Starting phenix.real_space_refine on Tue Feb 13 09:45:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7etw_31303/02_2024/7etw_31303_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7etw_31303/02_2024/7etw_31303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7etw_31303/02_2024/7etw_31303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7etw_31303/02_2024/7etw_31303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7etw_31303/02_2024/7etw_31303_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7etw_31303/02_2024/7etw_31303_updated.pdb" } resolution = 4.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3204 2.51 5 N 784 2.21 5 O 944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 445": "NH1" <-> "NH2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 631": "NH1" <-> "NH2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4952 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1525 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3059 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 25, 'TRANS': 457} Chain breaks: 3 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 852 Unresolved non-hydrogen angles: 1104 Unresolved non-hydrogen dihedrals: 724 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 6, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 456 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 340 Unusual residues: {'AJP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.52, per 1000 atoms: 0.71 Number of scatterers: 4952 At special positions: 0 Unit cell: (85.098, 86.189, 123.283, 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 20 16.00 O 944 8.00 N 784 7.00 C 3204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN B 641 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 969.5 milliseconds 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 3 sheets defined 58.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 19 through 47 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 71 through 94 Proline residue: A 75 - end of helix Proline residue: A 89 - end of helix removed outlier: 3.812A pdb=" N ASP A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 130 through 146 removed outlier: 4.027A pdb=" N ALA A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 175 removed outlier: 3.575A pdb=" N GLY A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.028A pdb=" N LEU A 186 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 188 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 213 removed outlier: 4.175A pdb=" N TYR A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.578A pdb=" N ALA B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 113 through 130 removed outlier: 3.626A pdb=" N SER B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Proline residue: B 118 - end of helix removed outlier: 3.951A pdb=" N GLN B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.705A pdb=" N ARG B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 159 " --> pdb=" O GLY B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 192 through 198 removed outlier: 4.708A pdb=" N HIS B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 245 through 258 removed outlier: 4.300A pdb=" N SER B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 305 Proline residue: B 287 - end of helix removed outlier: 3.911A pdb=" N LYS B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 335 removed outlier: 3.993A pdb=" N ALA B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.509A pdb=" N VAL B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 369 removed outlier: 5.421A pdb=" N LEU B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 408 removed outlier: 4.004A pdb=" N SER B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 432 removed outlier: 4.607A pdb=" N LEU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 Processing helix chain 'B' and resid 515 through 532 Processing