Starting phenix.real_space_refine on Tue Feb 13 12:59:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li6_23361/02_2024/7li6_23361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li6_23361/02_2024/7li6_23361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li6_23361/02_2024/7li6_23361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li6_23361/02_2024/7li6_23361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li6_23361/02_2024/7li6_23361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li6_23361/02_2024/7li6_23361_updated.pdb" } resolution = 3.5 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= 0.040 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4178 2.51 5 N 958 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 87": "OD1" <-> "OD2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6249 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4284 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 515} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} 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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 196 Unusual residues: {' CL': 1, 'D10': 6, 'D12': 3, 'HP6': 9, 'LNK': 4, 'R16': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Time building chain proxies: 4.30, per 1000 atoms: 0.69 Number of scatterers: 6249 At special positions: 0 Unit cell: (70.066, 79.981, 123.607, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 1078 8.00 N 958 7.00 C 4178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 4 sheets defined 43.8% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 89 through 92 No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 160 through 191 removed outlier: 4.039A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 253 through 269 removed outlier: 4.324A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.634A pdb=" N LEU A 310 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 361 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 403 through 416 removed outlier: 4.119A pdb=" N LEU A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 408 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 442 removed outlier: 4.000A pdb=" N ALA A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 4.103A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 475 removed outlier: 3.521A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 491 through 494 No H-bonds generated for 'chain 'A' and resid 491 through 494' Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.105A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 558 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.656A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing sheet with id= A, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.827A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.174A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 112 through 114 removed outlier: 5.851A pdb=" N GLN C 61 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU C 70 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 87 through 89 211 hydrogen bonds defined for protein. 609 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: 1.63 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1808 1.34 - 1.46: 1610 1.46 - 1.58: 2936 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6403 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 6398 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.37: 217 107.37 - 114.03: 3578 114.03 - 120.68: 2645 120.68 - 127.34: 2110 127.34 - 134.00: 82 Bond angle restraints: 8632 Sorted by residual: angle pdb=" N TYR A 495 " pdb=" CA TYR A 495 " pdb=" C TYR A 495 " ideal model delta sigma weight residual 114.04 110.66 3.38 1.24e+00 6.50e-01 7.43e+00 angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.39 109.50 3.89 1.47e+00 4.63e-01 7.01e+00 angle pdb=" C ALA C 74 " pdb=" N ALA C 75 " pdb=" CA ALA C 75 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.38e+00 angle pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" O GLY C 90 " ideal model delta sigma weight residual 122.22 120.64 1.58 6.50e-01 2.37e+00 5.92e+00 angle pdb=" C ARG A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 ... (remaining 8627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3426 17.66 - 35.32: 225 35.32 - 52.98: 48 52.98 - 70.64: 6 70.64 - 88.30: 6 Dihedral angle restraints: 3711 sinusoidal: 1505 harmonic: 2206 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual -86.00 -150.