Starting phenix.real_space_refine on Tue Feb 13 07:58:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnc_34910/02_2024/8hnc_34910_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnc_34910/02_2024/8hnc_34910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnc_34910/02_2024/8hnc_34910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnc_34910/02_2024/8hnc_34910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnc_34910/02_2024/8hnc_34910_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnc_34910/02_2024/8hnc_34910_updated.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2825 2.51 5 N 678 2.21 5 O 736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4272 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4187 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 21, 'TRANS': 548} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "B" 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'BLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.98, per 1000 atoms: 0.70 Number of scatterers: 4272 At special positions: 0 Unit cell: (101.504, 59.904, 79.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 736 8.00 N 678 7.00 C 2825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.01 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " 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=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 704 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 779.6 milliseconds 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 1 sheets defined 60.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 27 through 49 Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 63 through 78 removed outlier: 4.505A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.946A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 87' Processing helix chain 'A' and resid 93 through 116 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.706A pdb=" N LEU A 180 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.844A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 4.404A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 259 through 278 Proline residue: A 275 - end of helix removed outlier: 5.049A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 336 through 366 removed outlier: 5.253A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 399 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.767A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 549 removed outlier: 3.827A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 565 through 583 removed outlier: 4.087A pdb=" N LYS A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N SER A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY A 583 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 removed outlier: 4.268A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 Processing sheet with id= A, first strand: chain 'A' and resid 473 through 475 234 hydrogen bonds defined for protein. 630 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: 1.12 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 664 1.32 - 1.45: 1233 1.45 - 1.57: 2432 1.57 - 1.69: 0 1.69 - 1.82: 49 Bond restraints: 4378 Sorted by residual: bond pdb=" CGD BLR A 701 " pdb=" O1D BLR A 701 " ideal model delta sigma weight residual 1.231 1.308 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N LEU A 545 " pdb=" CA LEU A 545 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.28e-02 6.10e+03 1.31e+01 bond pdb=" C TYR A 352 " pdb=" O TYR A 352 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" CA LEU A 545 " pdb=" C LEU A 545 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.35e-02 5.49e+03 9.96e+00 bond pdb=" CA TYR A 352 " pdb=" C TYR A 352 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.32e-02 5.74e+03 9.53e+00 ... (remaining 4373 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.12: 85 105.12 - 112.33: 2214 112.33 - 119.54: 1333 119.54 - 126.75: 2255 126.75 - 133.95: 64 Bond angle restraints: 5951 Sorted by residual: angle pdb=" N VAL A 509 " pdb=" CA VAL A 509 " pdb=" C VAL A 509 " ideal model delta sigma weight residual 110.62 118.68 -8.06 1.02e+00 9.61e-01 6.25e+01 angle pdb=" N ASN A 503 " pdb=" CA ASN A 503 " pdb=" C ASN A 503 " ideal model delta sigma weight residual 111.56 122.66 -11.10 1.43e+00 4.89e-01 6.02e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.65 115.05 6.60 1.01e+00 9.80e-01 4.27e+01 angle pdb=" C TRP A 254 " pdb=" N VAL A 255 " pdb=" CA VAL A 255 " ideal model delta sigma weight residual 122.99 114.19 8.80 1.39e+00 