helix chain 'B' and resid 534 through 537 Processing helix chain 'B' and resid 633 through 640 removed outlier: 4.035A pdb=" N PHE B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 232 through 240 removed outlier: 3.805A pdb=" N VAL B 232 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 98 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 240 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR B 92 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 654 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 97 " --> pdb=" O VAL B 654 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.882A pdb=" N LEU B 134 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 272 through 275 removed outlier: 4.460A pdb=" N VAL B 272 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 651 " --> pdb=" O VAL B 272 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 747 1.32 - 1.44: 1388 1.44 - 1.56: 2907 1.56 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 5072 Sorted by residual: bond pdb=" C LYS B 277 " pdb=" O LYS B 277 " ideal model delta sigma weight residual 1.235 1.281 -0.047 1.18e-02 7.18e+03 1.57e+01 bond pdb=" N ARG B 660 " pdb=" CA ARG B 660 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.18e-02 7.18e+03 1.55e+01 bond pdb=" N VAL B 654 " pdb=" CA VAL B 654 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.14e-02 7.69e+03 1.45e+01 bond pdb=" N VAL B 657 " pdb=" CA VAL B 657 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.18e-02 7.18e+03 1.32e+01 bond pdb=" N LYS B 99 " pdb=" CA LYS B 99 " ideal model delta sigma weight residual 1.457 1.501 -0.045 1.24e-02 6.50e+03 1.30e+01 ... (remaining 5067 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.02: 93 105.02 - 112.27: 2960 112.27 - 119.52: 1573 119.52 - 126.76: 2345 126.76 - 134.01: 53 Bond angle restraints: 7024 Sorted by residual: angle pdb=" N PRO B 104 " pdb=" CA PRO B 104 " pdb=" C PRO B 104 " ideal model delta sigma weight residual 113.84 104.13 9.71 1.30e+00 5.92e-01 5.58e+01 angle pdb=" N ILE A 51 " pdb=" CA ILE A 51 " pdb=" C ILE A 51 " ideal model delta sigma weight residual 106.32 116.68 -10.36 1.61e+00 3.86e-01 4.14e+01 angle pdb=" CA SER B 173 " pdb=" C SER B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 117.95 122.09 -4.14 7.70e-01 1.69e+00 2.90e+01 angle pdb=" C ARG B 267 " pdb=" CA ARG B 267 " pdb=" CB ARG B 267 " ideal model delta sigma weight residual 116.54 111.29 5.25 1.15e+00 7.56e-01 2.08e+01 angle pdb=" C PRO B 89 " pdb=" N VAL B 90 " pdb=" CA VAL B 90 " ideal model delta sigma weight residual 122.48 128.15 -5.67 1.25e+00 6.40e-01 2.05e+01 ... (remaining 7019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 3423 22.75 - 45.51: 171 45.51 - 68.26: 26 68.26 - 91.02: 6 91.02 - 113.77: 2 Dihedral angle restraints: 3628 sinusoidal: 1663 harmonic: 1965 Sorted by residual: dihedral pdb=" C ILE A 51 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " pdb=" CB ILE A 51 " ideal model delta harmonic sigma weight residual -122.00 -133.18 11.18 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" CA LYS A 102 " pdb=" C LYS A 102 " pdb=" N ARG A 103 " pdb=" CA ARG A 103 " ideal model delta harmonic sigma weight residual 180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA VAL A 55 " pdb=" C VAL A 55 " pdb=" N THR A 56 " pdb=" CA THR A 56 " ideal model delta harmonic sigma weight residual 180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 3625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 958 0.254 - 0.509: 5 0.509 - 0.763: 0 0.763 - 1.018: 0 1.018 - 1.272: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-02 2.50e+03 4.04e+03 chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C11 AJP A 302 " pdb=" C10 AJP A 302 " pdb=" C12 AJP A 302 " pdb=" C16 AJP A 302 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 961 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.157 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG D 2 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.219 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 641 " 0.093 2.00e-02 2.50e+03 1.35e-01 2.26e+02 pdb=" CG ASN B 641 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 641 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 641 " -0.238 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.113 2.00e-02 2.50e+03 9.24e-02 1.07e+02 pdb=" C7 NAG D 1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.084 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.147 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 30 2.45 - 3.07: 4075 3.07 - 3.68: 6986 3.68 - 4.29: 9702 4.29 - 4.90: 14677 Nonbonded interactions: 35470 Sorted by model distance: nonbonded pdb=" O53 AJP A 302 " pdb=" O76 AJP A 302 " model vdw 1.843 2.440 nonbonded pdb=" O43 AJP A 304 " pdb=" O50 AJP A 304 " model vdw 2.094 2.440 nonbonded pdb=" O60 AJP A 303 " pdb=" O77 AJP A 303 " model vdw 2.245 2.440 nonbonded pdb=" O ILE B 280 " pdb=" O GLY B 281 " model vdw 2.262 3.040 nonbonded pdb=" O ALA B 382 " pdb=" OG SER B 386 " model vdw 2.268 2.440 ... (remaining 35465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.980 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.460 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.009 0.055 5072 Z= 0.619 Angle : 1.207 10.452 7024 Z= 0.682 Chirality : 0.076 1.272 964 Planarity : 0.008 0.135 812 Dihedral : 13.698 113.769 2354 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 1.94 % Allowed : 11.64 % Favored : 86.42 % Rotamer: Outliers : 1.36 % Allowed : 4.90 % Favored : 93.73 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.24), residues: 670 helix: -3.25 (0.19), residues: 375 sheet: -1.07 (1.06), residues: 26 loop : -4.37 (0.28), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 633 HIS 0.024 0.004 HIS B 632 PHE 0.013 0.002 PHE A 155 TYR 0.027 0.002 TYR A 88 ARG 0.005 0.001 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7952 (ttt90) cc_final: 0.6893 (tmt170) REVERT: A 167 VAL cc_start: 0.9082 (t) cc_final: 0.8821 (p) REVERT: A 208 ARG cc_start: 0.8669 (mtt180) cc_final: 0.7914 (mtt180) REVERT: A 209 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7542 (tp-100) REVERT: B 359 GLU cc_start: 0.7777 (mp0) cc_final: 0.7517 (mp0) REVERT: B 378 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8018 (ttmm) REVERT: B 383 GLN cc_start: 0.9147 (tt0) cc_final: 0.8482 (mt0) REVERT: B 388 GLU cc_start: 0.8434 (tp30) cc_final: 0.7911 (tp30) REVERT: B 442 ILE cc_start: 0.8824 (tp) cc_final: 0.8532 (mm) REVERT: B 445 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8018 (mmm160) REVERT: B 447 MET cc_start: 0.7903 (ttt) cc_final: 0.7536 (ttm) REVERT: B 626 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7315 (mmp80) REVERT: B 627 LYS cc_start: 0.7899 (mttt) cc_final: 0.7563 (pttm) REVERT: B 641 ASN cc_start: 0.6111 (t0) cc_final: 0.5609 (t0) outliers start: 5 outliers final: 1 residues processed: 160 average time/residue: 0.1960 time to fit residues: 38.4104 Evaluate side-chains 106 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 39 optimal weight: 40.0000 chunk 60 optimal weight: 8.9990 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 52 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS A 132 GLN B 17 ASN B 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5072 Z= 0.240 Angle : 0.789 6.854 7024 Z= 0.376 Chirality : 0.045 0.373 964 Planarity : 0.005 0.076 812 Dihedral : 9.338 73.370 1629 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.06 % Favored : 91.19 % Rotamer: Outliers : 0.27 % Allowed : 7.90 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.30), residues: 670 helix: -0.97 (0.25), residues: 383 sheet: -1.35 (0.82), residues: 37 loop : -3.19 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.011 0.003 HIS B 632 PHE 0.019 0.002 PHE B 301 TYR 0.028 0.003 TYR A 178 ARG 0.007 