Starting phenix.real_space_refine on Mon Apr 8 18:25:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8je2_36183/04_2024/8je2_36183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8je2_36183/04_2024/8je2_36183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8je2_36183/04_2024/8je2_36183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8je2_36183/04_2024/8je2_36183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8je2_36183/04_2024/8je2_36183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8je2_36183/04_2024/8je2_36183.pdb" } resolution = 3.63 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4937 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 67 5.16 5 C 5868 2.51 5 N 1606 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 529": "OD1" <-> "OD2" Residue "H PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9271 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3757 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 13, 'TRANS': 440} Chain breaks: 1 Chain: "B" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain breaks: 3 Chain: "C" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain breaks: 1 Chain: "D" Number of atoms: 3930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3919 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 494, 3919 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3972 Chain: "H" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 188 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8853 SG CYS D 599 40.605 84.257 37.400 1.00126.88 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 177 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG D 177 " occ=0.57 Time building chain proxies: 7.16, per 1000 atoms: 0.77 Number of scatterers: 9271 At special positions: 0 Unit cell: (117.86, 135.29, 141.93, 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) Zn 1 29.99 S 67 16.00 O 1729 8.00 N 1606 7.00 C 5868 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 Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 627 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 599 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 565 " 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 1 sheets defined 70.1% alpha, 2.1% 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 9 through 26 removed outlier: 3.535A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.694A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.895A pdb=" N CYS A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.567A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 173 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 230 Processing helix chain 'A' and resid 231 through 253 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.649A pdb=" N LEU A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 306 through 330 removed outlier: 4.320A pdb=" N HIS A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 358 removed outlier: 4.191A pdb=" N PHE A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 385 through 400 removed outlier: 4.018A pdb=" N GLU A 389 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.003A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 450 through 463 Processing helix chain 'B' and resid 23 through 36 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.526A pdb=" N THR C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 removed outlier: 4.622A pdb=" N LEU C 101 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 189 through 197 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 245 through 263 Processing helix chain 'D' and resid 268 through 284 Processing helix chain 'D' and resid 310 through 318 removed outlier: 3.532A pdb=" N LEU D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 338 removed outlier: 4.568A pdb=" N ALA D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.072A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 378 Processing helix chain 'D' and resid 381 through 398 removed outlier: 4.004A pdb=" N PHE D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 429 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 433 through 457 Processing helix chain 'D' and resid 460 through 477 removed outlier: 4.084A pdb=" N LEU D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 