5.18e-01 4.01e+01 angle pdb=" C THR A 510 " pdb=" N GLY A 511 " pdb=" CA GLY A 511 " ideal model delta sigma weight residual 121.58 116.85 4.73 8.60e-01 1.35e+00 3.02e+01 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 2389 21.20 - 42.40: 142 42.40 - 63.60: 13 63.60 - 84.79: 11 84.79 - 105.99: 8 Dihedral angle restraints: 2563 sinusoidal: 936 harmonic: 1627 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 506 " pdb=" CB CYS A 506 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual 93.00 14.62 78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" C LEU A 143 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " ideal model delta harmonic sigma weight residual -122.60 -110.31 -12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 2560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 691 0.294 - 0.587: 3 0.587 - 0.881: 0 0.881 - 1.175: 0 1.175 - 1.468: 1 Chirality restraints: 695 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-02 2.50e+03 5.39e+03 chirality pdb=" CA ASN A 503 " pdb=" N ASN A 503 " pdb=" C ASN A 503 " pdb=" CB ASN A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 692 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.82e+02 pdb=" C7 NAG B 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.286 2.00e-02 2.50e+03 2.44e-01 7.46e+02 pdb=" C7 NAG B 1 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " -0.159 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" C7 NAG A 704 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " 0.210 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.022 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 56 2.64 - 3.21: 4313 3.21 - 3.77: 6621 3.77 - 4.34: 8596 4.34 - 4.90: 13883 Nonbonded interactions: 33469 Sorted by model distance: nonbonded pdb=" ND BLR A 701 " pdb=" O2A BLR A 701 " model vdw 2.079 2.520 nonbonded pdb=" O MET A 233 " pdb=" N ALA A 257 " model vdw 2.204 2.520 nonbonded pdb=" O ASN A 460 " pdb=" N CYS A 463 " model vdw 2.224 2.520 nonbonded pdb=" OG SER A 418 " pdb=" ND2 ASN A 544 " model vdw 2.293 2.520 nonbonded pdb=" ND1 HIS A 115 " pdb=" CD1 TRP A 259 " model vdw 2.364 3.340 ... (remaining 33464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.700 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.006 0.077 4378 Z= 0.391 Angle : 1.009 11.099 5951 Z= 0.640 Chirality : 0.081 1.468 695 Planarity : 0.015 0.266 726 Dihedral : 15.074 105.991 1506 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.49 % Allowed : 5.11 % Favored : 94.40 % Cbeta Deviations : 0.39 % 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: -2.79 (0.31), residues: 562 helix: -1.27 (0.24), residues: 343 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 92 PHE 0.029 0.001 PHE A 591 TYR 0.025 0.002 TYR A 352 ARG 0.001 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8898 (tpt) cc_final: 0.8483 (tpp) REVERT: A 185 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 381 ILE cc_start: 0.8682 (tp) cc_final: 0.8426 (tp) REVERT: A 617 ASN cc_start: 0.7996 (t0) cc_final: 0.7607 (t0) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.1879 time to fit residues: 24.3173 Evaluate side-chains 75 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4378 Z= 0.206 Angle : 0.637 8.606 5951 Z= 0.307 Chirality : 0.043 0.281 695 Planarity : 0.004 0.031 726 Dihedral : 8.694 87.852 680 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.46 % Allowed : 12.90 % Favored : 85.64 % 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: -0.73 (0.35), residues: 562 helix: 0.39 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.89 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.001 0.001 HIS A 555 PHE 0.015 0.001 PHE A 591 TYR 0.022 0.002 TYR A 590 ARG 0.005 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8927 (tpt) cc_final: 0.8500 (tpp) REVERT: A 217 MET cc_start: 0.8423 (mmp) cc_final: 0.8186 (mmp) REVERT: A 253 ARG cc_start: 0.6861 (mtm180) cc_final: 0.6427 (mtm180) REVERT: A 381 ILE cc_start: 0.8760 (tp) cc_final: 0.8455 (tp) REVERT: A 390 MET cc_start: 0.8363 (mmt) cc_final: 0.7771 (mmt) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.1330 time to fit residues: 14.8074 Evaluate side-chains 81 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4378 Z= 0.227 Angle : 0.585 7.174 5951 Z= 0.285 Chirality : 0.042 0.266 695 Planarity : 0.004 0.035 726 Dihedral : 7.161 83.787 680 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.16 % Allowed : 15.33 % Favored : 81.51 % 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: -0.10 (0.36), residues: 562 helix: 