Starting phenix.real_space_refine on Sun Jan 19 02:53:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xse_38617/01_2025/8xse_38617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xse_38617/01_2025/8xse_38617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xse_38617/01_2025/8xse_38617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xse_38617/01_2025/8xse_38617.map" model { file = "/net/cci-nas-00/data/ceres_data/8xse_38617/01_2025/8xse_38617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xse_38617/01_2025/8xse_38617.cif" } resolution = 2.5 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= 0.001 sd= 0.021 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 6364 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5117 2.51 5 N 1368 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1658 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1611 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 201} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1673 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1621 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.47, per 1000 atoms: 0.67 Number of scatterers: 8120 At special positions: 0 Unit cell: (75.65, 107.95, 153, 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 31 16.00 O 1604 8.00 N 1368 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 22 sheets defined 8.5% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.581A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.139A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.281A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.823A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 163 through 168 removed outlier: 3.546A pdb=" N GLY H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA H 168 " --> pdb=" O TRP H 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 163 through 168' Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.552A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.658A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.722A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 166 through 168 No H-bonds generated for 'chain 'M' and resid 166 through 168' Processing helix chain 'M' and resid 197 through 199 No H-bonds generated for 'chain 'M' and resid 197 through 199' Processing helix chain 'M' and resid 212 through 214 No H-bonds generated for 'chain 'M' and resid 212 through 214' Processing helix chain 'N' and resid 121 through 126 removed outlier: 3.671A pdb=" N LYS N 126 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 187 removed outlier: 3.751A pdb=" N GLU N 187 " --> pdb=" O LYS N 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.636A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.102A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 130 through 134 Processing sheet with id=AA7, first strand: chain 'H' and resid 130 through 134 Processing sheet with id=AA8, first strand: chain 'H' and resid 161 through 162 Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.784A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.465A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.044A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.027A pdb=" N GLY M 10 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 130 through 134 removed outlier: 4.031A pdb=" N GLY M 149 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 130 through 134 removed outlier: 4.031A pdb=" N GLY M 149 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 160 through 164 Processing sheet with id=AB9, first strand: chain 'M' and resid 160 through 164 removed outlier: 4.510A pdb=" N TYR M 204 " --> pdb=" O VAL M 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.496A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 114 through 118 removed outlier: 5.965A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 145 through 149 321 hydrogen bonds defined for protein. 828 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: 2.71 Time building geometry restraints manager: 2.36 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: 2607 1.34 - 1.46: 2123 1.46 - 1.58: 3548 1.58 - 1.70: 1 1.70 - 1.82: 38 Bond restraints: 8317 Sorted by residual: bond pdb=" CB PRO L 113 " pdb=" CG PRO L 113 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" C ASP M 111 " pdb=" N PRO M 112 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.20e-02 6.94e+03 2.92e+00 bond pdb=" CB PRO L 120 " pdb=" CG PRO L 120 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" CB PRO N 204 " pdb=" CG PRO N 204 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.59e+00 bond pdb=" CG PRO N 204 " pdb=" CD PRO N 204 " ideal model delta sigma weight residual 1.503 1.553 -0.050 3.40e-02 8.65e+02 2.20e+00 ... (remaining 8312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11190 2.49 - 4.98: 103 4.98 - 7.47: 15 7.47 - 9.96: 4 9.96 - 12.45: 1 Bond angle restraints: 11313 Sorted by residual: angle pdb=" CA PRO L 113 " pdb=" N PRO L 113 " pdb=" CD PRO L 113 " ideal model delta sigma weight residual 112.00 99.55 12.45 1.40e+00 5.10e-01 7.91e+01 angle pdb=" N PRO L 113 " pdb=" CD PRO L 113 " pdb=" CG PRO L 113 " ideal model delta sigma weight residual 103.20 95.54 7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" CA