Starting phenix.real_space_refine on Fri Dec 27 10:01:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymh_33928/12_2024/7ymh_33928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymh_33928/12_2024/7ymh_33928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ymh_33928/12_2024/7ymh_33928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymh_33928/12_2024/7ymh_33928.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymh_33928/12_2024/7ymh_33928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymh_33928/12_2024/7ymh_33928.cif" } resolution = 3.52 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= 0.051 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 24 5.16 5 C 2577 2.51 5 N 657 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3948 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2038 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1389 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 197, 1384 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 183 Conformer: "B" Number of residues, atoms: 197, 1384 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 183 bond proxies already assigned to first conformer: 1403 Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 509 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA B 158 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 158 " occ=0.50 Time building chain proxies: 3.43, per 1000 atoms: 0.87 Number of scatterers: 3948 At special positions: 0 Unit cell: (58.1887, 61.4824, 139.433, 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 24 16.00 O 690 8.00 N 657 7.00 C 2577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " 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: 0.99 Conformation dependent library (CDL) restraints added in 633.6 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 53.9% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 26 through 50 Processing helix chain 'A' and resid 59 through 90 removed outlier: 3.636A pdb=" N LEU A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 96 through 129 removed outlier: 3.719A pdb=" N ALA A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.734A pdb=" N PHE A 163 " --> pdb=" O GLY A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.889A pdb=" N PHE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 211 Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.915A pdb=" N LYS A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 298 removed outlier: 4.635A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 304 through 329 removed outlier: 3.946A pdb=" N GLY A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 3.576A pdb=" N TYR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.556A pdb=" N LYS B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.380A pdb=" N GLN B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.605A pdb=" N GLU B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 205 through 225 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'B' and resid 88 through 93 Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.275A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D 91 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 66 through 69 224 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1232 1.34 - 1.46: 961 1.46 - 1.58: 1813 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4037 Sorted by residual: bond pdb=" CAJ E5E A 401 " pdb=" OAC E5E A 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" CAI E5E A 401 " pdb=" OAB E5E A 401 " ideal model delta sigma weight residual 1.354 1.400 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 1.469 1.482 -0.013 7.40e-03 1.83e+04 3.25e+00 bond pdb=" CAH E5E A 401 " pdb=" NAA E5E A 401 " ideal model delta sigma weight residual 1.486 1.451 0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C LEU A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.47e+00 ... (remaining 4032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 5268 1.60 - 3.21: 204 3.21 - 4.81: 38 4.81 - 6.41: 10 6.41 - 8.02: 4 Bond angle restraints: 5524 Sorted by residual: angle pdb=" N ILE A 159 " pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 111.91 106.40 5.51 8.90e-01 1.26e+00 3.83e+01 angle pdb=" N ASP A 300 " pdb=" CA ASP A 300 " pdb=" C ASP A 300 " ideal model delta sigma weight residual 114.31 108.59 5.72 1.29e+00 6.01e-01 1.97e+01 angle pdb=" N ILE A 178 " pdb=" CA ILE A 178 " pdb=" C ILE A 178 " ideal model delta sigma weight residual 110.05 106.05 4.00 1.09e+00 8.42e-01 1.35e+01 angle pdb=" C ILE A 321 " pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta sigma weight residual 120.06 124.17 -4.11 1.19e+00 7.06e-01 1.19e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 116.27 -6.46 2.21e+00 2.05e-01 8.54e+00 ... (remaining 5519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 2063 15.48 - 30.95: 209 30.95 - 