485 removed outlier: 3.850A pdb=" N PHE D 485 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 Processing helix chain 'D' and resid 511 through 521 removed outlier: 3.842A pdb=" N THR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 541 removed outlier: 3.576A pdb=" N ILE D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 575 through 580 Processing helix chain 'D' and resid 582 through 593 Processing helix chain 'D' and resid 596 through 609 Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.810A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE D 623 " --> pdb=" O THR D 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 50 removed outlier: 5.020A pdb=" N LYS C 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2457 1.33 - 1.45: 1603 1.45 - 1.57: 5279 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 9443 Sorted by residual: bond pdb=" N ILE C 90 " pdb=" CA ILE C 90 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.70e-03 1.32e+04 1.87e+01 bond pdb=" N ARG C 82 " pdb=" CA ARG C 82 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.36e+00 bond pdb=" N TYR A 49 " pdb=" CA TYR A 49 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.30e+00 bond pdb=" N VAL D 528 " pdb=" CA VAL D 528 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.01e+00 bond pdb=" N VAL C 81 " pdb=" CA VAL C 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.88e+00 ... (remaining 9438 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.51: 132 104.51 - 111.89: 4618 111.89 - 119.27: 3273 119.27 - 126.65: 4622 126.65 - 134.03: 103 Bond angle restraints: 12748 Sorted by residual: angle pdb=" N PRO D 510 " pdb=" CA PRO D 510 " pdb=" CB PRO D 510 " ideal model delta sigma weight residual 103.25 111.19 -7.94 1.05e+00 9.07e-01 5.71e+01 angle pdb=" CA PHE C 93 " pdb=" C PHE C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 118.85 122.58 -3.73 9.50e-01 1.11e+00 1.54e+01 angle pdb=" N ILE A 185 " pdb=" CA ILE A 185 " pdb=" CB ILE A 185 " ideal model delta sigma weight residual 110.54 115.79 -5.25 1.36e+00 5.41e-01 1.49e+01 angle pdb=" CA THR C 84 " pdb=" C THR C 84 " pdb=" O THR C 84 " ideal model delta sigma weight residual 121.78 116.97 4.81 1.28e+00 6.10e-01 1.41e+01 angle pdb=" N GLU A 237 " pdb=" CA GLU A 237 " pdb=" CB GLU A 237 " ideal model delta sigma weight residual 110.28 116.05 -5.77 1.55e+00 4.16e-01 1.39e+01 ... (remaining 12743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5268 16.89 - 33.79: 422 33.79 - 50.68: 75 50.68 - 67.57: 13 67.57 - 84.47: 5 Dihedral angle restraints: 5783 sinusoidal: 2385 harmonic: 3398 Sorted by residual: dihedral pdb=" C TYR A 49 " pdb=" N TYR A 49 " pdb=" CA TYR A 49 " pdb=" CB TYR A 49 " ideal model delta harmonic sigma weight residual -122.60 -133.13 10.53 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" CA GLU D 400 " pdb=" C GLU D 400 " pdb=" N THR D 401 " pdb=" CA THR D 401 " ideal model delta harmonic sigma weight residual 180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" N TYR A 49 " pdb=" C TYR A 49 " pdb=" CA TYR A 49 " pdb=" CB TYR A 49 " ideal model delta harmonic sigma weight residual 122.80 132.21 -9.41 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1283 0.071 - 0.141: 134 0.141 - 0.212: 13 0.212 - 0.283: 4 0.283 - 0.353: 1 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA TYR A 49 " pdb=" N TYR A 49 " pdb=" C TYR A 49 " pdb=" CB TYR A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PRO D 510 " pdb=" N PRO D 510 " pdb=" C PRO D 510 " pdb=" CB PRO D 510 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA LYS D 574 " pdb=" N LYS D 574 " pdb=" C LYS D 574 " pdb=" CB LYS D 574 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1432 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 233 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C SER A 233 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 233 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 234 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 37 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 38 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 367 " -0.015 2.00e-02 2.50e+03 9.90e-03 2.45e+00 pdb=" CG TRP D 367 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 367 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 