 helix: -4.39 (0.72), residues: 18 sheet: -0.81 (0.33), residues: 260 loop : -2.01 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 97 HIS 0.002 0.001 HIS H 207 PHE 0.014 0.002 PHE I 423 TYR 0.019 0.002 TYR H 183 ARG 0.002 0.000 ARG K 62 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 113) hydrogen bonds : angle 5.72494 ( 233) SS BOND : bond 0.00315 ( 8) SS BOND : angle 0.99836 ( 16) covalent geometry : bond 0.00392 ( 4939) covalent geometry : angle 0.71246 ( 6732) *********************** 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 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 171 HIS cc_start: 0.7521 (m170) cc_final: 0.7309 (m170) REVERT: K 13 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6824 (mt) REVERT: K 75 THR cc_start: 0.7210 (OUTLIER) cc_final: 0.6864 (p) REVERT: K 76 ILE cc_start: 0.7046 (mt) cc_final: 0.6692 (mt) REVERT: K 143 ARG cc_start: 0.6474 (mtp85) cc_final: 0.6154 (ttm-80) outliers start: 31 outliers final: 23 residues processed: 100 average time/residue: 0.2281 time to fit residues: 30.1095 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 : 0.413 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 47 optimal weight: 0.0040 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.3890 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.163254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144725 restraints weight = 22669.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.148180 restraints weight = 11267.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149912 restraints weight = 5940.263| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- 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 = 0.34 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4947 Z= 0.127 Angle : 0.673 10.821 6748 Z= 0.337 Chirality : 0.045 0.224 774 Planarity : 0.004 0.035 861 Dihedral : 6.548 50.722 703 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.82 % Favored : 90.71 % Rotamer: Outliers : 4.91 % Allowed : 20.18 % Favored : 74.91 % 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: -2.31 (0.33), residues: 637 helix: -3.80 (0.79), residues: 24 sheet: -0.72 (0.33), residues: 261 loop : -2.04 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 97 HIS 0.001 0.000 HIS I 486 PHE 0.011 0.001 PHE I 423 TYR 0.013 0.002 TYR H 183 ARG 0.003 0.000 ARG K 62 Details of bonding type rmsd hydrogen bonds : bond 0.02804 ( 113) hydrogen bonds : angle 5.51433 ( 233) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.90720 ( 16) covalent geometry : bond 0.00296 ( 4939) covalent geometry : angle 0.67224 ( 6732) *********************** 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 171 HIS cc_start: 0.7551 (m170) cc_final: 0.7330 (m170) REVERT: H 211 ASN cc_start: 0.6778 (m-40) cc_final: 0.6542 (t0) REVERT: K 75 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6670 (p) REVERT: K 76 ILE cc_start: 0.7022 (mt) cc_final: 0.6669 (mt) REVERT: K 143 ARG cc_start: 0.6457 (mtp85) cc_final: 0.6146 (ttm-80) outliers start: 27 outliers final: 20 residues processed: 94 average time/residue: 0.2414 time to fit residues: 29.2641 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.162423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144220 restraints weight = 20468.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147510 restraints weight = 11560.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148652 restraints weight = 6139.757| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4947 Z= 0.141 Angle : 0.689 13.815 6748 Z= 0.346 Chirality : 0.046 0.204 774 Planarity : 0.004 0.036 861 Dihedral : 6.328 50.057 701 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.92 % Favored : 89.61 % Rotamer: Outliers : 4.55 % Allowed : 19.82 % 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: -2.28 (0.32), residues: 637 helix: -3.80 (0.78), residues: 24 sheet: -0.68 (0.33), residues: 261 loop : -2.04 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 97 HIS 0.001 0.001 HIS I 486 PHE 0.012 0.001 PHE I 423 TYR 0.019 0.002 TYR H 32 ARG 0.004 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 113) hydrogen bonds : angle 5.48052 ( 233) SS BOND : bond 0.00294 ( 8) SS BOND : angle 0.88136 ( 16) covalent geometry : bond 0.00330 ( 4939) covalent geometry : angle 0.68850 ( 6732) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7609 (t80) REVERT: H 171 HIS cc_start: 0.7546 (m170) cc_final: 0.7315 (m170) REVERT: H 211 ASN cc_start: 0.6817 (m-40) cc_final: 0.6563 (t0) REVERT: K 75 THR cc_start: 0.7034 (OUTLIER) cc_final: 0.6687 (p) REVERT: K 76 ILE cc_start: 0.6692 (mt) cc_final: 0.6436 (mt) REVERT: K 143 ARG cc_start: 0.6461 (mtp85) cc_final: 0.6129 (ttm-80) outliers start: 25 outliers final: 19 residues processed: 94 average time/residue: 0.1774 time to fit residues: 21.5654 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 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: 0.0970 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 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 = 0.4027 r_free = 0.4027 target = 0.165456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146493 restraints weight = 25629.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151178 restraints weight = 17876.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.154215 restraints weight = 5634.526| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4947 Z= 0.111 Angle : 0.662 13.690 6748 Z= 0.330 Chirality : 0.045 0.192 774 Planarity : 0.004 0.034 861 Dihedral : 6.039 51.208 701 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.50 % Favored : 91.02 % 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: -2.15 (0.33), residues: 637 helix: -3.93 (0.69), residues: 30 sheet: -0.49 (0.32), residues: 269 loop : -2.01 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 97 HIS 0.001 0.000 HIS H 207 PHE 0.010 0.001 PHE I 423 TYR 0.015 0.002 TYR H 32 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 113) hydrogen bonds : angle 5.16816 ( 233) SS BOND : bond 0.00229 ( 8) SS BOND : angle 0.83502 ( 16) covalent geometry : bond 0.00257 ( 4939) covalent geometry : angle 0.66106 ( 6732) *********************** 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: 23 poor density : 79 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: H 211 ASN cc_start: 0.6838 (m-40) cc_final: 0.6619 (t0) REVERT: K 75 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6659 (p) REVERT: K 143 ARG cc_start: 0.6463 (mtp85) cc_final: 0.5996 (ttm170) outliers start: 23 outliers final: 18 residues processed: 95 average time/residue: 0.1606 time to fit residues: 20.1103 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 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 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: 0.4980 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.163355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144874 restraints weight = 19765.