Starting phenix.real_space_refine on Sat Jul 26 04:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grx_34216/07_2025/8grx_34216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grx_34216/07_2025/8grx_34216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8grx_34216/07_2025/8grx_34216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grx_34216/07_2025/8grx_34216.map" model { file = "/net/cci-nas-00/data/ceres_data/8grx_34216/07_2025/8grx_34216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grx_34216/07_2025/8grx_34216.cif" } resolution = 3.0 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= 0.002 sd= 0.116 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 42 5.16 5 C 5256 2.51 5 N 1474 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8328 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1140 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3024 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 352} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: D, C Time building chain proxies: 6.75, per 1000 atoms: 0.81 Number of scatterers: 8328 At special positions: 0 Unit cell: (124.063, 150.412, 77.9509, 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 42 16.00 O 1556 8.00 N 1474 7.00 C 5256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 245 " - pdb=" SG CYS B 296 " distance=2.02 Simple disulfide: pdb=" SG CYS B 345 " - pdb=" SG CYS B 396 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 245 " - pdb=" SG CYS D 296 " distance=2.02 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 396 " distance=2.04 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: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 22 sheets defined 27.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 removed outlier: 3.953A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 54 through 82 Processing helix chain 'A' and resid 87 through 125 Processing helix chain 'A' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.953A pdb=" N LEU C 43 " --> pdb=" O TRP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 54 through 82 Processing helix chain 'C' and resid 87 through 125 Processing helix chain 'C' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET B 117 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP B 192 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG B 193 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU B 241 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU B 235 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN B 320 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 317 " --> pdb=" O LEU B 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 268 Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL B 341 " --> pdb=" O MET B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336 Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET D 117 " --> pdb=" O TRP D 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 129 Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP D 192 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG D 193 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU D 241 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU D 235 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN D 320 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET D 317 " --> pdb=" O LEU D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 268 Processing sheet with id=AC3, first strand: chain 'D' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL D 341 " --> pdb=" O MET D 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 334 through 336 439 hydrogen bonds defined for protein. 1167 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: 2.59 Time building geometry restraints manager: 2.51 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: 1926 1.33 - 1.45: 1864 1.45 - 1.57: 4692 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8550 Sorted by residual: bond pdb=" C HIS D 363 " pdb=" N PRO D 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C HIS B 363 " pdb=" N PRO B 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C GLY D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C GLY B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C PHE B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 8.46e+00 ... (remaining 8545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 10724 2.13 - 4.25: 712 4.25 - 6.38: 112 6.38 - 8.50: 32 8.50 - 10.63: 18 Bond angle restraints: 11598 Sorted by residual: angle pdb=" C GLU B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C GLU D 67 " pdb=" N PRO D 68 " pdb=" CA PRO D 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C ARG D 267 " pdb=" N PRO D 268 " pdb=" CA PRO D 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C ARG B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C GLY D 184 " pdb=" N