Starting phenix.real_space_refine on Mon Mar 11 04:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/03_2024/8dtk_27703_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/03_2024/8dtk_27703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/03_2024/8dtk_27703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/03_2024/8dtk_27703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/03_2024/8dtk_27703_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/03_2024/8dtk_27703_neut_trim.pdb" } resolution = 3.77 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= -0.004 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2248 2.51 5 N 596 2.21 5 O 692 1.98 5 H 3363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6914 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3134 Classifications: {'peptide': 203} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1749 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106} Chain: "C" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2003 Classifications: {'peptide': 133} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "A" 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 Time building chain proxies: 3.87, per 1000 atoms: 0.56 Number of scatterers: 6914 At special positions: 0 Unit cell: (69.828, 92.046, 85.698, 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) S 15 16.00 O 692 8.00 N 596 7.00 C 2248 6.00 H 3363 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " 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 NAG-ASN " NAG A 601 " - " ASN A 331 " " NAG A 602 " - " ASN A 343 " Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 776.0 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.4% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.753A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.151A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.571A pdb=" N GLN C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.666A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.853A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.839A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.551A pdb=" N VAL B 85 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.968A pdb=" N VAL C 5 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 23 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.637A pdb=" N GLU C 10 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 110 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.543A pdb=" N VAL C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 82 " --> pdb=" O VAL C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 78 hydrogen bonds defined for protein. 177 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: 2.16 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3363 1.03 - 1.23: 9 1.23 - 1.42: 1608 1.42 - 1.62: 2005 1.62 - 1.81: 18 Bond restraints: 7003 Sorted by residual: bond pdb=" CB GLU C 81 " pdb=" CG GLU C 81 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CB ASP C 95 " pdb=" CG ASP C 95 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" CB ASP B 9 " pdb=" CG ASP B 9 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.56e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" CB MET B 4 " pdb=" CG MET B 4 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 6998 not shown) Histogram of bond angle deviations from ideal: 71.17 - 83.74: 3 83.74 - 96.31: 3 96.31 - 108.87: 2814 108.87 - 121.44: 8260 121.44 - 134.01: 1456 Bond angle restraints: 12536 Sorted by residual: angle pdb=" C PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 109.00 71.17 37.83 3.00e+00 1.11e-01 1.59e+02 angle pdb=" N PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 110.00 74.48 35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 109.00 78.57 30.43 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CB LEU C 4 " pdb=" CG LEU C 4 " pdb=" HG LEU C 4 " ideal model delta sigma weight residual 109.00 85.17 23.83 3.00e+00 1.11e-01 6.31e+01 angle pdb=" CD2 LEU C 4 " pdb=" CG LEU C 4 " pdb=" HG LEU C 4 " ideal model delta sigma weight residual 108.00 84.21 23.79 3.00e+00 1.11e-01 6.29e+01 ... (remaining 12531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 3126 22.08 - 44.16: 208 44.16 - 66.23: 51 66.23 - 88.31: 15 88.31 - 110.39: 5 Dihedral angle restraints: 3405 sinusoidal: 1818 harmonic: 1587 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA VAL A 524 " pdb=" C VAL A 524 " pdb=" N CYS A 525 " pdb=" CA CYS A 525 " ideal model delta harmonic sigma weight residual 180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 125.03 -32.03 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 3402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 537 0.352 - 0.705: 0 0.705 - 1.057: 0 1.057 - 1.409: 0 1.409 - 1.762: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" CG LEU C 4 " pdb=" CB LEU C 4 " pdb=" CD1 LEU C 4 " pdb=" CD2 LEU C 4 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.76e+01 chirality pdb=" CA PHE C 100N" pdb=" N PHE C 100N" pdb=" C PHE C 100N" pdb=" CB PHE C 100N" both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 535 not shown) Planarity restraints: 1068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 61 " 