PRO N 204 " pdb=" N PRO N 204 " pdb=" CD PRO N 204 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CA PRO L 120 " pdb=" N PRO L 120 " pdb=" CD PRO L 120 " ideal model delta sigma weight residual 112.00 107.20 4.80 1.40e+00 5.10e-01 1.17e+01 angle pdb=" CA ILE H 205 " pdb=" CB ILE H 205 " pdb=" CG1 ILE H 205 " ideal model delta sigma weight residual 110.40 116.00 -5.60 1.70e+00 3.46e-01 1.08e+01 ... (remaining 11308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4205 17.93 - 35.87: 547 35.87 - 53.80: 165 53.80 - 71.73: 31 71.73 - 89.66: 12 Dihedral angle restraints: 4960 sinusoidal: 1893 harmonic: 3067 Sorted by residual: dihedral pdb=" CA PRO M 212 " pdb=" C PRO M 212 " pdb=" N SER M 213 " pdb=" CA SER M 213 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA SER H 52 " pdb=" C SER H 52 " pdb=" N GLY H 53 " pdb=" CA GLY H 53 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU N 187 " pdb=" CG GLU N 187 " pdb=" CD GLU N 187 " pdb=" OE1 GLU N 187 " ideal model delta sinusoidal sigma weight residual 0.00 89.66 -89.66 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 926 0.043 - 0.085: 239 0.085 - 0.127: 81 0.127 - 0.170: 10 0.170 - 0.212: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA PRO L 113 " pdb=" N PRO L 113 " pdb=" C PRO L 113 " pdb=" CB PRO L 113 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CB ILE L 2 " pdb=" CA ILE L 2 " pdb=" CG1 ILE L 2 " pdb=" CG2 ILE L 2 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1254 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 203 " -0.064 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO N 204 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO N 204 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO N 204 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 112 " -0.059 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO L 113 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO L 113 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 113 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 119 " -0.038 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO L 120 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO L 120 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 120 " -0.032 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 395 2.72 - 3.26: 7017 3.26 - 3.81: 12438 3.81 - 4.35: 15502 4.35 - 4.90: 27723 Nonbonded interactions: 63075 Sorted by model distance: nonbonded pdb=" OG SER M 213 " pdb=" OG1 THR M 215 " model vdw 2.174 3.040 nonbonded pdb=" OD2 ASP L 105 " pdb=" OH TYR L 173 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN N 137 " pdb=" OG SER N 174 " model vdw 2.251 3.040 nonbonded pdb=" O SER M 85 " pdb=" OG SER M 85 " model vdw 2.261 3.040 nonbonded pdb=" O THR A 333 " pdb=" OG1 THR A 333 " model vdw 2.262 3.040 ... (remaining 63070 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 Found NCS groups: ncs_group { reference = (chain 'H' and (resid 1 through 32 or resid 34 or resid 36 through 48 or resid 5 \ 1 through 52 or resid 55 or resid 59 through 97 or resid 99 or resid 106 or resi \ d 110 or resid 113 through 223)) selection = (chain 'M' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG1)) or resid 6 through 32 or resid 34 or resid 36 \ through 48 or resid 51 through 52 or resid 55 or resid 59 through 97 or resid 99 \ or resid 106 or resid 110 or resid 113 through 223)) } ncs_group { reference = (chain 'L' and (resid 1 through 10 or resid 12 through 17 or resid 19 through 27 \ or resid 29 through 30 or resid 33 or resid 35 through 38 or resid 40 through 5 \ 1 or resid 54 or resid 57 through 76 or resid 78 through 79 or resid 81 through \ 90 or resid 93 or resid 95 or resid 97 through 99 or resid 101 through 212)) selection = (chain 'N' and (resid 1 through 10 or resid 12 through 17 or resid 19 through 27 \ or resid 29 through 30 or resid 33 or resid 35 through 38 or resid 40 through 5 \ 1 or resid 54 or resid 57 through 76 or resid 78 through 79 or resid 81 through \ 90 or resid 93 or resid 95 or resid 97 through 99 or resid 101 through 212)) } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.980 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 8317 Z= 0.233 Angle : 0.644 12.454 11313 Z= 0.346 Chirality : 0.043 0.212 1257 Planarity : 0.006 0.094 1458 Dihedral : 17.935 89.664 2970 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 5.41 % Allowed : 27.62 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1055 helix: -3.51 (0.63), residues: 33 sheet: 0.79 (0.25), residues: 444 loop : -1.09 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 111 PHE 0.007 0.001 PHE N 139 TYR 0.012 0.001 TYR A 495 ARG 0.012 0.000 ARG L 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.849 Fit side-chains REVERT: A 408 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (ppt170) REVERT: H 217 VAL cc_start: 0.7722 (p) cc_final: 0.7406 (t) REVERT: M 145 THR cc_start: 0.7641 (p) cc_final: 0.7416 (t) outliers start: 49 outliers final: 47 residues processed: 152 average time/residue: 0.8703 time to fit residues: 143.7044 Evaluate side-chains 148 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 220 ARG Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 188 