PRO D 185 " pdb=" CA PRO D 185 " ideal model delta sigma weight residual 119.84 126.74 -6.90 1.25e+00 6.40e-01 3.05e+01 ... (remaining 11593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.18: 4966 25.18 - 50.36: 152 50.36 - 75.54: 18 75.54 - 100.72: 2 100.72 - 125.90: 4 Dihedral angle restraints: 5142 sinusoidal: 2098 harmonic: 3044 Sorted by residual: dihedral pdb=" CA GLN B 330 " pdb=" C GLN B 330 " pdb=" N PRO B 331 " pdb=" CA PRO B 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLN D 330 " pdb=" C GLN D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLY B 184 " pdb=" C GLY B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -67.33 -112.67 0 5.00e+00 4.00e-02 5.08e+02 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 758 0.040 - 0.080: 302 0.080 - 0.120: 116 0.120 - 0.159: 38 0.159 - 0.199: 2 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA SER A 54 " pdb=" N SER A 54 " pdb=" C SER A 54 " pdb=" CB SER A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA SER C 54 " pdb=" N SER C 54 " pdb=" C SER C 54 " pdb=" CB SER C 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CG LEU D 235 " pdb=" CB LEU D 235 " pdb=" CD1 LEU D 235 " pdb=" CD2 LEU D 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1213 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 131 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 132 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 131 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 132 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ALA A 86 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 87 " -0.009 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2944 2.88 - 3.38: 7335 3.38 - 3.89: 14411 3.89 - 4.39: 16410 4.39 - 4.90: 26746 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" OG SER D 102 " pdb=" O GLY D 105 " model vdw 2.373 3.040 nonbonded pdb=" OG SER B 102 " pdb=" O GLY B 105 " model vdw 2.373 3.040 nonbonded pdb=" NE ARG B 253 " pdb=" O HIS B 300 " model vdw 2.522 3.120 nonbonded pdb=" NE ARG D 253 " pdb=" O HIS D 300 " model vdw 2.522 3.120 nonbonded pdb=" O ARG B 223 " pdb=" OH TYR B 251 " model vdw 2.551 3.040 ... (remaining 67841 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.720 Find NCS groups from input model: 0.140 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.007 0.040 8558 Z= 0.480 Angle : 1.263 10.628 11614 Z= 0.794 Chirality : 0.051 0.199 1216 Planarity : 0.005 0.057 1514 Dihedral : 12.300 125.903 3170 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.27 % Favored : 96.15 % Rotamer: Outliers : 0.22 % Allowed : 5.83 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 8.11 % 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: -0.43 (0.25), residues: 1040 helix: 1.26 (0.28), residues: 256 sheet: -0.08 (0.28), residues: 310 loop : -1.28 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 26 HIS 0.003 0.001 HIS D 209 PHE 0.010 0.002 PHE B 177 TYR 0.020 0.002 TYR B 197 ARG 0.005 0.001 ARG D 253 Details of bonding type rmsd hydrogen bonds : bond 0.15753 ( 429) hydrogen bonds : angle 7.61385 ( 1167) SS BOND : bond 0.00819 ( 8) SS BOND : angle 1.03658 ( 16) covalent geometry : bond 0.00651 ( 8550) covalent geometry : angle 1.26351 (11598) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 1.5825 time to fit residues: 257.4543 Evaluate side-chains 98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 58 GLN A 81 GLN A 117 GLN A 128 GLN A 140 HIS A 156 GLN B 92 HIS B 190 HIS B 205 GLN B 266 GLN B 280 ASN B 290 HIS B 301 ASN B 346 GLN C 46 GLN C 58 GLN C 81 GLN C 117 GLN C 128 GLN C 140 HIS C 156 GLN D 92 HIS D 190 HIS D 205 GLN D 266 GLN D 280 ASN D 290 HIS D 301 ASN D 346 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.199061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150801 restraints weight = 8980.589| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.35 r_work: 0.3385 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8558 Z= 0.153 Angle : 0.570 7.172 11614 Z= 0.299 Chirality : 0.039 0.138 1216 Planarity : 0.006 0.095 1514 Dihedral : 5.719 91.399 1164 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.04 % Rotamer: Outliers : 1.57 % Allowed : 10.31 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 5.41 % 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 (0.26), residues: 1040 helix: 3.55 (0.28), residues: 254 sheet: 0.36 (0.28), residues: 316 loop : -0.28 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 32 HIS 0.004 0.001 HIS D 92 PHE 0.010 0.001 PHE D 351 TYR 0.018 0.002 TYR D 372 ARG 0.002 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 429) hydrogen bonds : angle 5.31192 ( 1167) SS BOND : bond 0.00492 ( 8) SS BOND : angle 0.67111 ( 16) covalent geometry : bond 0.00346 ( 8550) covalent geometry : angle 0.56936 (11598) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7714 (ptm) REVERT: A 125 MET cc_start: 0.8402 (mmm) cc_final: 0.8145 (mmt) REVERT: A 151 ASP cc_start: 0.8679 (m-30) cc_final: 0.8294 (m-30) REVERT: B 32 TRP cc_start: 0.7383 (p90) cc_final: 0.6797 (p90) REVERT: B 223 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8463 (ttp80) REVERT: B 248 ASP cc_start: 0.7760 (p0) cc_final: 0.7554 (p0) REVERT: B 339 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7474 (mt-10) REVERT: C 64 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7719 (ptm) REVERT: C 125 MET cc_start: 0.8434 (mmm) cc_final: 0.8179 (mmt) REVERT: C 151 ASP cc_start: 0.8686 (m-30) cc_final: 0.8300 (m-30) REVERT: D 32 TRP cc_start: 0.7381 (p90) cc_final: 0.6793 (p90) REVERT: D 223 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8457 (ttp80) REVERT: D 339 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7477 (mt-10) outliers start: 14 outliers final: 2 residues processed: 108 average time/residue: 1.8561 time to fit residues: 214.0054 Evaluate side-chains 102 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 266 GLN B 405 HIS C 46 GLN D 266 GLN D 405 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148097 restraints weight = 8990.487| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.98 r_work: 0.3386 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8558 Z= 0.146 Angle : 0.530 6.786 11614 Z= 0.276 Chirality : 0.038 0.131 1216 Planarity : 0.006 0.096 1514 Dihedral : 5.078 81.454 1164 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.50 % Favored : 97.31 % Rotamer: Outliers : 1.57 % Allowed : 11.32 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.77 (0.27), residues: 1040 helix: 3.92 (0.29), residues: 254 sheet: 0.74 (0.29), residues: 314 loop : -0.04 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 26 HIS 0.002 0.001 HIS A 140 PHE 0.008 0.001 PHE D 351 TYR 0.012 0.002 TYR B 197 ARG 0.004 0.000 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 429) hydrogen bonds : angle 4.77728 ( 1167) SS BOND : bond 0.00568 ( 8) SS BOND : angle 0.74540 ( 16) covalent geometry : bond 0.00341 ( 8550) covalent geometry : angle 0.52946 (11598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7987 (ttt-90) cc_final: 0.7737 (ttm170) REVERT: A 151 ASP cc_start: 0.8684 (m-30) cc_final: 0.8253 (m-30) REVERT: B 32 TRP cc_start: 0.7577 (p90) cc_final: 0.7025 (p90) REVERT: B 223 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8567 (ttp80) REVERT: B 339 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7616 (mt-10) REVERT: C 61 ARG cc_start: 0.7991 (ttt-90) cc_final: 0.7738 (ttm170) REVERT: C 151 ASP cc_start: 0.8702 (m-30) cc_final: 0.8273 (m-30) REVERT: D 32 TRP cc_start: 0.7575 (p90) cc_final: 0.7027 (p90) REVERT: D 223 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8551 (ttp80) REVERT: D 339 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7615 (mt-10) outliers start: 14 outliers final: 9 residues processed: 114 average time/residue: 1.3124 time to fit residues: 159.6747 Evaluate side-chains 109 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 21 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.195205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147441 restraints weight = 8981.783| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.14 r_work: 0.3322 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8558 Z= 0.123 Angle : 0.496 6.662 11614 Z= 0.257 Chirality : 0.037 0.138 1216 Planarity : 0.005 0.101 1514 Dihedral : 4.955 78.247 1164 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.35 % Favored : 98.46 % Rotamer: Outliers : 2.47 % Allowed : 11.10 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.79 (0.27), residues: 1040 helix: 3.95 (0.28), residues: 254 sheet: 0.67 (0.28), residues: 332 loop : 0.00 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.004 0.001 HIS D 363 PHE 0.005 0.001 PHE B 351 TYR 0.011 0.001 TYR D 377 ARG 0.004 0.000 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 429) hydrogen bonds : angle 4.57751 ( 1167) SS BOND : bond 0.00488 ( 8) SS BOND : angle 0.69278 ( 16) covalent geometry : bond 0.00287 ( 8550) covalent geometry : angle 0.49610 (11598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: A 151 ASP cc_start: 0.8586 (m-30) cc_final: 0.8176 (m-30) REVERT: B 32 TRP cc_start: 0.7417 (p90) cc_final: 0.7084 (p90) REVERT: B 223 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8501 (ttp80) REVERT: B 339 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7587 (mt-10) REVERT: C 132 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: C 151 ASP cc_start: 0.8591 (m-30) cc_final: 0.8183 (m-30) REVERT: D 32 TRP cc_start: 0.7404 (p90) cc_final: 0.7072 (p90) REVERT: D 223 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8415 (ttp80) REVERT: D 339 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7588 (mt-10) outliers start: 22 outliers final: 