0.214 9.50e-02 1.11e+02 7.17e-02 6.49e+00 pdb=" NE ARG B 61 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 61 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 61 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 61 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 61 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG B 61 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 61 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 61 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 497 " 0.013 2.00e-02 2.50e+03 1.04e-02 3.23e+00 pdb=" CG PHE A 497 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 497 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 497 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 497 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 497 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 497 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 497 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 497 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 497 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 497 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 497 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 13 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 14 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.024 5.00e-02 4.00e+02 ... (remaining 1065 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 838 2.24 - 2.83: 14848 2.83 - 3.42: 17054 3.42 - 4.01: 23693 4.01 - 4.60: 35931 Nonbonded interactions: 92364 Sorted by model distance: nonbonded pdb=" H PHE C 100N" pdb=" HA PHE C 100N" model vdw 1.653 1.816 nonbonded pdb=" HA PHE C 100N" pdb=" HB2 PHE C 100N" model vdw 1.710 1.952 nonbonded pdb=" H ALA A 363 " pdb=" O CYS A 525 " model vdw 1.732 1.850 nonbonded pdb="HH12 ARG A 454 " pdb=" O SER A 469 " model vdw 1.739 1.850 nonbonded pdb=" O VAL C 96 " pdb=" HG1 THR C 100L" model vdw 1.744 1.850 ... (remaining 92359 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: 1.810 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: 0.110 Extract box with map and model: 7.230 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 26.030 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.005 0.044 3640 Z= 0.305 Angle : 0.788 10.998 4953 Z= 0.414 Chirality : 0.091 1.762 538 Planarity : 0.006 0.095 640 Dihedral : 16.060 110.391 1326 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.29 (0.37), residues: 443 helix: -3.24 (0.52), residues: 40 sheet: -1.95 (0.44), residues: 124 loop : -1.00 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 100B HIS 0.005 0.002 HIS C 32 PHE 0.031 0.002 PHE A 497 TYR 0.021 0.002 TYR B 49 ARG 0.016 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3304 time to fit residues: 33.3728 Evaluate side-chains 69 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3640 Z= 0.254 Angle : 0.648 10.490 4953 Z= 0.331 Chirality : 0.089 1.744 538 Planarity : 0.004 0.041 640 Dihedral : 8.282 52.544 541 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.52 % Allowed : 8.57 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.18 (0.37), residues: 443 helix: -3.02 (0.63), residues: 40 sheet: -1.61 (0.45), residues: 111 loop : -1.14 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 100B HIS 0.004 0.002 HIS C 32 PHE 0.017 0.002 PHE A 490 TYR 0.013 0.001 TYR B 49 ARG 0.005 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 76 average time/residue: 0.3335 time to fit residues: 30.9649 Evaluate side-chains 74 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3640 Z= 0.214 Angle : 0.578 10.348 4953 Z= 0.297 Chirality : 0.088 1.741 538 Planarity : 0.004 0.041 640 Dihedral : 7.335 59.567 541 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.78 % Allowed : 9.61 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.23 (0.37), residues: 443 helix: -3.13 (0.60), residues: 40 sheet: -1.72 (0.48), residues: 108 loop : -1.13 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 100B HIS 0.003 0.001 HIS C 32 PHE 0.010 0.001 PHE A 429 TYR 0.012 0.001 TYR B 49 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.3600 time to fit residues: 33.8554 Evaluate side-chains 76 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3640 Z= 0.264 Angle : 0.590 10.530 4953 Z= 0.304 Chirality : 0.088 1.753 538 Planarity : 0.004 0.042 640 Dihedral : 6.551 49.190 541 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.08 % Allowed : 11.43 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.26 (0.37), residues: 443 helix: -3.18 (0.58), residues: 40 sheet: -1.72 (0.49), residues: 108 loop : -1.16 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 35 HIS 0.004 0.002 HIS C 32 PHE 0.011 0.001 PHE A 429 TYR 0.011 0.001 TYR B 49 ARG 0.005 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.3610 time to fit residues: 34.6688 Evaluate side-chains 76 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3640 Z= 0.208 Angle : 0.564 10.460 4953 Z= 0.287 Chirality : 0.088 1.747 538 Planarity : 0.004 0.052 640 Dihedral : 6.412 49.933 541 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.56 % Allowed : 12.47 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.20 (0.37), residues: 443 helix: -3.06 (0.60), residues: 40 sheet: -1.59 (0.49), residues: 108 loop : -1.17 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 100B HIS 0.003 0.001 HIS C 32 PHE 0.007 0.001 PHE A 490 TYR 0.012 0.001 TYR B 49 ARG 0.008 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.3624 time to fit residues: 33.6969 Evaluate side-chains 76 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3640 Z= 0.183 Angle : 0.550 10.516 4953 Z= 0.278 Chirality : 0.087 1.740 538 Planarity : 0.004 0.056 640 Dihedral : 6.126 48.277 541 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.56 % Allowed : 14.03 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.04 (0.37), residues: 443 helix: -2.66 (0.74), residues: 33 sheet: -1.56 (0.48), residues: 109 loop : -1.12 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 353 HIS 0.002 0.001 HIS C 32 PHE 0.006 0.001 PHE A 490 TYR 0.012 0.001 TYR B 49 ARG 0.008 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.3733 time to fit residues: 35.1010 Evaluate side-chains 77 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3640 Z= 0.256 Angle : 0.585 10.709 4953 Z= 0.298 Chirality : 0.088 1.752 538 Planarity : 0.004 0.058 640 Dihedral : 6.300 47.600 541 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 1.82 % Allowed : 14.29 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.10 (0.37), residues: 443 helix: -2.56 (0.75), residues: 33 sheet: -1.62 (0.48), residues: 109 loop : -1.17 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 103 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE C 29 TYR 0.012 0.001 TYR B 49 ARG 0.009 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 78 average time/residue: 0.3676 time to fit residues: 34.4996 Evaluate side-chains 77 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3640 Z= 0.262 Angle : 0.601 10.532 4953 Z= 0.306 Chirality : 0.088 1.758 538 Planarity : 0.004 0.068 640 Dihedral : 6.435 48.498 541 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.82 % Allowed : 14.81 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.21 (0.37), residues: 443 helix: -2.64 (0.74), residues: 33 sheet: -1.66 (0.48), residues: 108 loop : -1.27 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 103 HIS 0.003 0.001 HIS C 32 PHE 0.012 0.001 PHE C 29 TYR 0.012 0.001 TYR B 49 ARG 0.011 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7829 (m-10) cc_final: 0.7622 (m-80) REVERT: A 529 LYS cc_start: 0.7218 (tmtt) cc_final: 0.6964 (tmtt) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.3646 time to fit residues: 33.7755 Evaluate side-chains 78 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3640 Z= 0.253 Angle : 0.599 10.518 4953 Z= 0.305 Chirality : 0.088 1.756 538 Planarity : 0.004 0.071 640 Dihedral : 6.396 48.306 541 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.56 % Allowed : 15.58 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.26 (0.37), residues: 443 helix: -2.57 (0.75), residues: 33 sheet: -1.68 (0.48), residues: 108 loop : -1.33 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 103 HIS 0.003 0.001 HIS C 32 PHE 0.013 0.001 PHE C 29 TYR 0.012 0.001 TYR B 49 ARG 0.010 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7817 (m-10) cc_final: 0.7616 (m-80) REVERT: A 529 LYS cc_start: 0.7212 (tmtt) cc_final: 0.6968 (tmtt) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.3563 time to fit residues: 31.8892 Evaluate side-chains 74 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3640 Z= 0.222 Angle : 0.584 10.386 4953 Z= 0.296 Chirality : 0.088 1.751 538 Planarity : 0.004 0.074 640 Dihedral : 6.268 48.740 541 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.56 % Allowed : 15.84 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.24 (0.37), residues: 443 helix: -2.53 (0.76), residues: 33 sheet: -1.64 (0.49), residues: 108 loop : -1.33 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 353 HIS 0.003 0.001 HIS C 32 PHE 0.012 0.001 PHE C 29 TYR 0.012 0.001 TYR B 49 ARG 0.012 0.001 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7202 (tmtt) cc_final: 0.6945 (tmtt) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.3638 time to fit residues: 31.5891 Evaluate side-chains 73 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.174122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151245 restraints weight = 12455.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157180 restraints weight = 6504.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.160935 restraints weight = 4099.557| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3640 Z= 0.212 Angle : 0.589 10.351 4953 Z= 0.295 Chirality : 0.088 1.747 538 Planarity : 0.004 0.074 640 Dihedral : 6.146 48.022 541 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 1.56 % Allowed : 16.10 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.23 (0.38), residues: 443 helix: -2.52 (0.75), residues: 33 sheet: -1.63 (0.48), residues: 108 loop : -1.32 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 353 HIS 0.002 0.001 HIS C 32 PHE 0.011 0.001 PHE C 29 TYR 0.012 0.001 TYR B 49 ARG 0.011 0.001 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.51 seconds wall clock time: 52 minutes 0.28 seconds (3120.28 seconds total)