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7135 (ptp-170) REVERT: A 93 ARG cc_start: 0.8022 (ttt90) cc_final: 0.7055 (tmt170) REVERT: A 209 GLN cc_start: 0.8493 (tp-100) cc_final: 0.7908 (tp-100) REVERT: B 298 TYR cc_start: 0.8437 (t80) cc_final: 0.8070 (t80) REVERT: B 347 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 383 GLN cc_start: 0.9118 (tt0) cc_final: 0.8472 (mt0) REVERT: B 388 GLU cc_start: 0.8455 (tp30) cc_final: 0.8250 (tp30) REVERT: B 442 ILE cc_start: 0.8811 (tp) cc_final: 0.8533 (mm) REVERT: B 445 ARG cc_start: 0.8381 (ttt90) cc_final: 0.7859 (mmm160) REVERT: B 627 LYS cc_start: 0.7837 (mttt) cc_final: 0.7518 (pttm) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1926 time to fit residues: 32.5278 Evaluate side-chains 105 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5072 Z= 0.281 Angle : 0.752 6.779 7024 Z= 0.360 Chirality : 0.045 0.344 964 Planarity : 0.005 0.070 812 Dihedral : 8.197 64.934 1629 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.01 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.33), residues: 670 helix: 0.12 (0.26), residues: 390 sheet: 2.20 (1.24), residues: 18 loop : -3.18 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.022 0.004 HIS B 632 PHE 0.020 0.002 PHE B 420 TYR 0.012 0.002 TYR B 292 ARG 0.008 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7404 (ptp-170) REVERT: A 93 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7312 (tmt170) REVERT: A 132 GLN cc_start: 0.6485 (mm-40) cc_final: 0.6048 (mm-40) REVERT: A 209 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8240 (tp-100) REVERT: B 16 TYR cc_start: 0.8638 (t80) cc_final: 0.7990 (t80) REVERT: B 40 CYS cc_start: 0.6182 (m) cc_final: 0.5756 (m) REVERT: B 304 ARG cc_start: 0.8287 (mmm160) cc_final: 0.8073 (tpt90) REVERT: B 329 MET cc_start: 0.8269 (mtp) cc_final: 0.8020 (mtm) REVERT: B 359 GLU cc_start: 0.7988 (mp0) cc_final: 0.7555 (mp0) REVERT: B 383 GLN cc_start: 0.9126 (tt0) cc_final: 0.8602 (mt0) REVERT: B 388 GLU cc_start: 0.8760 (tp30) cc_final: 0.8461 (tp30) REVERT: B 442 ILE cc_start: 0.8922 (tp) cc_final: 0.8654 (mm) REVERT: B 445 ARG cc_start: 0.8420 (ttt90) cc_final: 0.7898 (mmm160) REVERT: B 627 LYS cc_start: 0.7914 (mttt) cc_final: 0.7672 (pttm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1764 time to fit residues: 29.8491 Evaluate side-chains 110 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 50.0000 chunk 40 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5072 Z= 0.242 Angle : 0.720 8.499 7024 Z= 0.340 Chirality : 0.043 0.334 964 Planarity : 0.004 0.038 812 Dihedral : 8.012 63.386 1629 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.16 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.34), residues: 670 helix: 0.48 (0.27), residues: 391 sheet: -0.30 (0.97), residues: 35 loop : -2.95 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.015 0.003 HIS B 632 PHE 0.013 0.002 PHE B 15 TYR 0.036 0.002 TYR A 88 ARG 0.005 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7585 (ptp-170) REVERT: A 93 ARG cc_start: 0.8280 (ttt90) cc_final: 0.7438 (tmt170) REVERT: A 132 GLN cc_start: 0.6494 (mm-40) cc_final: 0.5994 (mm-40) REVERT: A 209 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8135 (tp-100) REVERT: B 16 TYR cc_start: 0.8679 (t80) cc_final: 0.8082 (t80) REVERT: B 17 ASN cc_start: 0.9143 (p0) cc_final: 0.8812 (t0) REVERT: B 40 CYS cc_start: 0.6017 (m) cc_final: 0.5787 (m) REVERT: B 329 MET cc_start: 0.8250 (mtp) cc_final: 0.8025 (mtm) REVERT: B 359 GLU cc_start: 0.7992 (mp0) cc_final: 0.7519 (mp0) REVERT: B 378 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8391 (ttmt) REVERT: B 383 GLN cc_start: 0.9110 (tt0) cc_final: 0.8634 (mt0) REVERT: B 388 GLU cc_start: 0.8797 (tp30) cc_final: 0.8496 (tp30) REVERT: B 396 MET cc_start: 0.7490 (ttm) cc_final: 0.7142 (ttm) REVERT: B 442 ILE cc_start: 0.8929 (tp) cc_final: 0.8691 (mm) REVERT: B 445 ARG cc_start: 0.8380 (ttt90) cc_final: 