46.43: 49 46.43 - 61.90: 4 61.90 - 77.38: 4 Dihedral angle restraints: 2329 sinusoidal: 744 harmonic: 1585 Sorted by residual: dihedral pdb=" CA PRO A 161 " pdb=" C PRO A 161 " pdb=" N LEU A 162 " pdb=" CA LEU A 162 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ILE A 325 " pdb=" C ILE A 325 " pdb=" N TYR A 326 " pdb=" CA TYR A 326 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE A 193 " pdb=" C PHE A 193 " pdb=" N TYR A 194 " pdb=" CA TYR A 194 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 393 0.038 - 0.075: 190 0.075 - 0.113: 56 0.113 - 0.151: 21 0.151 - 0.189: 6 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CAL E5E A 401 " pdb=" CAH E5E A 401 " pdb=" CAK E5E A 401 " pdb=" OAD E5E A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.49 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA TYR A 326 " pdb=" N TYR A 326 " pdb=" C TYR A 326 " pdb=" CB TYR A 326 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 663 not shown) Planarity restraints: 688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 322 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO A 323 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO A 327 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 286 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 287 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.034 5.00e-02 4.00e+02 ... (remaining 685 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1341 2.84 - 3.35: 3524 3.35 - 3.87: 6319 3.87 - 4.38: 6842 4.38 - 4.90: 12224 Nonbonded interactions: 30250 Sorted by model distance: nonbonded pdb=" OH TYR B 194 " pdb=" OD2 ASP B 215 " model vdw 2.324 3.040 nonbonded pdb=" OD1 ASP A 172 " pdb=" OH TYR D 37 " model vdw 2.331 3.040 nonbonded pdb=" OG SER D 69 " pdb=" O TYR D 78 " model vdw 2.383 3.040 nonbonded pdb=" O THR A 139 " pdb=" N GLY A 143 " model vdw 2.383 3.120 nonbonded pdb=" O ASP A 72 " pdb=" OG1 THR A 76 " model vdw 2.417 3.040 ... (remaining 30245 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=0.50 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: 0.810 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: 14.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4037 Z= 0.264 Angle : 0.780 8.018 5524 Z= 0.448 Chirality : 0.050 0.189 666 Planarity : 0.007 0.075 688 Dihedral : 13.786 77.379 1300 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.28), residues: 527 helix: -2.63 (0.23), residues: 283 sheet: -3.00 (0.49), residues: 67 loop : -3.32 (0.39), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 111 HIS 0.006 0.001 HIS B 191 PHE 0.012 0.002 PHE A 308 TYR 0.018 0.001 TYR A 134 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8592 (mp) cc_final: 0.8371 (mp) REVERT: A 165 TRP cc_start: 0.4361 (m100) cc_final: 0.4151 (m100) REVERT: A 272 LYS cc_start: 0.8785 (tppp) cc_final: 0.8292 (tptt) REVERT: B 215 ASP cc_start: 0.8499 (t70) cc_final: 0.7595 (t0) REVERT: D 100 TYR cc_start: 0.8228 (p90) cc_final: 0.7856 (p90) REVERT: D 102 ASP cc_start: 0.8443 (t70) cc_final: 0.7816 (t70) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2070 time to fit residues: 28.6319 Evaluate side-chains 87 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.0040 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 10.0000 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 318 ASN A 331 GLN B 16 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4037 Z= 0.168 Angle : 0.547 6.042 5524 Z= 0.297 Chirality : 0.040 0.129 666 Planarity : 0.005 0.043 688 Dihedral : 4.402 17.981 583 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.36 % Allowed : 16.35 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.33), residues: 527 helix: -0.77 (0.29), residues: 282 sheet: -2.45 (0.54), residues: 67 loop : -2.95 (0.39), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS B 16 PHE 0.008 0.001 PHE B 197 TYR 0.012 0.001 TYR A 326 ARG 0.008 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8067 (mtp) cc_final: 0.7673 (mtt) REVERT: A 165 TRP cc_start: 0.4009 (m100) cc_final: 0.3617 (m100) REVERT: A 272 LYS cc_start: 0.8714 (tppp) cc_final: 0.8209 (tptt) REVERT: B 215 ASP cc_start: 0.8542 (t70) cc_final: 0.7827 (t0) REVERT: D 100 TYR cc_start: 0.8212 (p90) cc_final: 0.7923 (p90) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.1789 time to fit residues: 21.9056 Evaluate side-chains 91 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain D residue 61 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 4037 Z= 0.498 Angle : 0.691 6.715 5524 Z= 0.367 Chirality : 0.046 0.155 666 Planarity : 0.005 0.040 688 Dihedral : 4.767 20.608 583 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.18 % Allowed : 17.98 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.34), residues: 527 helix: -0.33 (0.29), residues: 288 sheet: -2.47 (0.55), residues: 69 loop : -2.58 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 