11 residues processed: 116 average time/residue: 1.2966 time to fit residues: 159.4616 Evaluate side-chains 109 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.192185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144062 restraints weight = 8970.349| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.15 r_work: 0.3243 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8558 Z= 0.200 Angle : 0.556 6.842 11614 Z= 0.284 Chirality : 0.039 0.137 1216 Planarity : 0.006 0.105 1514 Dihedral : 5.079 76.248 1164 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.88 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 11.21 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.64 (0.27), residues: 1040 helix: 3.58 (0.29), residues: 254 sheet: 0.65 (0.29), residues: 330 loop : 0.02 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.006 0.001 PHE B 351 TYR 0.014 0.002 TYR D 198 ARG 0.003 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 429) hydrogen bonds : angle 4.63121 ( 1167) SS BOND : bond 0.00812 ( 8) SS BOND : angle 1.00486 ( 16) covalent geometry : bond 0.00488 ( 8550) covalent geometry : angle 0.55557 (11598) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6968 (mt-10) REVERT: A 58 GLN cc_start: 0.7823 (mt0) cc_final: 0.7266 (tp-100) REVERT: A 132 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: A 151 ASP cc_start: 0.8582 (m-30) cc_final: 0.8246 (m-30) REVERT: B 32 TRP cc_start: 0.7465 (p90) cc_final: 0.7111 (p90) REVERT: B 223 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8474 (ttp80) REVERT: C 49 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6969 (mt-10) REVERT: C 58 GLN cc_start: 0.7821 (mt0) cc_final: 0.7265 (tp-100) REVERT: C 132 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: C 151 ASP cc_start: 0.8598 (m-30) cc_final: 0.8258 (m-30) REVERT: D 32 TRP cc_start: 0.7456 (p90) cc_final: 0.7109 (p90) REVERT: D 223 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8537 (ttp80) outliers start: 25 outliers final: 11 residues processed: 117 average time/residue: 1.2655 time to fit residues: 157.3388 Evaluate side-chains 108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 0.3980 chunk 74 optimal weight: 0.0030 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 0.0170 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.195958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150130 restraints weight = 8997.987| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.32 r_work: 0.3360 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8558 Z= 0.099 Angle : 0.482 6.260 11614 Z= 0.248 Chirality : 0.036 0.140 1216 Planarity : 0.006 0.116 1514 Dihedral : 4.806 72.655 1164 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.79 % Allowed : 12.33 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.98 (0.27), residues: 1040 helix: 4.05 (0.28), residues: 254 sheet: 0.65 (0.28), residues: 336 loop : 0.29 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 26 HIS 0.005 0.001 HIS B 363 PHE 0.005 0.001 PHE D 354 TYR 0.012 0.001 TYR D 377 ARG 0.002 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 429) hydrogen bonds : angle 4.36582 ( 1167) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.51290 ( 16) covalent geometry : bond 0.00221 ( 8550) covalent geometry : angle 0.48223 (11598) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7790 (ttt-90) cc_final: 0.7489 (ttm110) REVERT: A 64 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7916 (ptm) REVERT: A 112 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7436 (mtp85) REVERT: A 151 ASP cc_start: 0.8618 (m-30) cc_final: 0.8294 (m-30) REVERT: B 32 TRP cc_start: 0.7404 (p90) cc_final: 0.7071 (p90) REVERT: B 223 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8535 (ttp80) REVERT: C 61 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7490 (ttm110) REVERT: C 64 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7912 (ptm) REVERT: C 112 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7431 (mtp85) REVERT: C 151 ASP cc_start: 0.8629 (m-30) cc_final: 0.8305 (m-30) REVERT: D 32 TRP cc_start: 0.7414 (p90) cc_final: 0.7086 (p90) REVERT: D 223 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8531 (ttp80) outliers start: 16 outliers final: 8 residues processed: 106 average time/residue: 1.3214 time to fit residues: 149.3937 Evaluate side-chains 99 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.192991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144264 restraints weight = 9062.835| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.14 r_work: 0.3373 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8558 Z= 0.143 Angle : 0.506 6.035 11614 Z= 0.259 Chirality : 0.037 0.140 1216 Planarity : 0.006 0.112 1514 Dihedral : 4.836 70.484 1164 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.47 % Allowed : 12.11 