0.99 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.003 0.001 HIS A 54 PHE 0.014 0.001 PHE A 591 TYR 0.019 0.001 TYR A 590 ARG 0.006 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8935 (tpt) cc_final: 0.8504 (tpp) REVERT: A 170 MET cc_start: 0.7780 (mmm) cc_final: 0.7563 (mmm) REVERT: A 198 ASP cc_start: 0.8696 (t0) cc_final: 0.8455 (t0) REVERT: A 381 ILE cc_start: 0.8774 (tp) cc_final: 0.8488 (tp) REVERT: A 390 MET cc_start: 0.8294 (mmt) cc_final: 0.7667 (mmt) REVERT: A 395 TYR cc_start: 0.7918 (t80) cc_final: 0.7716 (t80) REVERT: A 600 ILE cc_start: 0.9070 (tp) cc_final: 0.8764 (tp) REVERT: A 615 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7388 (p) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.1363 time to fit residues: 15.7018 Evaluate side-chains 85 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4378 Z= 0.197 Angle : 0.556 6.812 5951 Z= 0.275 Chirality : 0.041 0.207 695 Planarity : 0.004 0.036 726 Dihedral : 6.833 79.703 680 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.68 % Allowed : 17.52 % Favored : 79.81 % 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: 0.23 (0.36), residues: 562 helix: 1.25 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.59 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 254 HIS 0.002 0.001 HIS A 92 PHE 0.014 0.001 PHE A 591 TYR 0.018 0.001 TYR A 590 ARG 0.006 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8877 (tpt) cc_final: 0.8483 (tpp) REVERT: A 381 ILE cc_start: 0.8771 (tp) cc_final: 0.8474 (tp) REVERT: A 390 MET cc_start: 0.8205 (mmt) cc_final: 0.7595 (mmt) REVERT: A 395 TYR cc_start: 0.7764 (t80) cc_final: 0.7504 (t80) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.1296 time to fit residues: 14.4235 Evaluate side-chains 80 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 422 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4378 Z= 0.179 Angle : 0.545 6.399 5951 Z= 0.269 Chirality : 0.040 0.210 695 Planarity : 0.004 0.036 726 Dihedral : 6.658 77.816 680 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.89 % Allowed : 18.00 % Favored : 78.10 % 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: 0.41 (0.36), residues: 562 helix: 1.36 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.48 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 254 HIS 0.004 0.001 HIS A 92 PHE 0.013 0.001 PHE A 591 TYR 0.018 0.001 TYR A 590 ARG 0.006 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8848 (tpt) cc_final: 0.8469 (tpp) REVERT: A 356 PHE cc_start: 0.7297 (m-80) cc_final: 0.6806 (t80) REVERT: A 381 ILE cc_start: 0.8743 (tp) cc_final: 0.8457 (tp) REVERT: A 390 MET cc_start: 0.8154 (mmt) cc_final: 0.7522 (mmt) REVERT: A 395 TYR cc_start: 0.7650 (t80) cc_final: 0.7371 (t80) outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 0.1326 time to fit residues: 15.8609 Evaluate side-chains 85 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 520 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4378 Z= 0.162 Angle : 0.560 9.653 5951 Z= 0.271 Chirality : 0.039 0.188 695 Planarity : 0.004 0.041 726 Dihedral : 6.500 73.501 680 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.16 % Allowed : 19.95 % Favored : 76.89 % 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: 0.58 (0.36), residues: 562 helix: 1.47 (0.29), residues: 340 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 254 HIS 0.003 0.001 HIS A 92 PHE 0.011 0.001 PHE A 116 TYR 0.017 0.001 TYR A 590 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8814 (tpt) cc_final: 0.8480 (tpp) REVERT: A 170 MET cc_start: 0.7430 (mmm) cc_final: 0.7165 (mmt) REVERT: A 381 ILE cc_start: 0.8727 (tp) cc_final: 0.8429 (tp) REVERT: A 390 MET cc_start: 0.8087 (mmt) cc_final: 0.7364 (mmt) REVERT: A 395 TYR cc_start: 0.7572 (t80) cc_final: 0.7283 (t80) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1338 time to fit residues: 14.9825 Evaluate side-chains 79 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4378 Z= 0.198 Angle : 0.593 8.529 5951 Z= 0.285 Chirality : 0.040 0.180 695 Planarity : 0.003 0.026 726 Dihedral : 6.417 73.378 680 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.92 % Allowed : 20.92 % Favored : 76.16 % 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: 0.51 (0.36), residues: 562 helix: 1.38 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.43 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 92 PHE 0.010 0.001 PHE A 591 TYR 0.017 0.001 TYR A 590 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8846 (tpt) cc_final: 0.8492 (tpp) REVERT: A 381 ILE