0.7861 (mtp-110) REVERT: B 641 ASN cc_start: 0.5078 (t0) cc_final: 0.4865 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1863 time to fit residues: 30.0839 Evaluate side-chains 112 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS B 432 GLN B 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5072 Z= 0.177 Angle : 0.655 7.356 7024 Z= 0.310 Chirality : 0.042 0.310 964 Planarity : 0.003 0.038 812 Dihedral : 7.519 61.227 1629 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Rotamer: Outliers : 0.27 % Allowed : 3.81 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.34), residues: 670 helix: 0.77 (0.27), residues: 392 sheet: -0.26 (0.99), residues: 37 loop : -2.77 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.020 0.004 HIS B 632 PHE 0.019 0.002 PHE B 301 TYR 0.012 0.001 TYR B 300 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7574 (ptp-170) REVERT: A 92 ASP cc_start: 0.8002 (t0) cc_final: 0.7775 (t0) REVERT: A 93 ARG cc_start: 0.8287 (ttt90) cc_final: 0.7377 (tmt170) REVERT: A 132 GLN cc_start: 0.6619 (mm-40) cc_final: 0.6009 (mm-40) REVERT: A 149 ASP cc_start: 0.8657 (t0) cc_final: 0.8275 (t0) REVERT: A 166 THR cc_start: 0.9239 (m) cc_final: 0.9036 (m) REVERT: A 209 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8349 (tp-100) REVERT: B 16 TYR cc_start: 0.8624 (t80) cc_final: 0.8230 (t80) REVERT: B 17 ASN cc_start: 0.9116 (p0) cc_final: 0.8789 (t0) REVERT: B 40 CYS cc_start: 0.5747 (m) cc_final: 0.5544 (m) REVERT: B 329 MET cc_start: 0.8229 (mtp) cc_final: 0.7987 (mtm) REVERT: B 359 GLU cc_start: 0.7942 (mp0) cc_final: 0.7417 (mp0) REVERT: B 383 GLN cc_start: 0.9128 (tt0) cc_final: 0.8689 (mt0) REVERT: B 396 MET cc_start: 0.7138 (ttm) cc_final: 0.6924 (ttm) REVERT: B 442 ILE cc_start: 0.8923 (tp) cc_final: 0.8698 (mm) REVERT: B 445 ARG cc_start: 0.8291 (ttt90) cc_final: 0.8064 (ttt-90) REVERT: B 630 PHE cc_start: 0.7783 (t80) cc_final: 0.7314 (m-80) REVERT: B 639 TYR cc_start: 0.8906 (m-10) cc_final: 0.8689 (m-80) REVERT: B 641 ASN cc_start: 0.5072 (t0) cc_final: 0.4868 (t0) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1786 time to fit residues: 31.0352 Evaluate side-chains 113 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 40.0000 chunk 5 optimal weight: 0.0050 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5072 Z= 0.158 Angle : 0.655 8.172 7024 Z= 0.313 Chirality : 0.041 0.301 964 Planarity : 0.003 0.038 812 Dihedral : 7.266 59.772 1629 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.34), residues: 670 helix: 0.98 (0.27), residues: 387 sheet: -0.22 (0.99), residues: 37 loop : -2.54 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.004 0.002 HIS B 632 PHE 0.012 0.001 PHE B 15 TYR 0.031 0.001 TYR A 88 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7607 (m) cc_final: 0.7325 (p) REVERT: A 31 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7496 (ptp-170) REVERT: A 92 ASP cc_start: 0.8163 (t0) cc_final: 0.7874 (t70) REVERT: A 132 GLN cc_start: 0.6620 (mm-40) cc_final: 0.6000 (mm-40) REVERT: A 166 THR cc_start: 0.9318 (m) cc_final: 0.8963 (m) REVERT: A 170 GLN cc_start: 0.8839 (pm20) cc_final: 0.7919 (pm20) REVERT: A 209 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8386 (tp-100) REVERT: B 16 TYR cc_start: 0.8585 (t80) cc_final: 0.8210 (t80) REVERT: B 17 ASN cc_start: 0.9050 (p0) cc_final: 0.8822 (t0) REVERT: B 329 MET cc_start: 0.8103 (mtp) cc_final: 0.7876 (mtm) REVERT: B 359 GLU cc_start: 0.7958 (mp0) cc_final: 0.7457 (mp0) REVERT: B 378 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8670 (mtpp) REVERT: B 383 GLN cc_start: 0.9130 (tt0) cc_final: 0.8659 (mt0) REVERT: B 396 MET cc_start: 0.7321 (ttm) cc_final: 0.6970 (ttm) REVERT: B 430 PHE cc_start: 0.7050 (t80) cc_final: 0.6693 (t80) REVERT: B 442 ILE cc_start: 0.8928 (tp) cc_final: 0.8703 (mm) REVERT: B 639 TYR cc_start: 0.8879 (m-10) cc_final: 0.8661 (m-80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1740 