367 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 367 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 367 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 367 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 367 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 367 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 367 " 0.001 2.00e-02 2.50e+03 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1152 2.75 - 3.29: 9986 3.29 - 3.83: 15983 3.83 - 4.36: 18692 4.36 - 4.90: 30456 Nonbonded interactions: 76269 Sorted by model distance: nonbonded pdb=" NH1 ARG D 305 " pdb=" O THR D 306 " model vdw 2.215 2.520 nonbonded pdb=" OD1 ASP D 322 " pdb=" OH TYR D 354 " model vdw 2.225 2.440 nonbonded pdb=" NH2 ARG H 576 " pdb=" O CYS H 580 " model vdw 2.236 2.520 nonbonded pdb=" ND2 ASN D 155 " pdb=" O ASN H 579 " model vdw 2.258 2.520 nonbonded pdb=" NH1 ARG H 576 " pdb=" O CYS H 585 " model vdw 2.271 2.520 ... (remaining 76264 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=0.43 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: 9.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 27.570 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 32.220 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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: 72.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9443 Z= 0.259 Angle : 0.711 10.434 12748 Z= 0.446 Chirality : 0.046 0.353 1435 Planarity : 0.004 0.052 1639 Dihedral : 12.657 84.467 3569 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.16 % Rotamer: Outliers : 0.39 % Allowed : 0.29 % Favored : 99.32 % Cbeta Deviations : 0.09 % 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: 1.29 (0.25), residues: 1128 helix: 1.44 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.33 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 367 HIS 0.005 0.001 HIS D 627 PHE 0.018 0.001 PHE D 447 TYR 0.020 0.001 TYR A 90 ARG 0.006 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8890 (mtp) cc_final: 0.8597 (mtp) REVERT: A 294 MET cc_start: 0.8484 (mmp) cc_final: 0.8164 (mmp) REVERT: A 297 MET cc_start: 0.9152 (mmm) cc_final: 0.8737 (tpp) REVERT: A 406 MET cc_start: 0.8348 (tpt) cc_final: 0.8084 (tpt) REVERT: A 422 PHE cc_start: 0.9326 (t80) cc_final: 0.8951 (t80) REVERT: D 280 MET cc_start: 0.2391 (ttm) cc_final: 0.1758 (tpp) REVERT: D 395 MET cc_start: 0.9564 (ppp) cc_final: 0.9273 (ppp) REVERT: H 575 ILE cc_start: 0.9164 (mm) cc_final: 0.8713 (mm) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 0.2139 time to fit residues: 25.6770 Evaluate side-chains 66 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9443 Z= 0.196 Angle : 0.562 6.961 12748 Z= 0.300 Chirality : 0.040 0.147 1435 Planarity : 0.004 0.051 1639 Dihedral : 4.307 18.799 1247 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.31 % Favored : 97.60 % Rotamer: Outliers : 0.58 % Allowed : 5.35 % Favored : 94.07 % 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: 1.51 (0.25), residues: 1128 helix: 1.59 (0.19), residues: 775 sheet: None (None), residues: 0 loop : -0.22 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 PHE 0.020 0.002 PHE D 388 TYR 0.014 0.001 TYR A 219 ARG 0.005 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.8876 (mtp) cc_final: 0.8535 (mtp) REVERT: A 101 MET cc_start: 0.8374 (ppp) cc_final: 0.8137 (tmm) REVERT: A 294 MET cc_start: 0.8628 (mmp) cc_final: 0.8228 (mmm) REVERT: A 297 MET cc_start: 0.9022 (mmm) cc_final: 0.8681 (tpp) REVERT: A 406 MET cc_start: 0.8368 (tpt) cc_final: 0.8072 (tpt) REVERT: A 422 PHE cc_start: 0.9346 (t80) cc_final: 0.8971 (t80) REVERT: A 457 MET cc_start: 0.8991 (ppp) cc_final: 0.8650 (ppp) REVERT: D 597 LEU cc_start: 0.9179 (mt) cc_final: 0.8975 (mt) REVERT: H 575 ILE cc_start: 0.9030 (mm) cc_final: 0.8779 (mm) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.1697 time to fit residues: 19.9729 Evaluate side-chains 65 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9443 Z= 0.176 Angle : 0.538 7.286 12748 Z= 0.283 Chirality : 0.039 0.176 1435 Planarity : 0.003 0.050 1639 Dihedral : 4.261 19.475 1247 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 1.07 % Allowed : 6.52 % Favored : 92.41 % 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: 1.67 (0.25), residues: 