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB GLU A 606 " pdb=" CG GLU A 606 " pdb=" CD GLU A 606 " pdb=" OE1 GLU A 606 " ideal model delta sinusoidal sigma weight residual 0.00 88.30 -88.30 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 412 " pdb=" CG GLU A 412 " pdb=" CD GLU A 412 " pdb=" OE1 GLU A 412 " ideal model delta sinusoidal sigma weight residual 0.00 83.56 -83.56 1 3.00e+01 1.11e-03 9.47e+00 ... (remaining 3708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 941 0.331 - 0.661: 0 0.661 - 0.992: 0 0.992 - 1.322: 0 1.322 - 1.653: 1 Chirality restraints: 942 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 -0.75 -1.65 2.00e-02 2.50e+03 6.83e+03 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CB ILE C 99 " pdb=" CA ILE C 99 " pdb=" CG1 ILE C 99 " pdb=" CG2 ILE C 99 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 939 not shown) Planarity restraints: 1045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 339 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 288 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 88 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C PHE A 88 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE A 88 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 89 " -0.007 2.00e-02 2.50e+03 ... (remaining 1042 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1968 2.83 - 3.35: 5474 3.35 - 3.86: 9860 3.86 - 4.38: 10771 4.38 - 4.90: 19061 Nonbonded interactions: 47134 Sorted by model distance: nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.310 2.440 nonbonded pdb=" O GLU A 229 " pdb=" OG1 THR A 233 " model vdw 2.311 2.440 nonbonded pdb=" NE2 GLN C 114 " pdb=" O SER C 119 " model vdw 2.312 2.520 nonbonded pdb=" O VAL A 297 " pdb=" OG1 THR A 301 " model vdw 2.328 2.440 nonbonded pdb=" OG SER C 87 " pdb=" OD1 ASN C 98 " model vdw 2.354 2.440 ... (remaining 47129 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: 3.250 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.060 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 : 0.002 0.030 6403 Z= 0.121 Angle : 0.667 5.560 8632 Z= 0.305 Chirality : 0.066 1.653 942 Planarity : 0.003 0.039 1044 Dihedral : 12.312 88.297 2302 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.72 % Allowed : 9.53 % Favored : 88.75 % 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: -3.07 (0.27), residues: 761 helix: -0.87 (0.25), residues: 343 sheet: -2.44 (0.62), residues: 76 loop : -3.22 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 282 HIS 0.001 0.000 HIS A 223 PHE 0.003 0.000 PHE A 88 TYR 0.011 0.001 TYR A 175 ARG 0.001 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.693 Fit side-chains REVERT: A 306 TRP cc_start: 0.7018 (t-100) cc_final: 0.6154 (p-90) REVERT: A 514 TRP cc_start: 0.7063 (m-10) cc_final: 0.6686 (m100) REVERT: A 535 TRP cc_start: 0.6493 (t60) cc_final: 0.6135 (p-90) REVERT: A 607 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7032 (mtt180) REVERT: B 99 TYR cc_start: 0.8296 (m-80) cc_final: 0.8051 (m-80) REVERT: C 69 LYS cc_start: 0.7459 (tttp) cc_final: 0.7254 (tttm) REVERT: C 71 LEU cc_start: 0.7884 (tp) cc_final: 0.7629 (tp) REVERT: C 116 LYS cc_start: 0.6969 (tttt) cc_final: 0.6637 (mttp) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.2845 time to fit residues: 38.4626 Evaluate side-chains 73 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 145 ASN A 254 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN B 24 GLN C 62 GLN C 66 GLN C 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6403 Z= 0.174 Angle : 0.510 9.701 8632 Z= 0.253 Chirality : 0.040 0.223 942 