Starting phenix.real_space_refine on Wed Apr 30 04:01:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ni2_9375/04_2025/6ni2_9375.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ni2_9375/04_2025/6ni2_9375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ni2_9375/04_2025/6ni2_9375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ni2_9375/04_2025/6ni2_9375.map" model { file = "/net/cci-nas-00/data/ceres_data/6ni2_9375/04_2025/6ni2_9375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ni2_9375/04_2025/6ni2_9375.cif" } resolution = 4.0 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= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4506 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 21 5.16 5 C 3402 2.51 5 N 910 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5381 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 865 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2699 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 72 Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 109 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 4.22, per 1000 atoms: 0.78 Number of scatterers: 5381 At special positions: 0 Unit cell: (95.68, 91.52, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 6 15.00 O 1042 8.00 N 910 7.00 C 3402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 751.0 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 15 sheets defined 2.8% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'H' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 23 removed outlier: 3.728A pdb=" N MET A 82 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.537A pdb=" N THR A 108 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.580A pdb=" N LYS B 10 " --> pdb=" O ALA V 361 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.700A pdb=" N VAL B 164 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 168 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 75 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.700A pdb=" N VAL B 164 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 168 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.680A pdb=" N HIS B 198 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 274 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 272 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 218 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 270 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 220 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 268 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.629A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS B 251 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 239 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 249 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 241 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.629A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 343 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.557A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.094A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.094A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.659A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.926A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 465 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: 3.52 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1685 1.34 - 1.46: 1215 1.46 - 1.58: 2547 1.58 - 1.70: 22 1.70 - 1.82: 28 Bond restraints: 5497 Sorted by residual: bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.625 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O1P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O2P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O2P TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 5492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 7216 3.13 - 6.26: 240 6.26 - 9.40: 27 9.40 - 12.53: 3 12.53 - 15.66: 2 Bond angle restraints: 7488 Sorted by residual: angle pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" C GLU B 156 " ideal model delta sigma weight residual 110.24 117.78 -7.54 1.41e+00 5.03e-01 2.86e+01 angle pdb=" C THR B 74 " pdb=" N PHE B 75 " pdb=" CA PHE B 75 " ideal model delta sigma weight residual 122.29 130.49 -8.20 1.65e+00 3.67e-01 2.47e+01 angle pdb=" C GLN B 189 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " ideal model delta sigma weight residual 122.07 112.79 9.28 2.01e+00 2.48e-01 2.13e+01 angle pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " pdb=" CG LEU A 85 " ideal model delta sigma weight residual 116.30 100.64 15.66 3.50e+00 8.16e-02 2.00e+01 angle pdb=" N PHE B 75 " pdb=" CA PHE B 75 " pdb=" C PHE B 75 " ideal model delta sigma weight residual 109.23 102.62 6.61 1.55e+00 4.16e-01 1.82e+01 ... (remaining 7483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.64: 3059 13.64 - 27.29: 185 27.29 - 40.93: 30 40.93 - 54.58: 7 54.58 - 68.22: 4 Dihedral angle restraints: 3285 sinusoidal: 1239 harmonic: 2046 