LYS Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.135363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119613 restraints weight = 11259.299| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.93 r_work: 0.3594 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8317 Z= 0.272 Angle : 0.616 8.624 11313 Z= 0.313 Chirality : 0.044 0.155 1257 Planarity : 0.005 0.053 1458 Dihedral : 8.347 64.500 1253 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 4.75 % Allowed : 26.63 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1055 helix: -2.82 (0.63), residues: 46 sheet: 0.86 (0.25), residues: 456 loop : -1.19 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 113 HIS 0.004 0.001 HIS H 111 PHE 0.012 0.001 PHE N 139 TYR 0.016 0.002 TYR N 49 ARG 0.005 0.000 ARG L 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.942 Fit side-chains REVERT: H 34 MET cc_start: 0.8680 (mmp) cc_final: 0.8173 (mmp) outliers start: 43 outliers final: 24 residues processed: 142 average time/residue: 0.8480 time to fit residues: 131.3162 Evaluate side-chains 129 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 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 = 0.134943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.119001 restraints weight = 11484.376| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.95 r_work: 0.3586 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8317 Z= 0.264 Angle : 0.600 8.859 11313 Z= 0.303 Chirality : 0.044 0.151 1257 Planarity : 0.005 0.051 1458 Dihedral : 6.501 61.464 1194 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 4.09 % Allowed : 25.97 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1055 helix: -2.57 (0.67), residues: 46 sheet: 1.00 (0.24), residues: 464 loop : -1.20 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 113 HIS 0.004 0.001 HIS H 111 PHE 0.012 0.001 PHE N 139 TYR 0.016 0.002 TYR N 49 ARG 0.004 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.850 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 146 average time/residue: 0.8980 time to fit residues: 142.3853 Evaluate side-chains 130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.135126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119183 restraints weight = 11350.755| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.96 r_work: 0.3590 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8317 Z= 0.233 Angle : 0.586 8.713 11313 Z= 0.295 Chirality : 0.043 0.148 1257 Planarity : 0.005 0.046 1458 Dihedral : 6.009 62.310 1186 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.93 % Rotamer: Outliers : 4.53 % Allowed : 26.19 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1055 helix: -2.45 (0.68), residues: 46 sheet: 1.04 (0.25), residues: 454 loop : -1.11 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 113 HIS 0.003 0.001 HIS H 111 PHE 0.011 0.001 PHE N 139 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.873 Fit side-chains outliers start: 41 outliers final: 23 residues processed: 156 average time/residue: 0.8243 time to fit residues: 140.6421 Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.117473 restraints weight = 11209.813| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.94 r_work: 0.3569 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8317 Z= 0.397 Angle : 0.675 9.240 11313 Z= 0.339 Chirality : 0.046 0.156 1257 Planarity : 0.005 0.050 1458 Dihedral : 5.611 55.592 1180 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.54 % Favored : 93.27 % Rotamer: Outliers : 4.64 % Allowed : 26.08 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1055 helix: -2.62 (0.68), residues: 46 sheet: 1.08 (0.25), residues: 462 loop : -1.21 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 113 HIS 0.005 0.001 HIS M 35 PHE 0.015 0.002 PHE N 139 TYR 0.023 0.002 TYR N 49 ARG 0.004 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.832 Fit side-chains outliers start: 42 outliers final: 27 residues processed: 147 average time/residue: 0.8115 time to fit residues: 130.4580 Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 77 ASN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN M 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.133675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117698 restraints weight = 11256.165| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.96 r_work: 0.3570 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8317 Z= 0.342 Angle : 0.642 9.100 11313 Z= 0.324 Chirality : 0.045 0.152 1257 Planarity : 0.005 0.051 1458 Dihedral : 5.541 56.802 1180 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.07 % Favored : 93.74 % Rotamer: Outliers : 3.98 % Allowed : 26.30 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1055 helix: -2.64 (0.68), residues: 46 sheet: 1.10 (0.25), residues: 460 loop : -1.22 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 113 HIS 0.005 0.001 HIS M 35 PHE 0.014 0.002 PHE N 139 TYR 0.019 0.002 TYR N 49 ARG 0.007 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.839 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 138 average time/residue: 0.8873 time to fit residues: 133.8976 Evaluate side-chains 133 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 88 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.135293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.119322 