Planarity : 0.004 0.037 1044 Dihedral : 5.308 56.414 1009 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.75 % Allowed : 13.28 % Favored : 82.97 % 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: -2.02 (0.30), residues: 761 helix: 0.09 (0.28), residues: 351 sheet: -2.12 (0.58), residues: 95 loop : -2.76 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 59 HIS 0.001 0.001 HIS A 223 PHE 0.011 0.001 PHE A 213 TYR 0.021 0.001 TYR A 176 ARG 0.006 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.608 Fit side-chains REVERT: A 370 MET cc_start: 0.7124 (mmp) cc_final: 0.6665 (mmt) REVERT: A 607 ARG cc_start: 0.7464 (mtt180) cc_final: 0.7162 (mtt180) REVERT: B 50 TYR cc_start: 0.7900 (m-80) cc_final: 0.7372 (m-80) REVERT: B 53 MET cc_start: 0.8268 (mmt) cc_final: 0.7902 (mmt) REVERT: C 69 LYS cc_start: 0.7622 (tttp) cc_final: 0.7330 (tttm) REVERT: C 116 LYS cc_start: 0.7485 (tttt) cc_final: 0.6791 (mtmt) outliers start: 24 outliers final: 11 residues processed: 93 average time/residue: 0.1912 time to fit residues: 23.1733 Evaluate side-chains 76 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 60 optimal weight: 0.0370 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6403 Z= 0.190 Angle : 0.513 9.383 8632 Z= 0.258 Chirality : 0.041 0.262 942 Planarity : 0.004 0.033 1044 Dihedral : 4.948 56.781 1003 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.06 % Allowed : 16.41 % Favored : 79.53 % 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: -1.61 (0.31), residues: 761 helix: 0.43 (0.29), residues: 355 sheet: -1.72 (0.59), residues: 92 loop : -2.67 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 535 HIS 0.001 0.000 HIS A 223 PHE 0.013 0.001 PHE A 213 TYR 0.022 0.002 TYR A 176 ARG 0.005 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 1.383 Fit side-chains REVERT: A 306 TRP cc_start: 0.7137 (t-100) cc_final: 0.6267 (p-90) REVERT: A 370 MET cc_start: 0.7168 (mmp) cc_final: 0.6797 (mmt) REVERT: A 607 ARG cc_start: 0.7502 (mtt180) cc_final: 0.7225 (mtt180) REVERT: B 53 MET cc_start: 0.8305 (mmt) cc_final: 0.7853 (mmt) REVERT: C 116 LYS cc_start: 0.7826 (tttt) cc_final: 0.6846 (mtmt) outliers start: 26 outliers final: 19 residues processed: 86 average time/residue: 0.1816 time to fit residues: 20.8495 Evaluate side-chains 81 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 19 optimal weight: 0.0060 chunk 60 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6403 Z= 0.153 Angle : 0.495 9.442 8632 Z= 0.247 Chirality : 0.040 0.256 942 Planarity : 0.003 0.030 1044 Dihedral : 4.914 56.614 1003 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.84 % Allowed : 16.25 % Favored : 78.91 % 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: -1.27 (0.32), residues: 761 helix: 0.68 (0.29), residues: 356 sheet: -1.46 (0.60), residues: 92 loop : -2.51 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 514 HIS 0.001 0.000 HIS C 100 PHE 0.012 0.001 PHE A 423 TYR 0.024 0.001 TYR A 176 ARG 0.003 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 65 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.4710 (t80) REVERT: A 306 TRP cc_start: 0.7145 (t-100) cc_final: 0.6259 (p-90) REVERT: A 370 MET cc_start: 0.7131 (mmp) cc_final: 0.6801 (mmt) REVERT: A 607 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7225 (mtt180) REVERT: B 25 GLN cc_start: 0.8497 (mt0) cc_final: 0.8181 (mt0) REVERT: B 53 MET cc_start: 0.8312 (mmt) cc_final: 0.7901 (mmt) REVERT: C 116 LYS cc_start: 0.7851 (tttt) cc_final: 0.6860 (mtmt) outliers start: 31 outliers final: 21 residues processed: 92 average time/residue: 0.1834 time to fit residues: 22.7431 Evaluate side-chains 84 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6403 Z= 0.374 Angle : 0.649 9.421 8632 Z= 0.329 Chirality : 0.046 0.259 942 Planarity : 0.004 0.029 1044 Dihedral : 6.474 57.285 1003 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.84 % Allowed : 16.88 % Favored : 78.28 % 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: -1.59 (0.32), residues: 761 helix: 0.31 (0.28), residues: 