102 HIS 0.005 0.001 HIS B 191 PHE 0.013 0.002 PHE A 288 TYR 0.018 0.002 TYR A 326 ARG 0.007 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.453 Fit side-chains REVERT: A 63 TYR cc_start: 0.7580 (m-10) cc_final: 0.7302 (m-10) REVERT: A 165 TRP cc_start: 0.4379 (m100) cc_final: 0.3982 (m100) REVERT: A 272 LYS cc_start: 0.8796 (tppp) cc_final: 0.8286 (tptt) REVERT: B 215 ASP cc_start: 0.8687 (t70) cc_final: 0.8389 (t0) REVERT: D 100 TYR cc_start: 0.8216 (p90) cc_final: 0.7857 (p90) outliers start: 19 outliers final: 15 residues processed: 94 average time/residue: 0.1703 time to fit residues: 19.4778 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4037 Z= 0.149 Angle : 0.516 6.638 5524 Z= 0.274 Chirality : 0.040 0.132 666 Planarity : 0.004 0.040 688 Dihedral : 4.134 18.138 583 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.54 % Allowed : 20.44 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.36), residues: 527 helix: 0.59 (0.32), residues: 279 sheet: -2.18 (0.57), residues: 69 loop : -2.61 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 PHE 0.009 0.001 PHE A 297 TYR 0.012 0.001 TYR A 326 ARG 0.007 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.483 Fit side-chains REVERT: A 115 MET cc_start: 0.7915 (mtp) cc_final: 0.7532 (mtt) REVERT: A 145 MET cc_start: 0.7618 (mmm) cc_final: 0.7218 (mtt) REVERT: A 165 TRP cc_start: 0.3882 (m100) cc_final: 0.3488 (m100) REVERT: A 272 LYS cc_start: 0.8715 (tppp) cc_final: 0.8174 (tptt) REVERT: B 215 ASP cc_start: 0.8561 (t70) cc_final: 0.7826 (t0) outliers start: 13 outliers final: 7 residues processed: 103 average time/residue: 0.1967 time to fit residues: 24.3778 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 126 ASN B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4037 Z= 0.159 Angle : 0.516 6.456 5524 Z= 0.271 Chirality : 0.040 0.130 666 Planarity : 0.004 0.035 688 Dihedral : 3.926 16.400 583 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.00 % Allowed : 21.53 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.37), residues: 527 helix: 0.83 (0.32), residues: 284 sheet: -1.89 (0.58), residues: 69 loop : -2.45 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.003 0.001 HIS B 191 PHE 0.009 0.001 PHE A 297 TYR 0.014 0.001 TYR A 91 ARG 0.006 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.349 Fit side-chains REVERT: A 115 MET cc_start: 0.7942 (mtp) cc_final: 0.7607 (mtt) REVERT: A 145 MET cc_start: 0.7664 (mmm) cc_final: 0.7295 (mtt) REVERT: A 165 TRP cc_start: 0.3970 (m100) cc_final: 0.3482 (m100) REVERT: A 272 LYS cc_start: 0.8696 (tppp) cc_final: 0.8222 (tptt) REVERT: B 215 ASP cc_start: 0.8507 (t70) cc_final: 0.7782 (t0) outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.1862 time to fit residues: 22.1871 Evaluate side-chains 94 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 chunk 42 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4037 Z= 0.162 Angle : 0.515 7.321 5524 Z= 0.268 Chirality : 0.040 0.128 666 Planarity : 0.004 0.033 688 Dihedral : 3.861 16.256 583 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.54 % Allowed : 22.07 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.37), residues: 527 helix: 1.02 (0.32), residues: 283 sheet: -1.69 (0.59), residues: 69 loop : -2.32 (0.43), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.003 0.001 HIS B 191 PHE 0.009 0.001 PHE A 297 TYR 0.012 0.001 TYR A 91 ARG 0.007 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.481 Fit side-chains REVERT: A 145 MET cc_start: 0.7642 (mmm) cc_final: 0.7274 (mtt) REVERT: A 165 TRP cc_start: 0.3897 (m100) cc_final: 0.3525 (m100) REVERT: A 178 ILE cc_start: 0.8536 (pp) cc_final: 0.8280 (pt) REVERT: A 272 LYS cc_start: 0.8680 (tppp) cc_final: 0.8196 (tptt) REVERT: A 313 TRP cc_start: 0.8821 (m100) cc_final: 0.8572 (m100) REVERT: B 215 ASP cc_start: 0.8496 (t70) cc_final: 0.7763 (t0) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.1836 time to fit residues: 20.9827 Evaluate side-chains 94 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.0000 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4037 Z= 0.158 Angle : 0.509 7.024 5524 Z= 0.266 Chirality : 0.039 0.128 666 Planarity : 0.003 0.032 688 Dihedral : 3.725 16.578 583 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.81 % Allowed : 20.16 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.38), residues: 527 helix: 1.14 (0.32), residues: 283 sheet: -1.53 (0.60), residues: 69 loop : -2.24 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 PHE 0.008 0.001 PHE A 297 TYR 0.009 0.001 TYR A 326 ARG 0.005 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.463 Fit side-chains REVERT: A 140 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: A 165 TRP cc_start: 0.3855 (m100) cc_final: 0.3428 (m100) REVERT: A 272 LYS cc_start: 0.8651 (tppp) cc_final: 0.8157 (tptt) REVERT: A 313 TRP