Sorted by residual: dihedral pdb=" CA ALA A 51 " pdb=" C ALA A 51 " pdb=" N THR A 52 " pdb=" CA THR A 52 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA TYR A 59 " pdb=" C TYR A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 3282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 641 0.077 - 0.154: 188 0.154 - 0.231: 23 0.231 - 0.308: 2 0.308 - 0.385: 2 Chirality restraints: 856 Sorted by residual: chirality pdb=" CB VAL B 164 " pdb=" CA VAL B 164 " pdb=" CG1 VAL B 164 " pdb=" CG2 VAL B 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA VAL B 164 " pdb=" N VAL B 164 " pdb=" C VAL B 164 " pdb=" CB VAL B 164 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 853 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 9 " 0.028 2.00e-02 2.50e+03 2.35e-02 9.65e+00 pdb=" CG PHE B 9 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 113 " 0.022 2.00e-02 2.50e+03 2.04e-02 8.32e+00 pdb=" CG TYR B 113 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 113 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 113 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 113 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 113 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 113 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 21 " 0.019 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR B 21 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 21 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 21 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 21 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 21 " -0.005 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1065 2.78 - 3.31: 4502 3.31 - 3.84: 8646 3.84 - 4.37: 9354 4.37 - 4.90: 16512 Nonbonded interactions: 40079 Sorted by model distance: nonbonded pdb=" OD1 ASP B 204 " pdb=" OH TYR B 208 " model vdw 2.245 3.040 nonbonded pdb=" O ASP A 89 " pdb=" OH TYR A 93 " model vdw 2.256 3.040 nonbonded pdb=" OG SEP V 363 " pdb=" N SEP V 364 " model vdw 2.314 3.120 nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.337 3.040 ... (remaining 40074 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=1.00 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.400 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.010 0.121 5500 Z= 0.431 Angle : 1.328 15.660 7492 Z= 0.729 Chirality : 0.070 0.385 856 Planarity : 0.007 0.055 951 Dihedral : 9.614 68.220 1967 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.50 (0.31), residues: 682 helix: -0.31 (1.30), residues: 12 sheet: -0.88 (0.30), residues: 271 loop : -1.06 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 36 HIS 0.012 0.004 HIS A 44 PHE 0.054 0.005 PHE B 9 TYR 0.051 0.005 TYR B 113 ARG 0.015 0.002 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.30825 ( 162) hydrogen bonds : angle 9.89892 ( 465) SS BOND : bond 0.01335 ( 2) SS BOND : angle 2.64714 ( 4) covalent geometry : bond 0.00957 ( 5497) covalent geometry : angle 1.32666 ( 7488) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6443 (tpt-90) cc_final: 0.6016 (tpp80) REVERT: A 64 LYS cc_start: 0.8636 (ptpt) cc_final: 0.8060 (ptpp) REVERT: A 67 PHE cc_start: 0.7543 (m-10) cc_final: 0.7182 (m-10) REVERT: A 85 LEU cc_start: 0.7294 (mt) cc_final: 0.7091 (mt) REVERT: B 42 LEU cc_start: 0.7307 (tp) cc_final: 0.6995 (pp) REVERT: B 77 LYS cc_start: 0.8015 (tppt) cc_final: 0.7525 (mmtm) REVERT: B 232 LYS cc_start: 0.6625 (mttt) cc_final: 0.5500 (tttt) REVERT: H 48 LEU cc_start: 0.9402 (mt) cc_final: 0.9089 (tp) REVERT: H 71 PHE cc_start: 0.8088 (m-10) cc_final: 0.6749 (m-10) REVERT: L 25 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8169 (mtm-85) REVERT: L 28 GLN cc_start: 0.8997 (tt0) cc_final: 0.8639 (mt0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2188 time to fit residues: 41.4193 Evaluate side-chains 75 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.0000 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.106715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091466 restraints weight = 18999.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.093793 restraints weight = 11509.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.095485 restraints weight = 8013.776| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5500 Z= 0.189 Angle : 0.778 13.486 7492 Z= 0.401 Chirality : 0.047 0.154 856 Planarity : 0.005 0.058 951 Dihedral : 6.857 57.513 780 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.46 % Allowed : 13.51 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.59 (0.32), residues: 682 helix: 0.41 (1.44), residues: 12 sheet: -0.14 (0.31), residues: 274 loop : -0.54 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 36 HIS 0.008 0.002 HIS B 219 PHE 0.014 0.003 PHE B 277 TYR 0.030 0.002 TYR H 57 ARG 0.008 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 162) hydrogen bonds : angle 7.14450 ( 465) SS BOND : bond 0.01123 ( 2) SS BOND : angle 2.09663 ( 4) covalent geometry : bond 0.00419 ( 5497) covalent geometry : angle 0.77637 ( 7488) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6589 (tpt-90) cc_final: 0.6162 (tpp80) REVERT: A 22 CYS cc_start: 0.6771 (t) cc_final: 0.6541 (m) REVERT: A 64 LYS cc_start: 0.8571 (ptpt) cc_final: 0.8311 (ptpp) REVERT: A 75 LYS cc_start: 0.8506 (tttt) cc_final: 0.8253 (ttmt) REVERT: A 82 MET cc_start: 0.8177 (mtp) cc_final: 0.7570 (mtp) REVERT: B 77 LYS cc_start: 0.8234 (tppt) cc_final: 0.7753 (mmtm) REVERT: B 185 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6955 (mt-10) REVERT: B 241 ILE cc_start: 0.8748 (mt) cc_final: 0.8547 (tp) REVERT: H 40 VAL cc_start: 0.9139 (t) cc_final: 0.8891 (m) REVERT: L 28 GLN cc_start: 0.8859 (tt0) cc_final: 0.8579 (mt0) REVERT: L 82 GLU cc_start: 0.8462 (pm20) cc_final: 0.8164 (pp20) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.2170 time to fit residues: 29.0848 Evaluate side-chains 79 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.103777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.089399 restraints weight = 19813.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.091709 restraints weight = 11919.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.093355 restraints weight = 8235.650| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5500 Z= 0.222 Angle : 0.730 7.212 7492 Z= 0.379 Chirality : 0.046 0.156 856 Planarity : 0.005 0.055 951 Dihedral : 6.861 59.251 780 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.91 % Allowed : 12.46 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.43 (0.32), residues: 682 helix: 1.02 (1.48), residues: 12 sheet: 0.08 (0.31), residues: 283 loop : -0.55 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 36 HIS 0.008 0.002 HIS A 44 PHE 0.015 0.002 PHE A 67 TYR 0.026 0.002 TYR H 83 ARG 0.006 0.001 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 162) hydrogen bonds : angle 6.47401 ( 465) SS BOND : bond 0.00879 ( 2) SS BOND : angle 1.26586 ( 4) covalent geometry : bond 0.00502 ( 5497) covalent geometry : angle 0.72971 ( 7488) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.7577 (m-10) cc_final: 0.7345 (m-10) REVERT: A 82 MET cc_start: 0.7986 (mtp) cc_final: 0.7301 (mtp) REVERT: H 32 VAL cc_start: 0.7799 (p) cc_final: 0.7516 (t) REVERT: H 55 SER cc_start: 0.8782 (t) cc_final: 0.8539 (m) REVERT: L 28 GLN cc_start: 0.8907 (tt0) cc_final: 0.8639 (mt0) REVERT: L 88 TYR cc_start: 0.8454 (m-10) cc_final: 0.8159 (m-10) outliers start: 28 outliers final: 20 residues processed: 94 average time/residue: 0.1576 time to fit residues: 19.6934 Evaluate side-chains 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.109860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094808 restraints weight = 19513.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.097161 restraints weight = 11810.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.098833 restraints weight = 8196.057| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5500 Z= 0.135 Angle : 0.640 8.565 7492 Z= 0.329 Chirality : 0.044 0.145 856 Planarity : 0.004 0.045 951 Dihedral : 6.453 57.002 780 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.74 % Allowed : 13.33 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.23 (0.32), residues: 682 helix: 1.53 (1.58), residues: 12 sheet: 0.24 (0.31), residues: 281 loop : -0.45 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 36 HIS 0.004 0.001 HIS A 44 PHE 0.011 0.002 PHE A 29 TYR 0.020 0.002 TYR H 57 ARG 0.004 0.001 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 162) hydrogen bonds : angle 5.89849 ( 465) SS BOND : bond 0.00766 ( 2) SS BOND : angle 1.22283 ( 4) covalent geometry : bond 0.00307 ( 5497) covalent geometry : angle 0.63918 ( 7488) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.7490 (m-10) cc_final: 0.7283 (m-10) REVERT: A 82 MET cc_start: 0.7702 (mtp) cc_final: 0.7423 (mtp) REVERT: H 32 VAL cc_start: 0.7743 (p) cc_final: 0.7533 (t) REVERT: H 55 SER cc_start: 0.8812 (t) cc_final: 0.8551 (m) REVERT: L 28 GLN cc_start: 0.8985 (tt0) cc_final: 0.8712 (mt0) outliers start: 27 outliers final: 18 residues processed: 94 average time/residue: 0.1739 time to fit residues: 22.7106 Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094339 restraints weight = 19404.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096571 restraints weight = 11903.