363 sheet: -2.01 (0.54), residues: 103 loop : -2.43 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 514 HIS 0.002 0.001 HIS A 223 PHE 0.022 0.002 PHE A 373 TYR 0.028 0.002 TYR A 176 ARG 0.004 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6702 (t80) REVERT: A 176 TYR cc_start: 0.8180 (t80) cc_final: 0.7763 (t80) REVERT: A 306 TRP cc_start: 0.7248 (t-100) cc_final: 0.6177 (p-90) REVERT: A 385 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6711 (t80) REVERT: B 65 GLU cc_start: 0.7387 (tt0) cc_final: 0.7184 (tt0) REVERT: B 79 TYR cc_start: 0.8923 (m-80) cc_final: 0.8692 (m-80) REVERT: B 127 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.5475 (mtp) outliers start: 31 outliers final: 23 residues processed: 100 average time/residue: 0.1636 time to fit residues: 22.3565 Evaluate side-chains 92 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6403 Z= 0.160 Angle : 0.543 9.802 8632 Z= 0.267 Chirality : 0.041 0.252 942 Planarity : 0.003 0.028 1044 Dihedral : 5.318 56.431 1001 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.28 % Allowed : 20.00 % Favored : 76.72 % 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: -1.16 (0.32), residues: 761 helix: 0.65 (0.29), residues: 359 sheet: -1.25 (0.61), residues: 90 loop : -2.36 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 514 HIS 0.002 0.000 HIS A 235 PHE 0.011 0.001 PHE A 133 TYR 0.022 0.001 TYR A 176 ARG 0.004 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6394 (t80) REVERT: A 306 TRP cc_start: 0.7240 (t-100) cc_final: 0.6179 (p-90) REVERT: A 564 ARG cc_start: 0.8108 (ttt90) cc_final: 0.7849 (ptm160) REVERT: B 53 MET cc_start: 0.8231 (tpt) cc_final: 0.7980 (mmt) REVERT: B 79 TYR cc_start: 0.8912 (m-80) cc_final: 0.8598 (m-80) REVERT: C 85 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7659 (ttm170) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.2032 time to fit residues: 22.9307 Evaluate side-chains 80 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6403 Z= 0.223 Angle : 0.551 9.401 8632 Z= 0.276 Chirality : 0.042 0.261 942 Planarity : 0.004 0.027 1044 Dihedral : 5.396 57.123 1001 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.06 % Allowed : 20.31 % Favored : 75.62 % 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 (0.32), residues: 761 helix: 0.66 (0.29), residues: 360 sheet: -1.15 (0.60), residues: 90 loop : -2.39 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 514 HIS 0.001 0.001 HIS A 235 PHE 0.011 0.001 PHE A 380 TYR 0.028 0.002 TYR A 176 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6446 (t80) REVERT: A 176 TYR cc_start: 0.8116 (t80) cc_final: 0.7694 (t80) REVERT: A 204 TRP cc_start: 0.2179 (OUTLIER) cc_final: 0.0273 (m-90) REVERT: A 306 TRP cc_start: 0.7268 (t-100) cc_final: 0.6198 (p-90) REVERT: A 385 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6450 (t80) REVERT: A 564 ARG cc_start: 0.8174 (ttt90) cc_final: 0.7629 (ttt90) REVERT: B 53 MET cc_start: 0.8210 (tpt) cc_final: 0.7977 (mmt) REVERT: B 79 TYR cc_start: 0.8911 (m-80) cc_final: 0.8596 (m-80) REVERT: C 69 LYS cc_start: 0.7761 (tttp) cc_final: 0.7481 (tttm) outliers start: 26 outliers final: 20 residues processed: 90 average time/residue: 0.1941 time to fit residues: 23.2481 Evaluate side-chains 90 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6403 Z= 0.259 Angle : 0.579 9.395 8632 Z= 0.291 Chirality : 0.042 0.259 942 Planarity : 0.004 0.028 1044 Dihedral : 5.656 57.051 1001 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.53 % Allowed : 19.53 % Favored : 75.94 % 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: -1.21 (0.32), residues: 761 helix: 0.57 (0.29), residues: 360 sheet: -1.36 (0.56), residues: 99 loop : -2.32 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 514 HIS 0.002 0.001 HIS A 235 PHE 0.013 0.001 PHE A 373 TYR 0.025 0.002 TYR A 176 ARG 0.003 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 64 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6643 (t80) REVERT: A 176 TYR cc_start: 0.8161 (t80) cc_final: 0.7733 (t80) REVERT: A 204 TRP cc_start: 0.2338 (OUTLIER) cc_final: 0.0246 (m-90) REVERT: A 306 TRP cc_start: 0.7257 (t-100) cc_final: 0.6248 (p-90) REVERT: A 385 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6701 (t80) REVERT: B 53 MET cc_start: 0.8194 (tpt) cc_final: 0.7957 (mmt) REVERT: B 79 TYR cc_start: 0.8927 (m-80) cc_final: 0.8633 (m-80) REVERT: C 69 LYS cc_start: 0.7843 (tttp) cc_final: 0.7559 (tttm) outliers start: 29 outliers final: 22 residues processed: 88 average time/residue: 0.1753 time to fit residues: 21.2562 Evaluate side-chains 88 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.0040 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6403 Z= 0.158 Angle : 0.532 9.359 8632 Z= 0.266 Chirality : 0.041 0.254 942 Planarity : 0.003 0.028 1044 Dihedral : 5.192 56.983 1001 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.22 % Allowed : 20.16 % Favored : 75.62 % 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: -0.94 (0.32), residues: 761 helix: 0.86 (0.29), residues: 348 sheet: -0.94 (0.60), residues: 92 loop : -2.25 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 PHE 0.012 0.001 PHE A 133 TYR 0.021 0.001 TYR A 176 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6354 (t80) REVERT: A 176 TYR cc_start: 0.8112 (t80) cc_final: 0.7839 (t80) REVERT: A 204 TRP cc_start: 0.2274 (OUTLIER) cc_final: 0.0228 (m-90) REVERT: A 306 TRP cc_start: 0.7245 (t-100) cc_final: 0.6226 (p-90) REVERT: A 385 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6447 (t80) REVERT: A 389 MET cc_start: 0.6617 (tpp) cc_final: 0.5873 (mtt) REVERT: A 514 TRP cc_start: 0.8135 (m-10) cc_final: 0.7824 (m-10) REVERT: B 79 TYR cc_start: 0.8910 (m-80) cc_final: 0.8604 (m-80) outliers start: 27 outliers final: 19 residues processed: 87 average time/residue: 0.1750 time to fit residues: 20.7852 Evaluate side-chains 83 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 59 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6403 Z= 0.152 Angle : 0.525 9.365 8632 Z= 0.264 Chirality : 0.041 0.255 942 Planarity : 0.003 0.028 1044 Dihedral : 5.038 57.140 1001 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.28 % Allowed : 21.25 % Favored : 75.47 % 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: -0.92 (0.32), residues: 761 helix: 0.86 (0.29), residues: 349 sheet: -0.90 (0.60), residues: 94 loop : -2.25 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 PHE 0.016 0.001 PHE A 133 TYR 0.021 0.001 TYR A 176 ARG 0.003 0.000 ARG A 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6115 (t80) REVERT: A 204 TRP cc_start: 0.2263 (OUTLIER) cc_final: 0.0191 (m-90) REVERT: A 306 TRP cc_start: 0.7249 (t-100) cc_final: 0.6218 (p-90) REVERT: A 385 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6493 (t80) REVERT: A 514 TRP cc_start: 0.8139 (m-10) cc_final: 0.7867 (m-10) REVERT: B 79 TYR cc_start: 0.8894 (m-80) cc_final: 0.8591 (m-80) outliers start: 21 outliers final: 18 residues processed: 81 average time/residue: 0.1828 time to fit residues: 20.0057 Evaluate side-chains 82 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.155889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120527 restraints weight = 7370.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126053 restraints weight = 4273.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129769 restraints weight = 3015.400| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6403 Z= 0.155 Angle : 0.522 9.372 8632 Z= 0.262 Chirality : 0.040 0.256 942 Planarity : 0.003 0.028 1044 Dihedral : 4.950 57.225 1001 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.12 % Allowed : 21.41 % Favored : 75.47 % 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: -0.81 (0.33), residues: 761 helix: 0.94 (0.29), residues: 348 sheet: -0.79 (0.60), residues: 94 loop : -2.18 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 PHE 0.015 0.001 PHE A 133 TYR 0.026 0.001 TYR A 176 ARG 0.003 0.000 ARG A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.61 seconds wall clock time: 31 minutes 35.92 seconds (1895.92 seconds total)