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149664 restraints weight = 13815.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151156 restraints weight = 5086.049| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 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 = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4947 Z= 0.136 Angle : 0.684 13.953 6748 Z= 0.343 Chirality : 0.046 0.193 774 Planarity : 0.004 0.036 861 Dihedral : 6.027 50.926 700 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.24 % Favored : 89.29 % Rotamer: Outliers : 3.82 % Allowed : 20.91 % 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: -2.09 (0.33), residues: 637 helix: -3.70 (0.82), residues: 24 sheet: -0.54 (0.32), residues: 269 loop : -1.94 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 97 HIS 0.001 0.001 HIS I 486 PHE 0.013 0.001 PHE I 423 TYR 0.016 0.002 TYR H 32 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 113) hydrogen bonds : angle 5.26191 ( 233) SS BOND : bond 0.00283 ( 8) SS BOND : angle 0.87328 ( 16) covalent geometry : bond 0.00318 ( 4939) covalent geometry : angle 0.68364 ( 6732) *********************** 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 : 0.492 Fit side-chains revert: symmetry clash REVERT: I 536 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7486 (mt-10) REVERT: K 75 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6703 (p) REVERT: K 143 ARG cc_start: 0.6638 (mtp85) cc_final: 0.6184 (ttm170) outliers start: 21 outliers final: 19 residues processed: 90 average time/residue: 0.1916 time to fit residues: 22.0961 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL 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 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 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: 0.9980 chunk 36 optimal weight: 0.0040 chunk 31 optimal weight: 0.0040 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 overall best weight: 0.1160 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.168505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148378 restraints weight = 25433.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153255 restraints weight = 15136.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.156165 restraints weight = 5422.846| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4947 Z= 0.104 Angle : 0.650 13.350 6748 Z= 0.324 Chirality : 0.044 0.161 774 Planarity : 0.004 0.038 861 Dihedral : 5.659 51.813 700 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.24 % Favored : 92.28 % Rotamer: Outliers : 3.09 % Allowed : 22.00 % Favored : 74.91 % 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: -1.95 (0.33), residues: 637 helix: -3.79 (0.72), residues: 30 sheet: -0.44 (0.33), residues: 269 loop : -1.79 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 97 HIS 0.001 0.000 HIS H 207 PHE 0.009 0.001 PHE H 107 TYR 0.011 0.001 TYR I 523 ARG 0.002 0.000 ARG K 109 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 113) hydrogen bonds : angle 5.06886 ( 233) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.77062 ( 16) covalent geometry : bond 0.00235 ( 4939) covalent geometry : angle 0.64979 ( 6732) ********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: H 119 SER cc_start: 0.7172 (m) cc_final: 0.6927 (p) REVERT: I 536 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7427 (mt-10) REVERT: K 75 THR cc_start: 0.6941 (OUTLIER) cc_final: 0.6628 (p) REVERT: K 136 LEU cc_start: 0.8337 (tp) cc_final: 0.8106 (tt) REVERT: K 143 ARG cc_start: 0.6249 (mtp85) cc_final: 0.5772 (ttm170) outliers start: 17 outliers final: 13 residues processed: 94 average time/residue: 0.1836 time to fit residues: 21.6101 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL 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 I residue 417 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 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 = 0.3994 r_free = 0.3994 target = 0.162136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142846 restraints weight = 23769.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147921 restraints weight = 15011.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150130 restraints weight = 4974.171| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4947 Z= 0.178 Angle : 0.716 14.276 6748 Z= 0.361 Chirality : 0.046 0.199 774 Planarity : 0.005 0.051 861 Dihedral : 5.988 51.233 699 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.55 % Favored : 88.98 % Rotamer: Outliers : 3.45 % Allowed : 22.18 % Favored : 74.36 % 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: -2.12 (0.33), residues: 637 helix: -3.91 (0.68), residues: 30 sheet: -0.58 (0.32), residues: 276 loop : -1.90 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 97 HIS 0.002 0.001 HIS K 199 PHE 0.017 0.002 PHE H 29 TYR 0.018 0.002 TYR H 183 ARG 0.004 0.001 ARG K 55 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 113) hydrogen bonds : angle 5.41498 ( 233) SS BOND : bond 0.00350 ( 8) SS BOND : angle 1.00445 ( 16) covalent geometry : bond 0.00424 ( 4939) covalent geometry : angle 0.71504 ( 6732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.80 seconds wall clock time: 47 minutes 34.52 seconds (2854.52 seconds total)