restraints weight = 11323.569| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.97 r_work: 0.3593 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8317 Z= 0.192 Angle : 0.570 8.648 11313 Z= 0.288 Chirality : 0.043 0.150 1257 Planarity : 0.005 0.048 1458 Dihedral : 5.178 59.609 1179 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 3.43 % Allowed : 26.96 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1055 helix: -2.47 (0.68), residues: 46 sheet: 1.11 (0.25), residues: 449 loop : -1.10 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 111 PHE 0.011 0.001 PHE L 139 TYR 0.013 0.001 TYR L 49 ARG 0.005 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.015 Fit side-chains outliers start: 31 outliers final: 22 residues processed: 135 average time/residue: 0.8421 time to fit residues: 124.1608 Evaluate side-chains 130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.0570 chunk 52 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 0.1980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN 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 = 0.135914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119815 restraints weight = 11457.947| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.00 r_work: 0.3609 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8317 Z= 0.181 Angle : 0.558 8.643 11313 Z= 0.282 Chirality : 0.042 0.149 1257 Planarity : 0.005 0.048 1458 Dihedral : 4.990 58.769 1179 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 2.54 % Allowed : 28.07 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1055 helix: -2.28 (0.71), residues: 46 sheet: 1.09 (0.25), residues: 454 loop : -1.01 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS H 111 PHE 0.010 0.001 PHE L 139 TYR 0.013 0.001 TYR L 49 ARG 0.005 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.922 Fit side-chains outliers start: 23 outliers final: 21 residues processed: 130 average time/residue: 0.8905 time to fit residues: 125.9143 Evaluate side-chains 130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 0.0000 chunk 67 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.136233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120126 restraints weight = 11443.014| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.00 r_work: 0.3606 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8317 Z= 0.192 Angle : 0.566 8.709 11313 Z= 0.286 Chirality : 0.042 0.147 1257 Planarity : 0.005 0.048 1458 Dihedral : 4.961 58.632 1178 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 2.65 % Allowed : 27.96 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1055 helix: -2.27 (0.71), residues: 46 sheet: 1.17 (0.25), residues: 452 loop : -0.99 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 111 PHE 0.011 0.001 PHE L 139 TYR 0.013 0.001 TYR L 49 ARG 0.004 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.069 Fit side-chains REVERT: H 34 MET cc_start: 0.8600 (mmp) cc_final: 0.8342 (mmp) REVERT: M 215 THR cc_start: 0.7727 (m) cc_final: 0.7449 (m) outliers start: 24 outliers final: 23 residues processed: 127 average time/residue: 0.8887 time to fit residues: 123.3304 Evaluate side-chains 130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.134606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118756 restraints weight = 11230.937| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.94 r_work: 0.3587 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8317 Z= 0.234 Angle : 0.587 8.745 11313 Z= 0.296 Chirality : 0.043 0.152 1257 Planarity : 0.005 0.048 1458 Dihedral : 5.064 59.098 1178 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.59 % Favored : 94.22 % Rotamer: Outliers : 2.54 % Allowed : 27.96 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1055 helix: -2.32 (0.70), residues: 46 sheet: 1.13 (0.25), residues: 455 loop : -0.99 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 113 HIS 0.003 0.001 HIS M 35 PHE 0.011 0.001 PHE N 139 TYR 0.014 0.001 TYR L 49 ARG 0.005 0.000 ARG L 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.918 Fit side-chains REVERT: M 215 THR cc_start: 0.7727 (m) cc_final: 0.7457 (m) outliers start: 23 outliers final: 23 residues processed: 133 average time/residue: 0.8357 time to fit residues: 121.4433 Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 89 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN 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 = 0.135784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119731 restraints weight = 11390.688| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.99 r_work: 0.3612 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8317 Z= 0.174 Angle : 0.554 8.625 11313 Z= 0.280 Chirality : 0.042 0.143 1257 Planarity : 0.005 0.050 1458 Dihedral : 4.858 57.675 1178 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 2.76 % Allowed : 27.62 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1055 helix: -2.22 (0.71), residues: 46 sheet: 1.12 (0.25), residues: 456 loop : -0.93 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS H 111 PHE 0.010 0.001 PHE L 139 TYR 0.013 0.001 TYR L 49 ARG 0.004 0.000 ARG L 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6739.99 seconds wall clock time: 120 minutes 46.68 seconds (7246.68 seconds total)