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.91 (0.27), residues: 1040 helix: 3.89 (0.28), residues: 254 sheet: 0.61 (0.28), residues: 334 loop : 0.31 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 26 HIS 0.005 0.001 HIS B 363 PHE 0.004 0.001 PHE D 381 TYR 0.012 0.001 TYR B 198 ARG 0.002 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 429) hydrogen bonds : angle 4.38192 ( 1167) SS BOND : bond 0.00569 ( 8) SS BOND : angle 0.80945 ( 16) covalent geometry : bond 0.00346 ( 8550) covalent geometry : angle 0.50513 (11598) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7002 (mt-10) REVERT: A 64 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7861 (ptm) REVERT: A 112 ARG cc_start: 0.7575 (mtm110) cc_final: 0.7324 (mtp85) REVERT: A 132 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: A 151 ASP cc_start: 0.8547 (m-30) cc_final: 0.8218 (m-30) REVERT: B 32 TRP cc_start: 0.7518 (p90) cc_final: 0.7201 (p90) REVERT: B 223 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8508 (ttp80) REVERT: C 49 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7011 (mt-10) REVERT: C 64 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7868 (ptm) REVERT: C 112 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7321 (mtp85) REVERT: C 132 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: C 151 ASP cc_start: 0.8557 (m-30) cc_final: 0.8229 (m-30) REVERT: D 32 TRP cc_start: 0.7509 (p90) cc_final: 0.7198 (p90) REVERT: D 223 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8454 (ttp80) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 1.8335 time to fit residues: 212.9746 Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.192869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145175 restraints weight = 9087.399| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.12 r_work: 0.3301 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8558 Z= 0.136 Angle : 0.492 5.818 11614 Z= 0.253 Chirality : 0.037 0.137 1216 Planarity : 0.005 0.107 1514 Dihedral : 4.785 69.521 1164 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.24 % Allowed : 13.00 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 2.03 (0.27), residues: 1040 helix: 3.94 (0.28), residues: 254 sheet: 0.66 (0.29), residues: 334 loop : 0.43 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 26 HIS 0.005 0.001 HIS B 363 PHE 0.004 0.001 PHE B 381 TYR 0.011 0.001 TYR D 377 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 429) hydrogen bonds : angle 4.32726 ( 1167) SS BOND : bond 0.00500 ( 8) SS BOND : angle 0.76716 ( 16) covalent geometry : bond 0.00327 ( 8550) covalent geometry : angle 0.49169 (11598) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7020 (mt-10) REVERT: A 61 ARG cc_start: 0.7961 (ttt-90) cc_final: 0.7602 (ttm110) REVERT: A 64 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7889 (ptm) REVERT: A 112 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7384 (mtp85) REVERT: A 132 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: A 151 ASP cc_start: 0.8640 (m-30) cc_final: 0.8314 (m-30) REVERT: B 32 TRP cc_start: 0.7493 (p90) cc_final: 0.7216 (p90) REVERT: B 223 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8506 (ttp80) REVERT: C 49 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7017 (mt-10) REVERT: C 64 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7890 (ptm) REVERT: C 112 ARG cc_start: 0.7614 (mtm110) cc_final: 0.7374 (mtp85) REVERT: C 132 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: C 151 ASP cc_start: 0.8648 (m-30) cc_final: 0.8325 (m-30) REVERT: D 32 TRP cc_start: 0.7481 (p90) cc_final: 0.7212 (p90) REVERT: D 223 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8460 (ttp80) outliers start: 20 outliers final: 8 residues processed: 107 average time/residue: 1.2294 time to fit residues: 140.7044 Evaluate side-chains 102 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.192310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144607 restraints weight = 9097.869| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.13 r_work: 0.3235 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8558 Z= 0.144 Angle : 0.501 5.780 11614 Z= 0.257 Chirality : 0.037 0.136 1216 Planarity : 0.006 0.104 1514 Dihedral : 4.798 68.781 1164 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.79 % Allowed : 13.45 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.27), residues: 1040 helix: 3.88 (0.28), residues: 254 sheet: 0.71 (0.29), residues: 330 loop : 0.46 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.005 0.001 HIS B 363 PHE 0.007 0.001 PHE D 381 TYR 0.012 0.001 TYR D 377 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 429) hydrogen bonds : angle 4.32923 ( 1167) SS BOND : bond 0.00551 ( 8) SS BOND : angle 0.83398 ( 16) covalent geometry : bond 0.00348 ( 8550) covalent geometry : angle 0.50089 (11598) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7013 (mt-10) REVERT: A 64 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7836 (ptm) REVERT: A 112 ARG cc_start: 0.7499 (mtm110) cc_final: 0.7252 (mtp85) REVERT: A 132 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: A 151 ASP cc_start: 0.8538 (m-30) cc_final: 0.8218 (m-30) REVERT: B 32 TRP cc_start: 0.7513 (p90) cc_final: 0.7263 (p90) REVERT: B 223 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8438 (ttp80) REVERT: C 49 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7012 (mt-10) REVERT: C 64 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7839 (ptm) REVERT: C 112 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7250 (mtp85) REVERT: C 132 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: C 151 ASP cc_start: 0.8542 (m-30) cc_final: 0.8223 (m-30) REVERT: D 32 TRP cc_start: 0.7565 (p90) cc_final: 0.7294 (p90) REVERT: D 223 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8440 (ttp80) outliers start: 16 outliers final: 8 residues processed: 101 average time/residue: 1.2530 time to fit residues: 134.7846 Evaluate side-chains 103 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.0000 chunk 16 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.191715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145108 restraints weight = 9023.124| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.05 r_work: 0.3213 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8558 Z= 0.155 Angle : 0.511 5.744 11614 Z= 0.261 Chirality : 0.037 0.137 1216 Planarity : 0.005 0.103 1514 Dihedral : 4.855 68.570 1164 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.02 % Allowed : 13.34 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 2.00 (0.27), residues: 1040 helix: 3.83 (0.28), residues: 254 sheet: 0.68 (0.29), residues: 330 loop : 0.45 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.006 0.001 PHE B 381 TYR 0.012 0.001 TYR B 197 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 429) hydrogen bonds : angle 4.34897 ( 1167) SS BOND : bond 0.00596 ( 8) SS BOND : angle 0.86089 ( 16) covalent geometry : bond 0.00376 ( 8550) covalent geometry : angle 0.51007 (11598) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6878 (mt-10) REVERT: A 58 GLN cc_start: 0.7914 (mt0) cc_final: 0.7213 (tp-100) REVERT: A 64 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7717 (ptm) REVERT: A 112 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7411 (mtp85) REVERT: A 132 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: A 151 ASP cc_start: 0.8618 (m-30) cc_final: 0.8276 (m-30) REVERT: B 32 TRP cc_start: 0.7541 (p90) cc_final: 0.7281 (p90) REVERT: B 223 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8450 (ttp80) REVERT: B 416 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7318 (tp) REVERT: C 49 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6865 (mt-10) REVERT: C 58 GLN cc_start: 0.7912 (mt0) cc_final: 0.7208 (tp-100) REVERT: C 64 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7725 (ptm) REVERT: C 112 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7406 (mtp85) REVERT: C 132 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: C 151 ASP cc_start: 0.8617 (m-30) cc_final: 0.8278 (m-30) REVERT: D 32 TRP cc_start: 0.7569 (p90) cc_final: 0.7314 (p90) REVERT: D 223 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8446 (ttp80) REVERT: D 416 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7301 (tp) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 1.2550 time to fit residues: 148.3056 Evaluate side-chains 113 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 92 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 314 ASN D 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.190380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145773 restraints weight = 9017.324| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.02 r_work: 0.3349 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8558 Z= 0.120 Angle : 0.479 5.683 11614 Z= 0.247 Chirality : 0.036 0.136 1216 Planarity : 0.005 0.102 1514 Dihedral : 4.731 67.616 1164 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.68 % Allowed : 13.57 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 2.18 (0.28), residues: 1040 helix: 4.01 (0.28), residues: 254 sheet: 0.77 (0.29), residues: 330 loop : 0.55 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.004 0.001 PHE D 381 TYR 0.012 0.001 TYR D 377 ARG 0.001 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 429) hydrogen bonds : angle 4.25517 ( 1167) SS BOND : bond 0.00413 ( 8) SS BOND : angle 0.70633 ( 16) covalent geometry : bond 0.00285 ( 8550) covalent geometry : angle 0.47850 (11598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6583.57 seconds wall clock time: 117 minutes 9.93 seconds (7029.93 seconds total)