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.098243 restraints weight = 8345.083| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5500 Z= 0.183 Angle : 0.673 6.992 7492 Z= 0.349 Chirality : 0.046 0.239 856 Planarity : 0.004 0.044 951 Dihedral : 6.511 59.283 780 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.74 % Allowed : 15.44 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.26 (0.32), residues: 682 helix: 1.82 (1.63), residues: 12 sheet: 0.21 (0.30), residues: 296 loop : -0.49 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 36 HIS 0.005 0.001 HIS A 44 PHE 0.011 0.002 PHE B 61 TYR 0.022 0.002 TYR B 321 ARG 0.004 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 162) hydrogen bonds : angle 5.73420 ( 465) SS BOND : bond 0.00871 ( 2) SS BOND : angle 1.31029 ( 4) covalent geometry : bond 0.00416 ( 5497) covalent geometry : angle 0.67227 ( 7488) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.7795 (m-10) cc_final: 0.7534 (m-10) REVERT: A 82 MET cc_start: 0.7845 (mtp) cc_final: 0.7354 (mtp) REVERT: B 240 ASP cc_start: 0.7450 (p0) cc_final: 0.7023 (m-30) REVERT: H 32 VAL cc_start: 0.7627 (p) cc_final: 0.7404 (t) REVERT: H 55 SER cc_start: 0.8845 (t) cc_final: 0.8601 (m) REVERT: L 28 GLN cc_start: 0.8904 (tt0) cc_final: 0.8690 (mt0) outliers start: 27 outliers final: 24 residues processed: 90 average time/residue: 0.1367 time to fit residues: 17.0150 Evaluate side-chains 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.109679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.094631 restraints weight = 19573.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.096988 restraints weight = 11892.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.098588 restraints weight = 8256.442| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5500 Z= 0.151 Angle : 0.649 6.786 7492 Z= 0.332 Chirality : 0.045 0.206 856 Planarity : 0.004 0.038 951 Dihedral : 6.306 57.791 780 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.86 % Allowed : 18.60 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.13 (0.32), residues: 682 helix: 2.01 (1.67), residues: 12 sheet: 0.50 (0.31), residues: 278 loop : -0.57 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 36 HIS 0.004 0.001 HIS A 44 PHE 0.010 0.002 PHE L 72 TYR 0.015 0.002 TYR H 83 ARG 0.003 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 162) hydrogen bonds : angle 5.50611 ( 465) SS BOND : bond 0.00795 ( 2) SS BOND : angle 1.19610 ( 4) covalent geometry : bond 0.00345 ( 5497) covalent geometry : angle 0.64868 ( 7488) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8079 (mtp) cc_final: 0.7585 (mtp) REVERT: B 240 ASP cc_start: 0.7415 (p0) cc_final: 0.6950 (m-30) REVERT: H 32 VAL cc_start: 0.7546 (p) cc_final: 0.7338 (t) REVERT: H 50 TRP cc_start: 0.8857 (t60) cc_final: 0.8397 (t60) outliers start: 22 outliers final: 21 residues processed: 83 average time/residue: 0.1848 time to fit residues: 21.1794 Evaluate side-chains 86 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 0.0010 chunk 40 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.108628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.093753 restraints weight = 19914.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096094 restraints weight = 12194.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.097800 restraints weight = 8471.242| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5500 Z= 0.185 Angle : 0.672 7.500 7492 Z= 0.344 Chirality : 0.045 0.183 856 Planarity : 0.004 0.038 951 Dihedral : 6.369 59.188 780 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.86 % Allowed : 18.60 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.23 (0.32), residues: 682 helix: 2.01 (1.67), residues: 12 sheet: 0.45 (0.31), residues: 278 loop : -0.66 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 36 HIS 0.003 0.001 HIS A 44 PHE 0.013 0.002 PHE A 67 TYR 0.017 0.002 TYR H 83 ARG 0.003 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 162) hydrogen bonds : angle 5.48318 ( 465) SS BOND : bond 0.00869 ( 2) SS BOND : angle 1.19446 ( 4) covalent geometry : bond 0.00423 ( 5497) covalent geometry : angle 0.67141 ( 7488) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: B 203 LEU cc_start: 0.8943 (mp) cc_final: 0.8719 (mp) REVERT: B 215 SER cc_start: 0.9012 (m) cc_final: 0.8653 (p) REVERT: B 240 ASP cc_start: 0.7285 (p0) cc_final: 0.6746 (m-30) REVERT: H 32 VAL cc_start: 0.7465 (p) cc_final: 0.7243 (t) outliers start: 22 outliers final: 21 residues processed: 81 average time/residue: 0.1530 time to fit residues: 17.0585 Evaluate side-chains 86 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.109223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.094436 restraints weight = 19517.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.096680 restraints weight = 11921.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.098433 restraints weight = 8337.581| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5500 Z= 0.153 Angle : 0.657 9.696 7492 Z= 0.333 Chirality : 0.045 0.180 856 Planarity : 0.004 0.039 951 Dihedral : 6.262 58.137 780 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.04 % Allowed : 19.30 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.21 (0.32), residues: 682 helix: 2.05 (1.68), residues: 12 sheet: 0.53 (0.31), residues: 271 loop : -0.67 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 36 HIS 0.003 0.001 HIS A 44 PHE 0.015 0.002 PHE A 67 TYR 0.016 0.002 TYR B 249 ARG 0.003 0.001 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 162) hydrogen bonds : angle 5.29607 ( 465) SS BOND : bond 0.00806 ( 2) SS BOND : angle 1.14355 ( 4) covalent geometry : bond 0.00352 ( 5497) covalent geometry : angle 0.65688 ( 7488) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.6684 (m-80) cc_final: 0.6163 (m-10) REVERT: A 75 LYS cc_start: 0.8467 (tttt) cc_final: 0.8110 (tptt) REVERT: B 215 SER cc_start: 0.9038 (m) cc_final: 0.8712 (p) REVERT: B 240 ASP cc_start: 0.7328 (p0) cc_final: 0.6826 (m-30) REVERT: B 243 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.5130 (pt) REVERT: H 32 VAL cc_start: 0.7464 (p) cc_final: 0.7239 (t) outliers start: 23 outliers final: 20 residues processed: 83 average time/residue: 0.1445 time to fit residues: 16.4989 Evaluate side-chains 86 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.095553 restraints weight = 19188.