1128 helix: 1.70 (0.19), residues: 776 sheet: 0.07 (1.20), residues: 16 loop : -0.12 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 35 HIS 0.003 0.001 HIS A 279 PHE 0.012 0.001 PHE D 388 TYR 0.018 0.001 TYR A 194 ARG 0.004 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.8856 (mtp) cc_final: 0.8527 (mtp) REVERT: A 86 MET cc_start: 0.9344 (tpp) cc_final: 0.9019 (mmm) REVERT: A 101 MET cc_start: 0.8372 (ppp) cc_final: 0.8096 (tmm) REVERT: A 137 MET cc_start: 0.8720 (ppp) cc_final: 0.8442 (ppp) REVERT: A 236 MET cc_start: 0.8298 (mtp) cc_final: 0.7383 (mtp) REVERT: A 294 MET cc_start: 0.8699 (mmp) cc_final: 0.8336 (mmm) REVERT: A 297 MET cc_start: 0.9152 (mmm) cc_final: 0.8585 (tpp) REVERT: A 311 MET cc_start: 0.9526 (tpp) cc_final: 0.9302 (tpp) REVERT: A 406 MET cc_start: 0.8485 (tpt) cc_final: 0.8186 (tpt) REVERT: A 422 PHE cc_start: 0.9369 (t80) cc_final: 0.8983 (t80) REVERT: B 29 ARG cc_start: 0.9215 (mmm-85) cc_final: 0.9004 (mmm-85) REVERT: H 575 ILE cc_start: 0.9027 (mm) cc_final: 0.8781 (mm) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.1858 time to fit residues: 20.3972 Evaluate side-chains 70 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9443 Z= 0.269 Angle : 0.586 9.284 12748 Z= 0.309 Chirality : 0.039 0.150 1435 Planarity : 0.004 0.048 1639 Dihedral : 4.342 22.428 1247 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 1.36 % Allowed : 8.46 % Favored : 90.18 % 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: 1.49 (0.25), residues: 1128 helix: 1.56 (0.19), residues: 785 sheet: 1.25 (1.30), residues: 12 loop : -0.31 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP D 367 HIS 0.004 0.001 HIS A 279 PHE 0.016 0.001 PHE D 626 TYR 0.015 0.002 TYR A 194 ARG 0.003 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.8819 (mtp) cc_final: 0.8566 (mtp) REVERT: A 86 MET cc_start: 0.9357 (tpp) cc_final: 0.8957 (mmm) REVERT: A 101 MET cc_start: 0.8311 (ppp) cc_final: 0.8046 (tmm) REVERT: A 137 MET cc_start: 0.8650 (ppp) cc_final: 0.8350 (ppp) REVERT: A 236 MET cc_start: 0.8409 (mtp) cc_final: 0.7731 (mtp) REVERT: A 294 MET cc_start: 0.8797 (mmp) cc_final: 0.8382 (mmm) REVERT: A 297 MET cc_start: 0.9241 (mmm) cc_final: 0.8653 (tpp) REVERT: A 406 MET cc_start: 0.8507 (tpt) cc_final: 0.8249 (tpt) REVERT: A 422 PHE cc_start: 0.9414 (t80) cc_final: 0.9026 (t80) REVERT: D 280 MET cc_start: 0.2761 (ttm) cc_final: 0.2327 (tpp) REVERT: D 395 MET cc_start: 0.9672 (ppp) cc_final: 0.9392 (ppp) REVERT: H 575 ILE cc_start: 0.8978 (mm) cc_final: 0.8715 (mm) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.1934 time to fit residues: 20.4741 Evaluate side-chains 67 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9443 Z= 0.336 Angle : 0.638 7.798 12748 Z= 0.335 Chirality : 0.041 0.142 1435 Planarity : 0.004 0.045 1639 Dihedral : 4.555 21.408 1247 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 1.36 % Allowed : 9.44 % Favored : 89.20 % 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: 1.28 (0.25), residues: 1128 helix: 1.40 (0.19), residues: 785 sheet: 1.74 (1.37), residues: 12 loop : -0.39 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 367 HIS 0.006 0.001 HIS A 363 PHE 0.019 0.002 PHE A 64 TYR 0.017 0.002 TYR A 219 ARG 0.006 0.001 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.140 Fit side-chains REVERT: A 26 MET cc_start: 0.8800 (mtp) cc_final: 0.8592 (mtm) REVERT: A 86 MET cc_start: 0.9363 (tpp) cc_final: 0.8922 (mmm) REVERT: A 101 MET cc_start: 0.8421 (ppp) cc_final: 0.8086 (tmm) REVERT: A 137 MET cc_start: 0.8789 (ppp) cc_final: 0.8452 (ppp) REVERT: A 236 MET cc_start: 0.8494 (mtp) cc_final: 0.8121 (mtp) REVERT: A 294 MET cc_start: 0.8902 (mmp) cc_final: 0.8460 (mmm) REVERT: A 297 MET cc_start: 0.9174 (mmm) cc_final: 0.8768 (tpp) REVERT: A 406 MET cc_start: 0.8517 (tpt) cc_final: 0.8212 (tpt) REVERT: A 422 PHE cc_start: 0.9428 (t80) cc_final: 0.9029 (t80) REVERT: D 280 MET cc_start: 0.3494 (ttm) cc_final: 0.3165 (tpp) REVERT: D 326 MET cc_start: 0.7425 (tpt) cc_final: 0.6633 (tpt) REVERT: H 575 ILE cc_start: 0.8915 (mm) cc_final: 0.8624 (mm) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.1667 time to fit residues: 18.4995 Evaluate side-chains 67 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.0270 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9443 