cc_start: 0.8757 (tp) cc_final: 0.8447 (tp) REVERT: A 390 MET cc_start: 0.8110 (mmt) cc_final: 0.7384 (mmt) REVERT: A 395 TYR cc_start: 0.7596 (t80) cc_final: 0.7321 (t80) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.1352 time to fit residues: 13.6938 Evaluate side-chains 78 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 40.0000 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 520 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4378 Z= 0.161 Angle : 0.578 10.039 5951 Z= 0.278 Chirality : 0.039 0.170 695 Planarity : 0.003 0.026 726 Dihedral : 6.303 69.513 680 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.92 % Allowed : 21.17 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.36), residues: 562 helix: 1.46 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.40 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.003 0.001 HIS A 92 PHE 0.010 0.001 PHE A 591 TYR 0.024 0.001 TYR A 234 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8771 (tpt) cc_final: 0.8452 (tpp) REVERT: A 381 ILE cc_start: 0.8721 (tp) cc_final: 0.8418 (tp) REVERT: A 390 MET cc_start: 0.8062 (mmt) cc_final: 0.7331 (mmt) REVERT: A 395 TYR cc_start: 0.7510 (t80) cc_final: 0.7236 (t80) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.1451 time to fit residues: 15.2996 Evaluate side-chains 81 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 0.1980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4378 Z= 0.194 Angle : 0.584 10.181 5951 Z= 0.283 Chirality : 0.040 0.167 695 Planarity : 0.003 0.027 726 Dihedral : 6.234 68.935 680 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.68 % Allowed : 22.87 % Favored : 74.45 % 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: 0.63 (0.36), residues: 562 helix: 1.47 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.38 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 254 HIS 0.004 0.001 HIS A 92 PHE 0.011 0.001 PHE A 591 TYR 0.030 0.001 TYR A 234 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8831 (tpt) cc_final: 0.8469 (tpp) REVERT: A 185 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 381 ILE cc_start: 0.8770 (tp) cc_final: 0.8432 (tp) REVERT: A 395 TYR cc_start: 0.7522 (t80) cc_final: 0.7266 (t80) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 0.1380 time to fit residues: 13.9892 Evaluate side-chains 79 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 40.0000 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4378 Z= 0.166 Angle : 0.576 10.541 5951 Z= 0.277 Chirality : 0.039 0.165 695 Planarity : 0.003 0.028 726 Dihedral : 6.202 67.254 680 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.43 % Allowed : 22.87 % Favored : 74.70 % 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: 0.67 (0.36), residues: 562 helix: 1.49 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 254 HIS 0.003 0.001 HIS A 92 PHE 0.011 0.001 PHE A 591 TYR 0.023 0.001 TYR A 234 ARG 0.007 0.001 ARG A 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8790 (tpt) cc_final: 0.8459 (tpp) REVERT: A 185 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 381 ILE cc_start: 0.8731 (tp) cc_final: 0.8403 (tp) REVERT: A 395 TYR cc_start: 0.7499 (t80) cc_final: 0.7252 (t80) outliers start: 10 outliers final: 10 residues processed: 74 average time/residue: 0.1342 time to fit residues: 13.3105 Evaluate side-chains 79 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.0030 chunk 38 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** 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 = 0.3754 r_free = 0.3754 target = 0.165961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.122321 restraints weight = 4837.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119789 restraints weight = 4163.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120695 restraints weight = 4034.244| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4378 Z= 0.193 Angle : 0.578 10.383 5951 Z= 0.279 Chirality : 0.039 0.162 695 Planarity : 0.003 0.029 726 Dihedral : 6.152 67.587 680 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.92 % Allowed : 23.36 % Favored : 73.72 % 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: 0.70 (0.36), residues: 562 helix: 1.53 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.37 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 254 HIS 0.004 0.001 HIS A 92 PHE 0.012 0.001 PHE A 591 TYR 0.023 0.001 TYR A 234 ARG 0.007 0.001 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1237.20 seconds wall clock time: 23 minutes 2.97 seconds (1382.97 seconds total)