cc_start: 0.8813 (m100) cc_final: 0.8598 (m100) REVERT: B 35 MET cc_start: 0.7803 (pmm) cc_final: 0.7548 (pmm) REVERT: B 215 ASP cc_start: 0.8485 (t70) cc_final: 0.7757 (t0) REVERT: B 226 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7994 (t0) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.1852 time to fit residues: 22.8987 Evaluate side-chains 99 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 71 GLN B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4037 Z= 0.179 Angle : 0.530 10.100 5524 Z= 0.274 Chirality : 0.039 0.127 666 Planarity : 0.003 0.029 688 Dihedral : 3.741 16.086 583 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.09 % Allowed : 20.71 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.38), residues: 527 helix: 1.17 (0.32), residues: 283 sheet: -1.57 (0.60), residues: 70 loop : -2.20 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.003 0.001 HIS B 191 PHE 0.019 0.001 PHE A 187 TYR 0.012 0.001 TYR D 99 ARG 0.006 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.467 Fit side-chains REVERT: A 140 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: A 145 MET cc_start: 0.7493 (mmm) cc_final: 0.7094 (mtt) REVERT: A 272 LYS cc_start: 0.8652 (tppp) cc_final: 0.8152 (tptt) REVERT: B 215 ASP cc_start: 0.8496 (t70) cc_final: 0.7778 (t0) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.1798 time to fit residues: 21.6104 Evaluate side-chains 101 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4037 Z= 0.161 Angle : 0.523 10.240 5524 Z= 0.269 Chirality : 0.039 0.129 666 Planarity : 0.003 0.030 688 Dihedral : 3.692 15.960 583 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.54 % Allowed : 21.25 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.38), residues: 527 helix: 1.20 (0.32), residues: 284 sheet: -1.51 (0.60), residues: 70 loop : -2.10 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.003 0.001 HIS B 191 PHE 0.018 0.001 PHE A 187 TYR 0.016 0.001 TYR A 91 ARG 0.006 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.472 Fit side-chains REVERT: A 63 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: A 89 LEU cc_start: 0.8556 (mp) cc_final: 0.8206 (mp) REVERT: A 140 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: A 145 MET cc_start: 0.7486 (mmm) cc_final: 0.7093 (mtt) REVERT: A 272 LYS cc_start: 0.8624 (tppp) cc_final: 0.8134 (tptt) REVERT: A 313 TRP cc_start: 0.8813 (m100) cc_final: 0.8551 (m100) REVERT: B 35 MET cc_start: 0.7785 (pmm) cc_final: 0.7513 (pmm) REVERT: B 215 ASP cc_start: 0.8451 (t70) cc_final: 0.7746 (t0) REVERT: B 226 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7945 (t0) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.1946 time to fit residues: 22.8028 Evaluate side-chains 100 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 71 GLN B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4037 Z= 0.222 Angle : 0.569 9.859 5524 Z= 0.295 Chirality : 0.040 0.123 666 Planarity : 0.004 0.029 688 Dihedral : 3.893 21.594 583 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.54 % Allowed : 20.98 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.38), residues: 527 helix: 1.16 (0.32), residues: 284 sheet: -1.55 (0.60), residues: 70 loop : -2.05 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 102 HIS 0.003 0.001 HIS B 191 PHE 0.016 0.001 PHE A 187 TYR 0.010 0.001 TYR A 326 ARG 0.006 0.000 ARG B 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.455 Fit side-chains REVERT: A 145 MET cc_start: 0.7505 (mmm) cc_final: 0.7094 (mtt) REVERT: A 272 LYS cc_start: 0.8658 (tppp) cc_final: 0.8163 (tptt) REVERT: B 35 MET cc_start: 0.7817 (pmm) cc_final: 0.7538 (pmm) REVERT: B 215 ASP cc_start: 0.8510 (t70) cc_final: 0.7785 (t0) outliers start: 13 outliers final: 12 residues processed: 97 average time/residue: 0.1914 time to fit residues: 22.6225 Evaluate side-chains 103 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0470 chunk 42 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108578 restraints weight = 5909.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109190 restraints weight = 3660.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110838 restraints weight = 2954.169| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4037 Z= 0.176 Angle : 0.543 9.943 5524 Z= 0.280 Chirality : 0.039 0.128 666 Planarity : 0.004 0.029 688 Dihedral : 3.800 17.437 583 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.81 % Allowed : 20.71 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.38), residues: 527 helix: 1.23 (0.32), residues: 284 sheet: -1.51 (0.60), residues: 70 loop : -2.00 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.003 0.001 HIS B 191 PHE 0.017 0.001 PHE A 187 TYR 0.015 0.001 TYR A 91 ARG 0.006 0.000 ARG B 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1282.96 seconds wall clock time: 24 minutes 4.78 seconds (1444.78 seconds total)