Z= 0.162 Angle : 0.552 8.624 12748 Z= 0.286 Chirality : 0.038 0.148 1435 Planarity : 0.003 0.044 1639 Dihedral : 4.367 21.249 1247 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 0.97 % Allowed : 10.02 % Favored : 89.01 % 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: 1.53 (0.26), residues: 1128 helix: 1.63 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 367 HIS 0.004 0.001 HIS A 279 PHE 0.016 0.001 PHE A 64 TYR 0.020 0.001 TYR A 219 ARG 0.004 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.186 Fit side-chains REVERT: A 26 MET cc_start: 0.8810 (mtp) cc_final: 0.8601 (mtm) REVERT: A 86 MET cc_start: 0.9292 (tpp) cc_final: 0.8872 (mmm) REVERT: A 101 MET cc_start: 0.8336 (ppp) cc_final: 0.7898 (tmm) REVERT: A 137 MET cc_start: 0.8806 (ppp) cc_final: 0.8473 (ppp) REVERT: A 294 MET cc_start: 0.8874 (mmp) cc_final: 0.8497 (mmm) REVERT: A 297 MET cc_start: 0.9171 (mmm) cc_final: 0.8703 (mmp) REVERT: A 406 MET cc_start: 0.8484 (tpt) cc_final: 0.8264 (tpt) REVERT: A 422 PHE cc_start: 0.9421 (t80) cc_final: 0.9031 (t80) REVERT: C 105 MET cc_start: 0.9152 (mtp) cc_final: 0.8834 (ttp) REVERT: D 280 MET cc_start: 0.3190 (ttm) cc_final: 0.2898 (tpp) REVERT: H 575 ILE cc_start: 0.8915 (mm) cc_final: 0.8613 (mm) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1736 time to fit residues: 18.7410 Evaluate side-chains 65 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.0670 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9443 Z= 0.170 Angle : 0.558 8.596 12748 Z= 0.286 Chirality : 0.038 0.144 1435 Planarity : 0.003 0.042 1639 Dihedral : 4.256 19.493 1247 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.97 % Allowed : 10.99 % Favored : 88.04 % 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 (0.26), residues: 1128 helix: 1.64 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 35 HIS 0.004 0.001 HIS A 279 PHE 0.018 0.001 PHE A 198 TYR 0.016 0.001 TYR A 219 ARG 0.004 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.179 Fit side-chains REVERT: A 26 MET cc_start: 0.8813 (mtp) cc_final: 0.8602 (mtm) REVERT: A 86 MET cc_start: 0.9304 (tpp) cc_final: 0.8888 (mmm) REVERT: A 101 MET cc_start: 0.8303 (ppp) cc_final: 0.7930 (tmm) REVERT: A 137 MET cc_start: 0.8807 (ppp) cc_final: 0.8438 (ppp) REVERT: A 206 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8840 (mt) REVERT: A 236 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: A 294 MET cc_start: 0.8878 (mmp) cc_final: 0.8521 (mmm) REVERT: A 297 MET cc_start: 0.9170 (mmm) cc_final: 0.8379 (tpp) REVERT: A 422 PHE cc_start: 0.9421 (t80) cc_final: 0.9040 (t80) REVERT: D 280 MET cc_start: 0.3174 (ttm) cc_final: 0.2873 (tpp) REVERT: H 575 ILE cc_start: 0.8931 (mm) cc_final: 0.8630 (mm) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 0.1690 time to fit residues: 17.6911 Evaluate side-chains 65 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 317 ASN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9443 Z= 0.383 Angle : 0.710 12.253 12748 Z= 0.368 Chirality : 0.042 0.173 1435 Planarity : 0.004 0.039 1639 Dihedral : 4.586 20.754 1247 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 1.36 % Allowed : 11.48 % Favored : 87.16 % 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: 1.17 (0.25), residues: 1128 helix: 1.36 (0.19), residues: 785 sheet: None (None), residues: 0 loop : -0.49 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 35 HIS 0.006 0.001 HIS D 241 PHE 0.016 0.002 PHE A 64 TYR 0.017 0.002 TYR A 219 ARG 0.006 0.001 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.149 Fit side-chains REVERT: A 26 MET cc_start: 0.8786 (mtp) cc_final: 0.8570 (mtm) REVERT: A 101 MET cc_start: 0.8414 (ppp) cc_final: 0.8057 (tmm) REVERT: A 137 MET cc_start: 0.8813 (ppp) cc_final: 0.8375 (ppp) REVERT: A 294 MET cc_start: 0.8927 (mmp) cc_final: 0.8503 (mmm) REVERT: A 297 MET cc_start: 0.9122 (mmm) cc_final: 0.8650 (mmm) REVERT: A 422 PHE cc_start: 0.9445 (t80) cc_final: 0.9062 (t80) REVERT: D 280 MET cc_start: 0.3788 (ttm) cc_final: 0.3410 (tpp) REVERT: D 593 MET cc_start: 0.9085 (mmm) cc_final: 0.8769 (mmm) REVERT: H 575 ILE cc_start: 0.8945 (mm) cc_final: 0.8648 (mm) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.1686 time to fit residues: 18.1659 Evaluate side-chains 68 