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.097946 restraints weight = 11582.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.099667 restraints weight = 8000.574| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5500 Z= 0.120 Angle : 0.677 11.401 7492 Z= 0.334 Chirality : 0.044 0.175 856 Planarity : 0.004 0.040 951 Dihedral : 6.027 56.008 780 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.33 % Allowed : 20.18 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.11 (0.33), residues: 682 helix: 2.17 (1.70), residues: 12 sheet: 0.61 (0.32), residues: 271 loop : -0.63 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 36 HIS 0.002 0.001 HIS B 198 PHE 0.012 0.002 PHE B 268 TYR 0.016 0.002 TYR B 249 ARG 0.003 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 162) hydrogen bonds : angle 5.12641 ( 465) SS BOND : bond 0.00753 ( 2) SS BOND : angle 0.93013 ( 4) covalent geometry : bond 0.00279 ( 5497) covalent geometry : angle 0.67732 ( 7488) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8446 (tttt) cc_final: 0.7604 (tptt) REVERT: B 215 SER cc_start: 0.9010 (m) cc_final: 0.8700 (p) REVERT: B 240 ASP cc_start: 0.7396 (p0) cc_final: 0.6890 (m-30) outliers start: 19 outliers final: 18 residues processed: 84 average time/residue: 0.1612 time to fit residues: 18.2187 Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.0470 chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.110704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.095916 restraints weight = 19419.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.098267 restraints weight = 11803.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.099979 restraints weight = 8161.752| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5500 Z= 0.120 Angle : 0.665 8.436 7492 Z= 0.330 Chirality : 0.044 0.169 856 Planarity : 0.004 0.038 951 Dihedral : 5.911 55.753 780 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.02 (0.33), residues: 682 helix: 2.18 (1.69), residues: 12 sheet: 0.62 (0.32), residues: 280 loop : -0.49 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 36 HIS 0.002 0.001 HIS B 198 PHE 0.053 0.002 PHE A 27 TYR 0.019 0.002 TYR B 47 ARG 0.003 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 162) hydrogen bonds : angle 5.08204 ( 465) SS BOND : bond 0.00820 ( 2) SS BOND : angle 1.12184 ( 4) covalent geometry : bond 0.00281 ( 5497) covalent geometry : angle 0.66473 ( 7488) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.6711 (m-80) cc_final: 0.6219 (m-80) REVERT: A 59 TYR cc_start: 0.5708 (m-80) cc_final: 0.5406 (m-10) REVERT: A 75 LYS cc_start: 0.8461 (tttt) cc_final: 0.7612 (tptt) REVERT: B 215 SER cc_start: 0.9011 (m) cc_final: 0.8720 (p) REVERT: B 240 ASP cc_start: 0.7180 (p0) cc_final: 0.6784 (m-30) REVERT: B 255 MET cc_start: 0.7629 (mmm) cc_final: 0.7117 (mmm) REVERT: H 84 LEU cc_start: 0.8315 (mp) cc_final: 0.8029 (mp) outliers start: 19 outliers final: 16 residues processed: 81 average time/residue: 0.1664 time to fit residues: 18.1576 Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.110437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.095594 restraints weight = 19804.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.097906 restraints weight = 12020.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099608 restraints weight = 8330.425| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5500 Z= 0.132 Angle : 0.662 8.373 7492 Z= 0.332 Chirality : 0.045 0.167 856 Planarity : 0.004 0.039 951 Dihedral : 5.901 56.666 780 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.63 % Allowed : 21.05 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.07 (0.33), residues: 682 helix: 2.29 (1.71), residues: 12 sheet: 0.64 (0.32), residues: 280 loop : -0.44 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 36 HIS 0.002 0.001 HIS A 44 PHE 0.022 0.002 PHE A 27 TYR 0.016 0.002 TYR B 47 ARG 0.005 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 162) hydrogen bonds : angle 5.06418 ( 465) SS BOND : bond 0.00746 ( 2) SS BOND : angle 1.37083 ( 4) covalent geometry : bond 0.00308 ( 5497) covalent geometry : angle 0.66118 ( 7488) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.40 seconds wall clock time: 38 minutes 21.37 seconds (2301.37 seconds total)