time to fit residues: 28.8906 Evaluate side-chains 116 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5072 Z= 0.358 Angle : 0.790 8.828 7024 Z= 0.375 Chirality : 0.046 0.363 964 Planarity : 0.004 0.030 812 Dihedral : 7.852 59.891 1629 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.76 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.34), residues: 670 helix: 0.63 (0.27), residues: 401 sheet: -0.64 (0.93), residues: 39 loop : -2.74 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 146 HIS 0.006 0.003 HIS B 18 PHE 0.013 0.002 PHE A 196 TYR 0.039 0.002 TYR A 88 ARG 0.013 0.001 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7670 (ptp-170) REVERT: A 92 ASP cc_start: 0.8148 (t0) cc_final: 0.7840 (t0) REVERT: A 93 ARG cc_start: 0.8338 (ttt90) cc_final: 0.7476 (tmt170) REVERT: A 103 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7761 (tpp80) REVERT: A 132 GLN cc_start: 0.6573 (mm-40) cc_final: 0.6356 (mm-40) REVERT: A 133 LEU cc_start: 0.7980 (tp) cc_final: 0.7695 (tp) REVERT: A 164 LEU cc_start: 0.7676 (mm) cc_final: 0.6873 (tt) REVERT: A 170 GLN cc_start: 0.8706 (pm20) cc_final: 0.7981 (pm20) REVERT: B 16 TYR cc_start: 0.8654 (t80) cc_final: 0.8275 (t80) REVERT: B 17 ASN cc_start: 0.9153 (p0) cc_final: 0.8775 (t0) REVERT: B 329 MET cc_start: 0.8228 (mtp) cc_final: 0.8006 (mtm) REVERT: B 347 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7473 (mt-10) REVERT: B 359 GLU cc_start: 0.8071 (mp0) cc_final: 0.7607 (mp0) REVERT: B 383 GLN cc_start: 0.9171 (tt0) cc_final: 0.8743 (mt0) REVERT: B 396 MET cc_start: 0.7441 (ttm) cc_final: 0.7051 (ttm) REVERT: B 442 ILE cc_start: 0.9004 (tp) cc_final: 0.8780 (mm) REVERT: B 444 ILE cc_start: 0.8650 (mm) cc_final: 0.8342 (mm) REVERT: B 447 MET cc_start: 0.8062 (ttt) cc_final: 0.7836 (ttt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1729 time to fit residues: 28.6862 Evaluate side-chains 111 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5072 Z= 0.189 Angle : 0.691 8.058 7024 Z= 0.330 Chirality : 0.043 0.320 964 Planarity : 0.004 0.035 812 Dihedral : 7.469 59.578 1629 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.52 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.34), residues: 670 helix: 0.86 (0.27), residues: 397 sheet: -0.60 (0.91), residues: 39 loop : -2.49 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 633 HIS 0.004 0.002 HIS B 18 PHE 0.021 0.001 PHE B 420 TYR 0.017 0.001 TYR A 178 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7682 (ptp-170) REVERT: A 92 ASP cc_start: 0.8232 (t0) cc_final: 0.7944 (t70) REVERT: A 103 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7750 (tpp80) REVERT: A 132 GLN cc_start: 0.6378 (mm-40) cc_final: 0.6129 (mm-40) REVERT: A 133 LEU cc_start: 0.7900 (tp) cc_final: 0.7576 (tp) REVERT: A 164 LEU cc_start: 0.7691 (mm) cc_final: 0.6957 (tt) REVERT: A 170 GLN cc_start: 0.8451 (pm20) cc_final: 0.8012 (pm20) REVERT: B 16 TYR cc_start: 0.8590 (t80) cc_final: 0.8145 (t80) REVERT: B 17 ASN cc_start: 0.9118 (p0) cc_final: 0.8791 (t0) REVERT: B 40 CYS cc_start: 0.5807 (m) cc_final: 0.5420 (m) REVERT: B 329 MET cc_start: 0.8192 (mtp) cc_final: 0.7936 (mtm) REVERT: B 347 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7471 (mt-10) REVERT: B 359 GLU cc_start: 0.7994 (mp0) cc_final: 0.7512 (mp0) REVERT: B 378 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8970 (mtpp) REVERT: B 383 GLN cc_start: 0.9133 (tt0) cc_final: 0.8822 (mt0) REVERT: B 396 MET cc_start: 0.7355 (ttm) cc_final: 0.6982 (ttm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1708 time to fit residues: 29.4865 Evaluate side-chains 111 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 30.0000 chunk 63 optimal weight: 0.0980 chunk 38 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5072 Z= 0.186 Angle : 0.696 8.649 7024 Z= 0.334 Chirality : 0.043 0.312 964 Planarity : 0.004 0.039 812 Dihedral : 7.322 58.338 1629 