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.0670 chunk 103 optimal weight: 0.2980 chunk 60 optimal weight: 0.0020 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9443 Z= 0.169 Angle : 0.643 11.342 12748 Z= 0.319 Chirality : 0.039 0.193 1435 Planarity : 0.003 0.040 1639 Dihedral : 4.404 20.378 1247 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.78 % Allowed : 12.45 % Favored : 86.77 % 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: 1.44 (0.26), residues: 1128 helix: 1.55 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -0.36 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 35 HIS 0.003 0.001 HIS A 279 PHE 0.017 0.001 PHE A 202 TYR 0.019 0.001 TYR A 219 ARG 0.004 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 1.080 Fit side-chains REVERT: A 26 MET cc_start: 0.8782 (mtp) cc_final: 0.8433 (mtp) REVERT: A 86 MET cc_start: 0.9302 (tpp) cc_final: 0.8874 (mmm) REVERT: A 101 MET cc_start: 0.8350 (ppp) cc_final: 0.7892 (tmm) REVERT: A 137 MET cc_start: 0.8837 (ppp) cc_final: 0.8499 (ppp) REVERT: A 294 MET cc_start: 0.8903 (mmp) cc_final: 0.8603 (mmm) REVERT: A 297 MET cc_start: 0.9105 (mmm) cc_final: 0.8612 (mmm) REVERT: A 422 PHE cc_start: 0.9424 (t80) cc_final: 0.9031 (t80) REVERT: B 46 LYS cc_start: 0.8132 (tmmt) cc_final: 0.7886 (ttpp) REVERT: D 280 MET cc_start: 0.3506 (ttm) cc_final: 0.3285 (tpp) REVERT: D 326 MET cc_start: 0.7590 (tpt) cc_final: 0.7128 (tpt) REVERT: H 575 ILE cc_start: 0.8934 (mm) cc_final: 0.8661 (mm) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.1853 time to fit residues: 18.9252 Evaluate side-chains 64 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.0040 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9443 Z= 0.197 Angle : 0.666 17.839 12748 Z= 0.328 Chirality : 0.040 0.186 1435 Planarity : 0.003 0.039 1639 Dihedral : 4.343 19.825 1247 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Rotamer: Outliers : 0.58 % Allowed : 12.94 % Favored : 86.48 % 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: 1.52 (0.26), residues: 1128 helix: 1.60 (0.19), residues: 789 sheet: None (None), residues: 0 loop : -0.34 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 35 HIS 0.003 0.001 HIS A 279 PHE 0.019 0.001 PHE D 447 TYR 0.016 0.001 TYR A 219 ARG 0.004 0.000 ARG B 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 1.160 Fit side-chains REVERT: A 26 MET cc_start: 0.8777 (mtp) cc_final: 0.8443 (mtp) REVERT: A 86 MET cc_start: 0.9320 (tpp) cc_final: 0.8886 (mmm) REVERT: A 101 MET cc_start: 0.8303 (ppp) cc_final: 0.7949 (tmm) REVERT: A 137 MET cc_start: 0.8858 (ppp) cc_final: 0.8477 (ppp) REVERT: A 294 MET cc_start: 0.8904 (mmp) cc_final: 0.8602 (mmm) REVERT: A 297 MET cc_start: 0.9105 (mmm) cc_final: 0.8669 (mmm) REVERT: A 422 PHE cc_start: 0.9411 (t80) cc_final: 0.9022 (t80) REVERT: C 75 MET cc_start: 0.8670 (mtm) cc_final: 0.8392 (pmm) REVERT: D 280 MET cc_start: 0.3342 (ttm) cc_final: 0.3032 (tpp) REVERT: D 326 MET cc_start: 0.7696 (tpt) cc_final: 0.7356 (tpp) REVERT: H 575 ILE cc_start: 0.8951 (mm) cc_final: 0.8684 (mm) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1685 time to fit residues: 16.9796 Evaluate side-chains 64 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 5 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.049274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.035311 restraints weight = 120381.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.036715 restraints weight = 51153.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.037602 restraints weight = 29956.046| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9443 Z= 0.165 Angle : 0.658 14.448 12748 Z= 0.321 Chirality : 0.039 0.170 1435 Planarity : 0.003 0.039 1639 Dihedral : 4.265 19.938 1247 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.58 % Allowed : 13.13 % Favored : 86.28 % 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: 1.57 (0.26), residues: 1128 helix: 1.67 (0.19), residues: 789 sheet: None (None), residues: 0 loop : -0.37 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 35 HIS 0.003 0.001 HIS A 279 PHE 0.015 0.001 PHE D 388 TYR 0.015 0.001 TYR A 219 ARG 0.004 0.000 ARG D 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.57 seconds wall clock time: 45 minutes 0.16 seconds (2700.16 seconds total)