Starting phenix.real_space_refine on Tue Nov 14 02:12:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/11_2023/8dtk_27703_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/11_2023/8dtk_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_27703/11_2023/8dtk_27703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/11_2023/8dtk_27703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/11_2023/8dtk_27703_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtk_27703/11_2023/8dtk_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-1.21rc1-5144/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 chiralities: 2 Time building chain proxies: 3.69, per 1000 atoms: 0.53 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: 5.16 Conformation dependent library (CDL) restraints added in 747.1 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: 0.59 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: 2.41 Time building geometry restraints manager: 5.39 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 - 17.86: 2605 17.86 - 35.73: 209 35.73 - 53.59: 31 53.59 - 71.46: 6 71.46 - 89.32: 7 Dihedral angle restraints: 2858 sinusoidal: 1271 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 2855 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: 1.580 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: 7.110 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 25.780 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- 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 : 13.590 89.322 1284 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 *********************** 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 : 0.539 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: 0.3355 time to fit residues: 34.3383 Evaluate side-chains 69 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6233 ------------------------------------------------------------------------------- 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: 0.0870 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: 0.5980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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: 0.7138 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3640 Z= 0.201 Angle : 0.602 10.402 4953 Z= 0.312 Chirality : 0.088 1.736 538 Planarity : 0.004 0.039 640 Dihedral : 5.258 21.178 499 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.52 % Allowed : 8.05 % Favored : 91.43 % 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: -1.98 (0.38), residues: 443 helix: -2.91 (0.66), residues: 40 sheet: -1.78 (0.47), residues: 107 loop : -0.86 (0.35), residues: 296 *********************** 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 74 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.3393 time to fit residues: 30.8402 Evaluate side-chains 73 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0803 time to fit residues: 0.9815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7192 moved from start: 0.1796 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= 0.234 Angle : 0.594 10.400 4953 Z= 0.305 Chirality : 0.088 1.740 538 Planarity : 0.004 0.041 640 Dihedral : 5.137 19.583 499 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.26 % Allowed : 9.61 % Favored : 90.13 % 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: -3.17 (0.59), residues: 40 sheet: -1.73 (0.47), residues: 108 loop : -1.08 (0.34), residues: 295 *********************** 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 77 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.3646 time to fit residues: 33.6963 Evaluate side-chains 73 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 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 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: 0.7225 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3640 Z= 0.255 Angle : 0.587 10.467 4953 Z= 0.301 Chirality : 0.088 1.752 538 Planarity : 0.004 0.048 640 Dihedral : 5.107 18.540 499 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.30 % Allowed : 11.17 % Favored : 87.53 % 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: -2.27 (0.37), residues: 443 helix: -3.17 (0.58), residues: 40 sheet: -1.78 (0.48), residues: 108 loop : -1.15 (0.34), residues: 295 *********************** 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 82 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 79 average time/residue: 0.3889 time to fit residues: 36.9868 Evaluate side-chains 75 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0827 time to fit residues: 1.1969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7225 moved from start: 0.2343 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= 0.212 Angle : 0.570 10.484 4953 Z= 0.290 Chirality : 0.088 1.748 538 Planarity : 0.004 0.053 640 Dihedral : 4.975 18.132 499 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.78 % Allowed : 13.25 % 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: -2.21 (0.37), residues: 443 helix: -3.12 (0.60), residues: 40 sheet: -1.65 (0.49), residues: 108 loop : -1.14 (0.34), residues: 295 *********************** 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 76 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.3763 time to fit residues: 34.0115 Evaluate side-chains 71 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0830 time to fit residues: 0.9964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7269 moved from start: 0.2577 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= 0.271 Angle : 0.597 10.810 4953 Z= 0.305 Chirality : 0.088 1.758 538 Planarity : 0.004 0.051 640 Dihedral : 5.079 19.120 499 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.26 % Allowed : 14.81 % Favored : 84.94 % 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: -2.22 (0.37), residues: 443 helix: -2.69 (0.74), residues: 33 sheet: -1.68 (0.48), residues: 108 loop : -1.27 (0.33), residues: 302 *********************** 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 74 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.3962 time to fit residues: 35.2936 Evaluate side-chains 71 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8237 time to fit residues: 1.5909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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: 0.7225 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3640 Z= 0.173 Angle : 0.554 10.559 4953 Z= 0.279 Chirality : 0.087 1.744 538 Planarity : 0.004 0.061 640 Dihedral : 4.808 17.445 499 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.26 % Allowed : 15.84 % 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: -2.17 (0.37), residues: 443 helix: -2.64 (0.75), residues: 33 sheet: -1.49 (0.45), residues: 118 loop : -1.28 (0.34), residues: 292 *********************** 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 72 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.3826 time to fit residues: 33.2389 Evaluate side-chains 70 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0761 time to fit residues: 0.7553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 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: 0.5980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.7260 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3640 Z= 0.237 Angle : 0.579 10.549 4953 Z= 0.293 Chirality : 0.088 1.751 538 Planarity : 0.004 0.066 640 Dihedral : 4.907 18.096 499 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 16.62 % 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: -2.28 (0.37), residues: 443 helix: -2.68 (0.75), residues: 33 sheet: -1.58 (0.45), residues: 118 loop : -1.36 (0.34), residues: 292 *********************** 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 71 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3731 time to fit residues: 31.9848 Evaluate side-chains 69 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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: 0.7252 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3640 Z= 0.210 Angle : 0.566 10.467 4953 Z= 0.286 Chirality : 0.088 1.748 538 Planarity : 0.004 0.073 640 Dihedral : 4.844 17.631 499 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 17.40 % 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: -2.28 (0.37), residues: 443 helix: -2.61 (0.77), residues: 33 sheet: -1.56 (0.44), residues: 120 loop : -1.37 (0.34), residues: 290 *********************** 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 68 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3764 time to fit residues: 31.0373 Evaluate side-chains 68 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7292 moved from start: 0.3041 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= 0.281 Angle : 0.605 10.624 4953 Z= 0.309 Chirality : 0.089 1.761 538 Planarity : 0.005 0.075 640 Dihedral : 5.071 18.490 499 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.26 % Allowed : 17.40 % 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: -2.41 (0.37), residues: 443 helix: -2.61 (0.77), residues: 33 sheet: -1.63 (0.45), residues: 118 loop : -1.49 (0.34), residues: 292 ********************** 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 70 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.3587 time to fit residues: 30.6712 Evaluate side-chains 68 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0768 time to fit residues: 0.8505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.174174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151715 restraints weight = 12392.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.157505 restraints weight = 6466.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161298 restraints weight = 4061.437| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3640 Z= 0.217 Angle : 0.582 10.421 4953 Z= 0.295 Chirality : 0.088 1.749 538 Planarity : 0.004 0.076 640 Dihedral : 5.017 23.027 499 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 16.62 % 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: -2.34 (0.37), residues: 443 helix: -2.63 (0.76), residues: 33 sheet: -1.59 (0.44), residues: 120 loop : -1.42 (0.34), residues: 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.17 seconds wall clock time: 53 minutes 25.91 seconds (3205.91 seconds total)