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.67 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.34), residues: 670 helix: 0.99 (0.27), residues: 399 sheet: -0.50 (0.92), residues: 39 loop : -2.33 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.004 0.002 HIS B 632 PHE 0.024 0.001 PHE B 435 TYR 0.031 0.002 TYR B 639 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7719 (ptp-170) REVERT: A 92 ASP cc_start: 0.8261 (t0) cc_final: 0.8050 (t70) REVERT: A 132 GLN cc_start: 0.6367 (mm-40) cc_final: 0.6061 (mm-40) REVERT: A 133 LEU cc_start: 0.7933 (tp) cc_final: 0.7585 (tp) REVERT: A 166 THR cc_start: 0.9307 (m) cc_final: 0.8998 (m) REVERT: A 170 GLN cc_start: 0.8423 (pm20) cc_final: 0.7924 (pm20) REVERT: B 13 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6927 (mtm-85) REVERT: B 16 TYR cc_start: 0.8583 (t80) cc_final: 0.8122 (t80) REVERT: B 17 ASN cc_start: 0.9103 (p0) cc_final: 0.8802 (t0) REVERT: B 347 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 359 GLU cc_start: 0.7993 (mp0) cc_final: 0.7468 (mp0) REVERT: B 378 LYS cc_start: 0.9297 (mtpt) cc_final: 0.9037 (mtpp) REVERT: B 383 GLN cc_start: 0.9153 (tt0) cc_final: 0.8894 (mt0) REVERT: B 396 MET cc_start: 0.7379 (ttm) cc_final: 0.6949 (ttm) REVERT: B 444 ILE cc_start: 0.8707 (mm) cc_final: 0.8300 (mm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1803 time to fit residues: 30.0498 Evaluate side-chains 112 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5072 Z= 0.165 Angle : 0.696 9.735 7024 Z= 0.332 Chirality : 0.043 0.295 964 Planarity : 0.004 0.046 812 Dihedral : 7.043 58.132 1629 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.93 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.34), residues: 670 helix: 1.17 (0.27), residues: 391 sheet: -0.18 (0.98), residues: 36 loop : -2.04 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 105 HIS 0.005 0.001 HIS B 632 PHE 0.021 0.001 PHE B 435 TYR 0.022 0.001 TYR B 639 ARG 0.003 0.000 ARG B 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7734 (ptp-170) REVERT: A 133 LEU cc_start: 0.7938 (tp) cc_final: 0.7634 (tp) REVERT: A 166 THR cc_start: 0.9296 (m) cc_final: 0.8968 (m) REVERT: A 170 GLN cc_start: 0.8375 (pm20) cc_final: 0.7849 (pm20) REVERT: B 16 TYR cc_start: 0.8549 (t80) cc_final: 0.8108 (t80) REVERT: B 300 TYR cc_start: 0.8520 (t80) cc_final: 0.8299 (t80) REVERT: B 347 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 359 GLU cc_start: 0.8006 (mp0) cc_final: 0.7420 (mp0) REVERT: B 362 LEU cc_start: 0.8697 (mt) cc_final: 0.7895 (tp) REVERT: B 378 LYS cc_start: 0.9235 (mtpt) cc_final: 0.8842 (mtpp) REVERT: B 383 GLN cc_start: 0.9086 (tt0) cc_final: 0.8876 (mt0) REVERT: B 416 GLU cc_start: 0.8222 (pp20) cc_final: 0.7859 (tm-30) REVERT: B 430 PHE cc_start: 0.6891 (t80) cc_final: 0.6601 (t80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1753 time to fit residues: 31.0876 Evaluate side-chains 113 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.0040 chunk 38 optimal weight: 40.0000 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120302 restraints weight = 12577.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123516 restraints weight = 7032.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125702 restraints weight = 4906.777| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5072 Z= 0.193 Angle : 0.665 7.556 7024 Z= 0.319 Chirality : 0.044 0.299 964 Planarity : 0.004 0.043 812 Dihedral : 7.017 59.127 1629 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.93 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.34), residues: 670 helix: 1.18 (0.28), residues: 396 sheet: 0.35 (1.01), residues: 34 loop : -2.08 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.004 0.001 HIS B 18 PHE 0.017 0.001 PHE B 435 TYR 0.016 0.001 TYR B 639 ARG 0.007 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.42 seconds wall clock time: 25 minutes 9.54 seconds (1509.54 seconds total)